PROF. SINA ADL (Orcid ID : 0000-0001-6324-6065)
Accepted Article
PROF. DAVID BASS (Orcid ID : 0000-0002-9883-7823)
DR. CÉDRIC BERNEY (Orcid ID : 0000-0001-8689-9907)
DR. PACO CÁRDENAS (Orcid ID : 0000-0003-4045-6718)
DR. IVAN CEPICKA (Orcid ID : 0000-0002-4322-0754)
DR. MICAH DUNTHORN (Orcid ID : 0000-0003-1376-4109)
PROF. BENTE EDVARDSEN (Orcid ID : 0000-0002-6806-4807)
DR. DENIS H. LYNN (Orcid ID : 0000-0002-1554-7792)
DR. EDWARD A.D MITCHELL (Orcid ID : 0000-0003-0358-506X)
PROF. JONG SOO PARK (Orcid ID : 0000-0001-6253-5199)
DR. GUIFRÉ TORRUELLA (Orcid ID : 0000-0002-6534-4758)
DR. VASILY V. ZLATOGURSKY (Orcid ID : 0000-0002-2688-3900)
Article type
: Original Article
Corresponding author mail id: sina.adl@usask.ca
Adl et al.---Classification of Eukaryotes
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
Sina M. Adla, David Bassb,c, Christopher E. Laned, Julius Lukeše,f, Conrad L. Schochg,
Alexey Smirnovh, Sabine Agathai, Cedric Berneyj, Matthew W. Brownk,l, Fabien Burkim,
Paco Cárdenasn, Ivan Čepičkao, Ludmila Chistyakovap, Javier del Campoq, Micah
Dunthornr,s, Bente Edvardsent, Yana Eglitu, Laure Guillouv, Vladimír Hamplw, Aaron A.
Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Sergey Karpovh, Eunsoo Kimx, Martin
Koliskoe, Alexander Kudryavtsevh,aa, Daniel J. G. Lahrab, Enrique Laraac,ad, Line Le
Gallae, Denis H. Lynnaf,ag, David G. Mannah, Ramon Massana i Moleraq, Edward A. D.
Mitchellac,ai , Christine Morrowaj, Jong Soo Parkak, Jan W. Pawlowskial, Martha J.
Powellam, Daniel J. Richteran, Sonja Rueckertao, Lora Shadwickap, Satoshi Shimanoaq,
Frederick W. Spiegelap, Guifré Torruella i Cortesar, Noha Youssefas, Vasily
Zlatogurskyh,at, Qianqian Zhangau,av.
This article has been accepted for publication and undergone full peer review but has not
been through the copyediting, typesetting, pagination and proofreading process, which may
lead to differences between this version and the Version of Record. Please cite this article as
doi: 10.1111/jeu.12691
This article is protected by copyright. All rights reserved.
a
Accepted Article
Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan,
Saskatoon, SK Canada, and
b
Dept of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, and
c
Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe,
Weymouth, Dorset DT4 8UB, and
d
Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881 USA,
and
e
Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice,
Czechia, and
f
Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia, and
g
National Institute for Biotechnology Information, National Library of Medicine, National Institutes of
Health, Bethesda, MD 20892, USA, and
h
Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034
Saint Petersburg, Russia, and
i
Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria,
and
j
CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystèmes Pélagiques, Station
Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France, and
k
Department of Biological Sciences, Mississippi State University, MS USA, and
l
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS USA, and
m
Department of Organismal Biology, Program in Systematic Biology, Science for Life Laboratory,
Uppsala University, Uppsala 75236, Sweden, and
n
Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, SE-75123
Uppsala, Sweden, and
o
Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czechia,
and
p
Core Facility Centre for Culture Collection of Microorganisms, Saint Petersburg State University,
198504 Saint Petersburg, Russia, and
q
Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49 08003 Barcelona,
Catalonia, Spain, and
r
Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, D-67663
Kaiserslautern, Germany, and
s
Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, D45141 Essen, Germany, and
t
Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway, and
u
Department of Biology, Dalhousie University, Halifax, NS, Canada, and
v
Sorbonne Université, Université Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station
Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff, France, and
w
Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252
42 Vestec, Czechia, and
x
Department of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024
USA, and
y
Senckenberg am Meer, DZMB – German Centre for Marine Biodiversity Research, D-26382
Wilhelmshaven, Germany, and
z
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA,
and
aa
Laboratory of Parasitic Worms and Protistology, Zoological Institute RAS, 199034 Saint Petersburg,
Russia, and
ab
Department of Zoology, Institute of Biosciences, University of Sao Paulo, Matao Travessa 14
Cidade Universitaria, Sao Paulo, 05508-090 SP, Brazil, and
ac
Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel,
Switzerland, and
This article is protected by copyright. All rights reserved.
ad
Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain, and
Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne
Universités, 57 rue Cuvier, CP 39 75005, Paris, France, and
af
Department of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph,
Ontario N1G 2W1 Canada, and
ag
Department of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver,
British Columbia V6T 1Z4 Canada, and
ah
Royal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom and Institute for Agrifood Research
and Technology, C/ Poble Nou km 5.5, Sant Carles de La Ràpita, E-43540 Spain , and
ai
Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, CH-2000 Neuchâtel, Switzerland,
and
aj
Department of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood
BT18 OEU, Northern Ireland, UK, and
ak
Department of Oceanography and Kyungpook Institute of Oceanography, School of Earth System
Sciences, Kyungpook National University, Daegu, Republic of Korea, and
al
Department of Genetics and Evolution, University of Geneva 1211, Geneva 4, Switzerland, and
am
Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA, and
an
Institut de Biologia Evolutiva (CSIC-Univeritat Pompeu Fabra), Passeig Marítim de la Barceloneta
37-49, 08003 Barcelona, Catalonia, Spain, and
ao
School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, United Kingdom,
and
ap
Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA, and
aq
Science Research Centre, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo, 102-8160, Japan,
and
ar
Laboratoire Evolution et Systématique, Université Paris-XI, 91405 Orsay, France, and
as
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
74074 USA, and
at
Department of Organismal Biology, Systematic Biology Program, Uppsala university, Uppsala,
Sweden, and
au
Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, China,
and
av
Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
Accepted Article
ae
Abstract:
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk.
Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the
resolution of many nodes in phylogenetic analyses. For some clades even families are being
clearly resolved. As we had predicted, environmental sampling in the intervening years has
massively increased the genetic information at hand. Consequently, we have discovered
novel clades, exciting new genera, and uncovered a massive species level diversity beyond
the morphological species descriptions. Several clades known from environmental samples
only have found their home. Sampling soils, deeper marine waters, and the deep sea will
continue to fill us with surprises. The main changes in this revision are the confirmation that
eukaryotes form at least two domains, the loss of monophyly in the Exavata, robust support
for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from
environmental samples that are effective for each clade. We have provided a guide to
trophic functional guilds in an appendix, to facilitate the interpretation of environmental
samples.
This article is protected by copyright. All rights reserved.
Accepted Article
THIS revision of the classification of eukaryotes updates that of the International Society of
Protistologists (Adl et al., 2012). Since then, there has been a massive increase in DNA
sequence information of phylogenetic relevance from environmental samples. We now have
a much better sense of the undescribed biodiversity in our environment (Pawlowski et al.,
2012; de Vargas et al., 2015). While significant, it still remains a partial estimation as several
continents and soils in general are poorly sampled, and the deeper ocean is hard to reach.
This new data clarified phylogenetic relationships and the new information is incorporated in
this revision.
Systematics. We assembled the classification according to the principles outlined
elsewhere, and we refer the reader to the introductions of both Adl et al., 2005 and 2012 for
background information, and to Adl et al. 2007 for a discussion. Briefly, we adopted a
hierarchical system without formal rank designations. The hierarchy is represented by
indented paragraphs. The nomenclatural priority is given to the oldest name (and its
authority) that correctly assembled genera or higher groups together into a clade, except
where its composition was substantially modified. In these cases, we have used a newer
term and its appropriate authorship. In cases where ranks were created to include a single
lower rank, the higher ranks were eliminated as superfluous. In this scheme, monotypic taxa
are represented by the genus only. Nested clades represent as best as we know,
monophyletic lineages, and para- or polyphyletic groups are so indicated.
This system of hierarchical nameless ranks, that ignores endings of clade names, has
proved its utility in providing name stability as we reconstructed a new phylogenetic
classification during the past 20 years. Clade names in this system do not change when their
rank or composition changes, and it is only the authority for the name that changes when
each clade description is adjusted (Cantino, 1998; Pleijel and Rouse, 2003). Where a new
term is introduced in this classification, it is identified with ‘‘Adl et al. 2019’’ as the authority,
or by the submitting author (e.g. Mann in Adl et al., 2019), and they are to be cited as
emended in this publication. The descriptions provided are not intended to substitute for
formal diagnoses. They are provided primarily for the student and general users to identify
common morphological features, such as synapomorphies and apomorphies, within
monophyletic lineages.
There are two novel components in this revision. First, we have provided trophic
assignments for most taxa. This will prove useful in interpreting communities from
environmental samples. Second, we informally suggest a phylum rank and classes in most
clades to provide a point of reference in the classification hierarchy for the non-specialist.
This became possible, as there has been some stability at this level in the molecular
phylogenetic reconstructions. It should be obvious that genera grouped into a clade then
represent a family, and families into an order.
Nomenclature. This committee of the Society has had the responsibility of arbitrating
nomenclature for protists in general. Historically, the task was simpler as most groups fell
under one or the other of the two Codes of Nomenclature (algae and some other protists
under the “International Code of Nomenclature for algae, fungi, and plants”, and protozoa
This article is protected by copyright. All rights reserved.
Accepted Article
under the “International Code of Zoological Nomenclature”), and few were described under
both Codes. The Society was represented on the relevant committees. Notwithstanding that
both Codes are incompatible, some have proposed to provide parallel classifications in each
Code, while others proposed to adopt a modern unified code of nomenclature. Since the
rearrangement of the classification along monophyletic lineages during the 90s, many clades
now include a mixture of taxa from both Codes. Several taxa, such as diatoms, are
described in parallel under both Codes with different names. This situation created and
perpetuates anomalies, such as the recent re-description of the dictyostellid amoebae with
the botanical Code (Sheikh et al. 2018) for genera that are unarguably in Amoebozoa
governed by the Zoological Code. Issues such as these have been thoroughly discussed in
the past (Adl et al., 2007; Lahr et al., 2012). It has been the responsibility of this committee
to discuss and arbitrate published phylogenetic hypotheses, proposals for new names and
name changes. Underlying these discussions are principles of nomenclatural priority in the
spirit of codes of nomenclature.
A classification is unlike a phylogenetic tree in a publication, where the discovery of new
clades, branches, or robust nodes requires proposing new names. Newly named clades and
nodes have their utility in phylogenetic analysis and discussion, but do not need to be
formalized in the classification immediately. An overwhelming number of spent names have
thus accumulated, with an increasing frequency over the past four decades, most of which
are no longer – or never were – in common use. Many of these names were ephemeral, as
their monophyly did not stand the test of (time) statistical analysis. The proliferation of these
names reflects a methodological error practiced by some. That is to formalize names
prematurely and pretend to re-organize classifications single-handedly. As we argued before
(Adl et al., 2012), this must be done with care, respecting nomenclatural priority, published
as a proposal or a phylogenetic hypothesis first, to be verified by the community, and only
eventually considered for change in the classification. The task of refereeing and classifying
falls on Society committees representing communities of professionals. The very formal and
slow process of voting to conserve or reject names through the tradition of the botanical
codes takes years as it has to proceed through committees and then approved by vote on
the floor of the congress at four-year intervals. That is, however, too slow for the pace of
changes today given the rate at which new information is becoming available.
In contrast to a phylogenetic tree, a classification system belongs to a community of users,
and it is generated through discussions of the available evidence, for pragmatic purposes of
teaching, curation, organizing data, archiving, and communicating with a common language.
It is a commonly agreed point of reference. It can hardly be re-imagined or re-done at will by
one individual. The Linnaean system that we have inherited has detailed codes of
nomenclature that guide and regulate how living organisms are named, names changed,
and classified. The elaborate rules arise from disputes and mistakes made in the past, in
part out of respect for each other’s work. Instead of providing a long list of rejected and
invalid names, we can specify that those not selected in this classification were considered
nomina ambigua, nomina perplexa, nomina dubia, nomina nuda, or did not have
nomenclatural priority and are declared nomina rejicienda.
Another proposed classification of prokaryotes and eukaryotes was published recently
(Ruggiero et al. 2015). This effort may be reasonable in their classification of the
prokaryotes, but the eukaryote section does not pass standards of modern biology.
Specifically, it is their refusal to use monophyly as a guiding principle, but to argue to retain
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Accepted Article
“ancestral (paraphyletic) taxa when it seemed beneficial to do so” instead, even where
monophyletic clades are already established. Their insistence on using a hodge-podge of
names that do not have nomenclatural priority and poorly describe the taxa included, further
reduces its usefulness.
Classification. The super-groups utilized since 2005 (Simpson and Roger 2004, Adl et al.,
2005) are revised as follows:
1) Eukaryotes now form two Domains called Amorphea and Diaphoretickes, with several
additional clades that do not group into a third Domain.
2) In the Amorphea, the Opisthokonta, Breviatea, and Apusomonadida now form a robust
clade, as noted earlier (Adl et al., 2012), called Obazoa. Within the Opisthokonta, the
Holozoa and Nucletmycea(/Holomycota) are robust clades with improved resolution of
the basal sister lineages. In the Holozoa, the sponges and the other animals group
together as the Metazoa (Porifera, Placozoa, Ctenophora, Cnidaria, Bilateria). In
addition, a sister clade to the Amorphea comprising several genera recently described as
CRuMs (Brown et al., 2018).
3) There are two sister clades in Opisthokonta, the Holozoa and the Nucletmycea
(/Holomycota). They share several characters, including synthesis of extracellular chitin
in exoskeleton, cyst/spore wall, or cell wall of filamentous growth and hyphae; the
extracellular digestion of substrates with osmotrophic absorption of nutrients; and other
cell biosynthetic and metabolic pathways. Genera at the base of each clade are
amoeboid and phagotrophic.
4) The Archaeplastida, Sar, and several other clades remain a monophyletic clade under
Diaphoretickes. The clade comprising the cryptomonads, kathablepharids, and
Palpitomonas is well recognized and robust, although placement of its node within the
Diaphoretickes remains problematic. In some but not all analyses, the clade appears
inside the Archaeplastida. This position has always occurred from time to time in some
phylogenies with weak support, but there is now stronger support for this association.
We are not committed to their inclusion within the Archaeplastida but do note its
likelihood. The inclusion of the Cryptista in the Archaeplastida would expand that group
without affecting its defining criteria. Questioning the single origin of a plastid within the
Archaeplastida is a rare minority opinion. Yet, the possibility of more than one plastid
origin must not be ruled-out until the cryptomonads are robustly positioned.
5) The new robust support for the Cryptista clade is accompanied by a similarly robust
support for a clade comprising the Centroplasthelida and Haptophyta as the Haptista
within the Diaphoretickes.
6) Nodes at the base of the Alveolata are better resolved with additional genera. The
placeholder name Protalveolata is no longer required.
7) The Excavata comprise three clades: the Metamonada, the Discoba and the
Malawimonada. Their mutual relationships, as well as their relationships to other clades
of eukaryotes, remain uncertain. We have dropped the supergoup Excavata in favour of
the informal Excavates when referring to the “Discoba, Metamonada, Malawimonada”,
as Incertae sedis in eukaryotes. The Excavates, and several clades and genera, fall
outside of the two principal domains, but do not cluster together into a third domain.
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Accepted Article
This classification will serve as a primary starting reference for the taxonomic framework
developed by UniEuk (unieuk.org; Berney et al. 2017), the Society supported, consensusdriven, community-based and expert-driven international initiative to maintain a universal
taxonomy for, at least, microbial eukaryotes. A specific aim of the UniEuk project is to apply
one taxonomic framework to all genetic data in the International Nucleotide Sequence
Database Collaboration (INSDC) repositories, which includes DDBJ (ddbj.nig.ac.jp),
GenBank (ncbi.nlm.nih.gov), and ENA (ebi.ac.uk/ena) databases. The system's broad use
and preservation will be ensured by a direct implementation of the UniEuk taxonomic
framework into the ENA (European Nucleotide Archive) at EMBL-EBI
(http://www.ebi.ac.uk/ena). The project will capture our collective knowledge on eukaryotic
diversity, evolution and ecology via three main modules (EukRef, EukBank, and EukMap).
EukRef (eukref.org; del Campo et al. 2018) uses a standardized, open-source bioinformatics
pipeline to generate homogenous, high-quality curation of sequences (primarily 18S rDNA)
available in INSDC databases. EukRef is fully operational; outputs include (on a lineage-bylineage basis) taxonomically curated sequences, sequence alignments, phylogenetic trees,
and metadata. EukBank is a public repository of (primarily V4 18S rDNA) high-throughput
metabarcoding datasets, centralised at ENA, with standardized protocols for submitting
datasets and metadata. EukMap (eukmap.unieuk.org) is an editable, user-friendly
representation of the UniEuk taxonomy in the form of a publicly navigable tree, where each
node/taxon is associated with contextual data (taxonomic, and ecological information, links
to representative images, etc.). It will be operational by 2019 and will allow registered
community members to directly interact with and inform the taxonomic framework, and to
flag taxonomy issues requiring revision. As a whole, the UniEuk system will represent a
community hub to centralize, standardize and promote global knowledge on eukaryotic
diversity, taxonomy, and ecology.
Clarification of terms for trophic functional groups. Several terms were clarified to
correct misuse of terminology in publications. In 2005, these were: eukaryote, prokaryote,
algae, zoosporic fungi, protozoa, zooplankton, phytoplankton, cyst, spore, and cilium. In
2012 they were related to the cytoskeleton and motility: lobopodia, lamellipodia, filopodia,
granuloreticulopodia, reticulopodia, axopodia, centriole, centrosome, microtubular organizing
centre (MTOC), basal body, kinetosome, kinetid, and mastigont. In this revision they pertain
to trophic functional groups, and a plea to improve sample site descriptions.
In addition to descriptions of morphology that accompany specimen, which is critical for
understanding cell function and interpreting phylogenetic trees, descriptions of site and food
preferences are required for an ecological interpretation of the role in the community and
ecosystem. Often species lack sufficient description of the collection site or feeding habit.
To compare environmental DNA data sets, adequate meta-data is necessary to select
appropriate samples for comparison. The same issue exists when trying to re-isolate a
species or to verify the type specimen. Therefore, it is important the environment and habitat
is sufficiently described. Stating marine, terrestrial, or soil is grossly inadequate. The soil for
example is heterogeneous horizontally at the sub-millimetre to regional scales. It is also
stratified through the profile, and across the diameter of each ped. Whether a soil or aquatic
sample, solution chemistry and site physical parameters contribute to define the nichespace.
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Accepted Article
Because we care about nomenclature and the exact meaning of words, and of names of
things, especially species and their groupings into nodes and stems on phylogenetic trees, it
is equally important to care for how we describe sampling sites and feeding habits. There
are two parts to describing the feeding habit: what is eaten, and how it is eaten.
Species that release enzymes extracellularly to digest substrates in their habitat, are
generally called saprotrophic, or lysotrophic, and contribute to the decomposition of
organic matter. One incredible resource is FunGuild (Nguyen et al., 2016,
(https://github.com/UMNFuN/FUNGuild) to determine substrate utilization for saprotrophic
fungi. Probably all eukaryotes are capable of osmotrophy, the acquisition of soluble nutrients
through the cell membrane. For example plants obtain their carbon for photosynthesis from
the air, as well as some oxygen – however they rely on osmotrophy through the roots to
obtain all the other elements they need. Osmotrophy occurs through the ciliary pit, by
pinocytosis, by diffusion, and by various membrane transport mechanisms. Some species
have no alternative form of acquiring energy, are very poor at decomposing substrates, and
are strict osmotrophs relying on dissolved nutrients. Detritus eaters ingest particles derived
from cells and tissues, decomposing organic matter, starch granules, plant or animal debris,
or wood (microchip) fragments.
Species that eat other species are called consumers, and there are a variety of terms to
describe the functional groups. Some acquire suspended particles in the solution and
accumulate the particles by filtration into an oral region or cytostome (not filter-feeders, as
they do not feed on filters). The size of particles filtered out of the liquid depend on the
current generated, and the structure of the feeding apparatus (Fenchel, 1986), and it is a
good idea to specify what size prey are ingested. The remaining consumers fall into two
categories, the grazers and predators. Grazers, like a cow in a field of grasses, browse and
ingest from surfaces covered with potential food items (for example an amoeba on a lawn of
bacteria, or on soil particle surfaces). Predators pursue scarce prey according to optimal
foraging theory, typically handle one prey at a time, and it is mathematically distinct (for
example a Jakoba ingesting one bacterium). Species ingest bacteria either by filtration, or by
phagotrophy as a grazer or predator; it is best to specify “bacteria by filtration”, or “bacteria
by phagocytosis”. A popular term bacterivore has the unintended implication of voraciously
devouring (voracitas L.) which is a false description of how many bacteria eaters acquire
their prey, and an incomplete description. Use it, but be aware that some readers and
reviewers will be more discriminating. In contrast, the more appropriate term –trophy (trophe
Gr.), to eat for food and nourishment, sounds more awkward in English. For species that
ingest unicellular protists by phagotrophy, the correct term is cytotrophy. Bacterium
(Ehrenberg 1838) has been the word used to refer to a prokaryotic cell, while cell (Dutrochet,
1824; Schwann, 1839; Schleiden 1839) has been used since to refer to a eukaryotic cell.
Mixotrophy refers to photosynthetic species that also ingest food by phagocytosis.
There are two distinct mechanisms to feed on algal filaments (cellulosic cell wall) or fungal
hyphae (chitinous cell wall). One mechanism is to slurp the filaments like noodles and ingest
them, the other is to penetrate through the cell wall. Those that puncture through
phagocytose cytoplasm, and some species even penetrate inside to ingest cytoplasm along
the tube or in the spore. It is best to distinguish between the cell wall material to digest and
the mechanism of ingestion. Thus, we have mycotrophy or phycotrophy, by either
swallowing (devoratis L.) or by penetrating (penetrando L.).
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Accepted Article
In microbial food webs there are also consumers of consumers, typically by predation, that
are equivalent above-ground or in aquatic systems to carnivores (meat eaters), or other
functional groups. Although 2°consumers, 3° consumers, and so on exist in microbial food
webs, it is hardly correct to refer to carnivores in food webs where there is no meat.
Another poorly crafted term one encounters, albeit rarely, is eukaryovory. Although there are
famous examples of eukaryovory (Saint-Exupéry, 1943), eukaryotes eating eukaryotes can
include parasitism, as intracellular or extracellular parasites, on hosts that are protists or
multicellular, with various grades of host specificity, and it is a poor substitute for cytotrophy.
We have summarized the higher level classification of eukaryotes in Table 1, with an
estimate of the known number of genera, and providing informal phylum and class
designations to help orient the student and users along the hierarchy, or nodes on a
phylogenetic tree. The revised classification of eukaryotes is presented in Table 2, and
genera that have not been studied enough to place in the classification are listed in Table 3
as incertae sedis Eukarya. Table 4 provides recommended primers for analyzing DNA from
environmental samples, noting that the choice of primers and depth of sequencing are
important sources of variation between studies. Appendix 1 provides additional supporting
literature that we considered important to understand the changes. Appendix 2 provides
more detail about the trophic functional assignments across protists, by noting exceptions at
the genus level.
Acknowledgments
After the first author, D. Bass, C.E Lane, J. Lukeš, C. L. Schoch, and A. Smirnov have
contributed equally and are to be considered second authors; subsequent authors are listed
alphabetically and are to be considered third authors.
We were saddened and hurt by the untimely loss of two dear colleagues, D.H Lynn, and J.
Clamp, both ciliatologists.
Research support was provided as follows: SMA by NSERC 249889-2007; DB by NERC
NE/H009426/1 and NE/H000887/1; MWB by NSF1456054; FB by a Fellowship from Science
for Life Laboratory and VR/2017-04563; PC by EU-Horizon 2020 research and innovation
program through the SponGES project (679849)*; BE by RCN TaxMArc 268286/GMR; LG
by ANR HAPAR (ANR-14-CE02-0007); VH MK JL by ERDF; MEYS with ERC 771592 CZ
1.05/1.1.00/02.0109 BIOCEV; SK by RSF 16-14-10302; MK by CSF GA18-28103S; CEL by
NSF1541510 and NIH-AI124092; EL by CAM: 2017-T1/AMB-5210; JL by ERC CZ LL1601
and OPVVV 16_019/0000759; MP by NSF DEB-1455611; DJR by the Beatriu de Pinós
postdoctoral programme of the Government of Catalonia's Secretariat for Universities and
Research of the Ministry of Economy and Knowledge; CLS by the intramural research
program of the National Library of Medicine, National Institutes of Health; AS by RSF
1.53.574.2017 and RFBR 16-04-01454 NY by NSF DEB 1557102; VZ by RFBR 16-3460102 mol-a-dk; UniEuk and EukRef by the Gordon and Betty Moore Foundation.
This article is protected by copyright. All rights reserved.
Accepted Article
We thank numerous colleagues who were consulted ad hoc throughout this process. In
addition, we specifically thank Alexander Ereskovsky (CNRS, Station marine d’Endoume,
Marseille, France) for help with the sponges; and Iñaki Ruiz-Trillo (ICREA - Institut de
Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain) with the
Holozoa; David S. Hibbett (Biology Department, Clark University, Worcester, MA USA, and
Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA) with the
Holomycota; Isabelle Florent (Institut de Systématique, Évolution, Biodiversité, Muséum
National d’Histoire Naturelle, Sorbonne Universités, Paris, France) with Apicomplexa;
Shauna Murray (Climate Change Cluster, University of Technology Sydney, Australia),
Albert Reñé (Dept. Biologia Marina i Oceanografia, Institut de Ciències del Mar, CMIMA
(CSIC), Barcelona, Spain) and Nicolas Chomérat (IFREMER, ODE/UL/LER Bretagne
Occidentale, Concarneau, France) for dinoflagellate primers and barcoding; Urban Tillmann
(Alfred Wegener Institut, Helmholz-Zentrum für Polar- und Meeresforschung, Bremerhaven,
Germany) and Per Juel Hansen (Marine Biological Section, Dept. of Biology, University of
Copenhagen, Denmark) for the dinoflagellate literature and functional assignments; Anna
Karnkowska (University of Warsaw) with Euglenophyta; William Bourland (Biology, Boise
State University) for discussions on ciliates; Alastair Simpson (Dalhousie University) for
discussions on higher level ranking and structure; Angela Mele (Philadelphia) for the cover
art.
*This document reflects only the authors’ view and the Executive Agency for Small and
Medium-sized Enterprises (EASME) is not responsible for any use that may be made of the
information it contains.
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Figure legend.
Figure 1. Overview of the diversity of protists amongst eukaryotes.
Supporting information
Appendix S1. Supplementary references.
Appendix S2. Functional group assignments.
Appendix S3. Translation guide for East Asian users.
Table 1. Higher ranks of the eukaryotes indicating the position of Linnaean ranks, and the number of
known genera. G genus, F family, O order, C class, P phylum, K kingdom. *The state of the
classification in online databases are too poor to evaluate or work with this clade.
AMORPHEA
CRuMs (O) 11
Collodictyonidae (F)
Rigifilida (F)
Mantamonas (G)
Amoebozoa 255
Incertae sedis 21
Tubulinea (P) 93
Corycida (C)
Echinamoebida (C)
Elardia (C) (Arcellinida 63)
Evosea (P) 106
Variosea (C)
Eumycetozoa (C)
Cutosea (C)
Archamoebea (C)
This article is protected by copyright. All rights reserved.
Discosea (P) 35
Accepted Article
Flabellinia (C)
Stygamoebida (C)
Centramoebia (C)
Obazoa
Apusomonadida (F) 6
Breviatea (F) 4
Opisthokonta
Holozoa 25 (without Choanoflagellata, Porifera and Metazoa)
Incertae sedis Holozoa: Corallochytrium, Syssomonas
Ichtyosporea (O)
Choanoflagellata (C) 57
Metazoa
Porifera (P) 742
Hexactinellida (C)
Demospongiae (C)
Calcarea (C)
Trichoplax (G/F?)
Cnidaria (P)
Ctenophora (P)
Bilateria (K, ~35 P)
Nucletmycea
(Fungi) ~8,600
Rotosphaerida (O) 9
Opisthosporidia (O)
Aphelidea (F) 4
Cryptomycota (F) 3
Microsporida (O?/F) >150
Blastocladiales (O) 14
Chytridiomycetes (C) 140
Dikarya ~8,000 Ascomycota (P) ~6,400
Basidiomycota (P) ~1,600
This article is protected by copyright. All rights reserved.
Mucoromycota (P) ~140
Accepted Article
Neocallimastigaceae (F) 11
Olpidium (G)
Zoopagomycota (P) ~200
DIAPHORETICKES
Incertae sedis: Microhelliela maris, Ancoracysta twista, Rappemonads, Telonemia, Picozoa
Cryptista (C) 21
Cryptophyceae (O)
Palpitomonas (G)
Haptista (P)
Haptophyta (C) 80
Pavlovales (F)
Prymnesiophyceae (O)
Centroplasthelida (C) 16
Pterocystida (O)
Panacanthocystida (O)
Archaeplastida
Glaucocystaceae (F) 4
Rhodophyceae (P) 850
Cyanidiales (O)
Proteorhodophytina (O/C)
Eurhodophytina (C)
Chloroplastida (72,000 sp + Embryophyta)
Chlorophyta (P)
Ulvophyceae (C)
Trebouxiophyceae (C)
Chlorophyceae (C)
Chlorodendrophyceae (C)
Pedinophyceae (C)
Chloropicophyceae (C)
Picocystophyceae (C)
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Pyramimonadales (C)
Accepted Article
Mamiellophyceae (C)
Nephroselmis (G)
Pycnococcaceae (C)
Palmophyllophyceae (C)
Streptophyta (P)
Chlorokybus atmophyticus
Mesostigma viridae
Klebsomidiophyceae (F)
Phragmoplastophyta (C)
Zygnemataceae (F)
Coleochaetophyceae (O)
Characeae (F)
Embryophyta (K)
Sar
Stramenopiles (P)
Bigyra (C) 49
Opalinata (O)
Placidida (F)
Bicosoecida (O/F)
Sagenista
Labyrinthulomycetes (O)
Pseudophyllomitidae (F?)
Gyrista (C) 31 excluding Peronosporomycetes and Ochrophyta
Developea (F)
Hyphochytriales (O)
Peronosporomycetes (C/O) 46
Pirsonia (G)
Actinophryidae (F)
Ochrophyta*
Chrysista (C)* Chrysophyceae (O)
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Eustigmatales (O)
Phaeophyceae (O)
Raphidophyceae (O)
Accepted Article
Schizocladia (O)
Xanthophyceae (O)
Diatomista
Bolidophyceae (F)
Diatomea (C) ~400
Alveolata, others 26
Colpodellida (O)
Perkinsidae (F)
Colponemidia (F)
Acavomonas (G)
Oxyrrhis marina
Dinoflagellata (P) 300
Syndiniales (O)
Noctilucales (O)
Dinophyceae (C)
Apicomplexa (P) ~350
Incertae sedis: Agamococcidiorida (F), Protococcidiorida (F)
Aconoidasida (C)
Conoidasida (C)
Ciliophora (P)
Karyorelictea (C) 18
Heterotrichida (O) 58
Spirotrichea (C) 139 + Hypotrichia
Hypotrichia 183
Armophorea (O) 41
Litostomatea (C) 263
Phyllopharyngea (C) 263
Colpodea (C) 73
Nassophorea (C) 23
Plagyopylea (C) 15
Oligomymenophorea (C) 433
This article is protected by copyright. All rights reserved.
Rhizaria
Accepted Article
Cercozoa (P) >>204
Cercomonadida (F)
Paracercomonadida (F)
Glissomonadida (O)
Viridiraptoridae (F)
Pansomonadidae (F)
Sainouridae (F)
Thecofilosea (C)
Imbricatea
Spongomonadida (F)
Marimonadida (F)
Variglissida (F)
Silicofilosea (C)
Metromonadea (F)
Granofilosea (O)
Chlorarachnea (F)
Endomyxa (P) >34
Vampyrellida (O)
Phytomyxea (O)
Filoreta (G)
Gromia (G)
Ascetosporea (C)
Retaria
Foraminifera (P) ~950
Monothalamea (C/O?)
Tubothalamea (C)
Globothalamea (C)
Radiolaria (P)
Acantharea (C) 50
Taxopodida (F) 1 + environmental clades
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Polycystinea (C) ~470
Accepted Article
Aquavalon (G)
Tremula (G)
Excavates
Metamonada 133
Fornicata
Parabasalia
Preaxostyla
Discoba 94
Jakobida
Tsukubamonas (G)
Heterolobosea
Euglenozoa (P)
Euglenida (C)
Diplonema (O)
Symbiontida (F)
Kinetoplastea (C)
Table 2. Classification of the higher ranks of the protists and multicellular organisms. The
authority to whom the taxon name is attributed appears immediately after the taxon name.
For purposes of nomenclature and stability of names in the classification, we have tried to
retain the oldest term that correctly described the grouping, emended if necessary; in the
square bracket following are inappropriate and incorrect names used in the literature, or that
do not have nomenclatural priority. If the taxon name has been emended herein, the
authority is indicated and the reference is to this manuscript (“emend. Adl et al. 2019”).
Selected references to the literature since 2012 can be found in Appendix 1. Citations in the
notes to this table can be found in the LITERATURE CITED. Named clades are
monophyletic as best as we can determine; if paraphyly or polyphyly is suspected, it is
indicated by P; robust clades recovered in phylogenetic analysis that do not have
morphological diagnosis are indicated by R (ribo-group); monotypic group with only one
described species are indicated by M; MTOC, microtubular organizing center. *Denotes
genera lacking DNA sequence information or known to require taxonomic revision.
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AMORPHEA Adl et al. 2012
Accepted Article
The least inclusive clade containing Homo sapiens Linnaeus 1758, Neurospora crassa
Shear and Dodge 1927 (both Opisthokonta), and Dictyostelium discoideum Raper 1935
(Amoebozoa). This is a node-based definition in which all of the specifiers are extant; it is
intended to apply to a crown clade; qualifying clause – the name does not apply if any of the
following fall within the specified clade – Arabidopsis thaliana (Linnaeus) Heynhold 1842
(Archaeplastida), Tetrahymena thermophila Nanney and McCoy 1976 (Alveolata),
Thalassiosira pseudonana Hasle and Hiemdal 1970 (Stramenopiles), Bigelowiella natans
Moestrup and Sengco 2001 (Rhizaria), Euglena gras Klebs 1883 (Excavata), and Emiliania
huxleyi (Lohmann) Hay and Mohler 1967 (Haptophyta).
Incertae sedis Amorphea: Obazoa Brown et al. 2013 (R)
Obazoa is a clade that is robustly recovered in phylogenetic trees and consits of the
Opisthokonta and two other clades, Apusomonadida and Breviatea. It is the least inclusive
clade containing Homo sapiens Linnaeus 1758 (Opisthokonta), Neurospora crassa Shear &
Dodge 1927 (Opisthokonta), P. biforma Brown et al. (Breviatea), and Thecamonas trahens
Larsen & Patterson 1990 (Apusomonadida).
● Apusomonadida Karpov & Mylnikov 1989
Gliding cells (5–15 µm), with dorsal cell membrane underlain by thin theca extending
laterally and ventrally as flanges that delimit a broad ventral region from which pseudopodia
develop in most genera; with two heterodynamic cilia, the anterior enclosed by sleeve-like
extension of flanges to form a proboscis and the posterior cilium lying within the ventral
region; tubular mitochondrial cristae; phagocytosis of bacteria. Amastigomonas,
Apusomonas, Chelonemonas, Manchomonas, Multimonas, Podomonas, Thecamonas.
● Breviatea Cavalier-Smith & 2004
Amoeboid gliding cells (10–15 µm) with single anteriorly-directed apical cilium and in some
isolates a second posteriorly-directed cilium; filopodia projecting unilaterally from cell,
perpendicular to anteroposterior axis and direction of movement; filopodia forming at anterior
end, moving posteriorly as cell moves forward (filopodia appearing attached to substrate),
and resorbed at posterior; cell can also produce broad lamellopodia; anaerobic or
microaerophilic, with large mitochondrion-like organelle; ingests bacteria; can form cysts.
Breviata, Lenisia, Pygsuia, Subulatomonas.
Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998
Organisms almost all demonstrating ‘amoeboid activity’1 in all or in certain stage(s) of their
life cycle. Amoeboid locomotion with steady flow of the cytoplasm or occasional eruptions in
some groups; alternatively, amoeboid locomotion involving the extension and retraction of
pseudopodia and/or subpseudopodia with little coordinated movement of the cytoplasm.
Cells naked, often with well-developed, differentiated glycocalyx; in several groups cells are
covered with a tectum2 or a cuticle3. Two groups are testate (enclosed in a flexible or hard
extracellular envelope with one to several opening(s)). Mitochondrial cristae tubular
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Accepted Article
(ramicristate), with few exceptions; mitochondria secondarily reduced to mitochondrionrelated organelles (MRO) in archamoebians. Most only reported to be asexual, but sex and
life cycles consistent with sex have been reported in all three major lineages – Tubulinea,
Evosea, and Discosea. Many taxa exhibit either sporocarpic4 or sorocarpic5 fruiting.
Biciliated, uniciliated, or multiciliated stages in the life cycle of some taxa; some taxa exhibit
reduction of the bikont kinetid to a unikont kinetid.
1
The ability of a unicellular organism or a cell type in a multicellular organism to actively
change the conformation of the entire cell body by extending and retracting pseudopodia;
pseudopodia are used for cell movement over the substratum and/or for feeding.
2
Monolayer of scales covering the cell adhering to the substratum from the dorsal surface;
the ventral surface of the cell remains free. Known in amoebae of the genus Cochliopodium.
3
Layer of fibrous material covering the cell, adhering to the substratum from the dorsal
surface; the ventral surface remains free. Known in amoebae of the genera Gocevia,
Paragocevia and Ovalopodium.
4
Single amoeboid cell differentiates into a usually stalked, subaerial structure that supports
one to many propagules termed spores. As defined here, this kind of sporocarp has only
ever been observed in Amoebozoa and is potentially synapomorphic for Amoebozoa. Should
this prove the case, non-sporocarpic amoebozoans are the products of reductive evolution.
5
Amoebae aggregate into a multicellular mass that develops into a multicellular, subaerial
fruiting body consisting of either distinct stalk cells and spores or non-differentiated encysted
cells (usually also called spores). Sorocarpic development is found in two lineages of
amoebozoans, the Dictyostelia (Eumycetozoa) and in Copromyxa (Tubulinea).
Incertae sedis Amoebozoa: Belonocystis*, Boveella*, Biomyxa, Corallomyxa, Gibbodiscus*,
Hartmannia*, Malamoeba*, Malpighamoeba*, Microcorycia*, Microglomus*, Oscillosignum*,
Parmulina*, Penardochlamys*, Pseudothecamoeba*, Rhabdamoeba*, Schoutedamoeba6,
Stereomyxa*7, Subulamoeba*, Thecochaos*, Triaenamoeba*, Unda*8, Zonomyxa*
6
The species Schoutedamoeba minuta described by Van Vichelen et al. (2016) has a
hartmannelid morphology (monopodial cells with pronounced frontal hyaline cap) but in SSU
tree it shows affinities with Variosea, although with no support. More robust data are
necessary to clarify its position among Amoebozoa.
7
The taxon name Stereomyxa ramosa is used in Tekle et al. (2016) and Tekle and Wood
(2017) for an isolate that is a distinct genus named Dracoamoeba (see Tice et al. 2016). To
date, no molecular data on a true Stereomyxa are available and thus it remains incertae
sedis.
8
The name Unda is used in Tekle et al. (2016) as well as in Tekle and Wood (2017) for an
isolate of Vannella as noted in Cavalier-Smith et al. (2016) and Kang et al. (2017).
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●Tubulinea Smirnov et al. 2005
Accepted Article
Organisms producing lobose pseudopodia (lobopodia)9. The entire cell or individual
pseudopodia (in polypodial cells) are tubular, cylindrical, or subcylindrical, rounded in crosssection. If cells are flattened or branched they are capable of altering the locomotive form
from a flattened, expanded one to monopodial or polypodial, with subcylindrical
pseudopodia. Monoaxial flow of the cytoplasm in every pseudopodium or in the entire cell.
No convincing evidence of ciliate stages 10. Two groups are testate, and two sorocarpic taxa
are known. No sporocarpy has been reported.
9
Variable cell projections, smooth in outline, with rounded tips, which participate in the
relocation of the main cytoplasmic mass of the cell and include both the granuloplasm and
the hyaloplasm (sensu Smirnov 2008).
10
Schaudinn (1899) reported a complex life cycle in Trichosphaerium (Corycida) that
included biciliated stages, which undergo copulation; no further confirmation of this
observation has been obtained.
●●Corycida Kang et al. 2017
Cells covered with flexible, leather-like coating forming one or several openings used to
protrude pseudopodia or are enclosed in hard test made of spicules with multiple apertures.
The least inclusive clade containing Amphizonella sp.11, Diplochlamys sp.11,
Trichosphaerium sp.11. Amphizonella, Diplochlamys, Trichosphaerium 12 .
11
Strain numbers and source data for these isolates are provided by Kang et al. (2017).
12
The genus Atrichosa Cavalier-Smith et al. 2016 is considered here a junior synonym of
Trichosphaerium until the opposite is shown. The position of the genera Penardochlamys,
Microcorycia, Zonomyxa and Parmulina, which were listed by Meisterfeld (2002) under
“Microcoryciidae” is not clear; by their morphological characters they may belong to this
lineage as well but this requires demonstration by molecular data.
●●Echinamoebida Cavalier-Smith 2004 (R)
Cells tubular, vermiform or flattened, with or without spine-like subpseudopodia; capable of
adopting subcylindrical monopodial form under certain conditions. The least inclusive clade
containing Vermamoeba vermiformis, Echinamoeba silvestris and Micriamoeba tesseris.
Echinamoeba, Micriamoeba, Vermamoeba.
●●Elardia Kang et al. 2017 (R)
Cells naked or covered with a hard test; tubular or produce tubular pseudopodia; if flattened
or branched, capable of altering the locomotive form to monopodial or polypodial, with
tubular pseudopodia. The least inclusive clade containing Amoeba proteus, Arcella
intermedia, and Rhizamoeba saxonica.
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●●●Leptomyxida Pussard & Pons 1976 sensu Smirnov et al. 2017
Accepted Article
Naked amoebae with locomotive form altering from a flattened expanded or reticulate one to
a subcylindrical monopodial one when in rapid movement or under specific conditions;
adhesive uroidal structures always present. Flabellula, Gephyramoeba*, Leptomyxa,
Rhizamoeba.
●●●Arcellinida Kent 1880
Cell covered with hard or highly rigid organic or mineral extracellular test consisting of either
self-secreted elements (calcareous, siliceous, or chitinoid), a sheet-like chitinoid structure, or
recycled organic or mineral particles bound together, with a single main opening.
Incertae sedis Arcellinida: Argynnia, Awerintzewia*, Geamphorella*, Jungia*,
Lagenodifflugia*, Lamtoquadrula*, Leptochlamys*, Maghrebia*, Microquadrula*,
Paraquadrula*, Pentagonia*, Pseudawerintzewia*, Pomoriella*, Pontigulasia*, Physochila,
Schoenbornia*, Sexangularia*, Zivkovicia*.
●●●●Sphaerothecina Kosakyan 2016
Test rigid or more or less flexible, either completely chitinoid or comprising recycled organic
or mineral particles held together by an organic cement, or composed of self-secreted
chitinoid or siliceous elements; always rounded in radial symmetry but varying in height from
flattened saucer-shaped, hemispheric or more elongated to egg-shaped; pseudostome
circular or lobed, surrounded by a collar; produce thick, digitate pseudopodia. Antarcella*,
Arcella, Cornuapyxis*, Cucurbitella*, Cyclopyxis*, Distomatopyxis*, Ellipsopyxella*,
Ellipsopyxis*, Geopyxella*, Lamptopyxis*, Netzelia, Protocucurbitella*, Pseudocucurbitella*,
Pyxidicula, Suiadifflugia*, Trigonopyxis*13.
13
The SSU rRNA sequence of Trigonopyxis arcula AY848967 is almost identical to
Bullinularia indica AY848970, and represents probably a contamination.
●●●●Difflugina Meisterfeld 2002 sensu Kosakyan et al. 2016
Test either completely chitinoid or comprising organic or mineral particles, or recycled diatom
frustules, scales or plates (often from Euglyphida), or composed of siliceous, calcite, or
chitinoid self-secreted plates (idiosomes) held together by an organic cement; may produce
thick, digitate pseudopodia, or move using a flattened, disc-like hyaline projection.
Alocodera, Apodera, Bullinularia, Centropyxis, Certesella, Cornutheca, Difflugia,
Geoplagiopyxis*, Gibbocarina, Hyalosphenia, Hoogenraadia*, Lesquereusia, Longinebela,
Mrabella, Nebela, Oopyxis*, Padaungiella, Paracentropyxis*, Plagiopyxis*,
Planhoogenraadia*, Planocarina, Porosia, Proplagiopyxis*, Protoplagipyxis*, Quadrulella,
Spumochlamys, probably Conicocassis*, Microchlamys*, Pseudonebela*.
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●●●●Heleopera sphagni Leidy 187414
Accepted Article
Test reinforced with mineral particles, slit-like aperture, numerous small digitate
pseudopodia; with symbiotic Chlorella.
14
This species typically positioned as sister clade of both Sphaerothecina and Difflugina in
beta tubulin (Lahr et al., 2011), SSU rRNA (Lara et al., 2008) and multigene phylogenies
(Lahr et al. 2013), so it is listed here as a separate lineage.
●●●●Phryganellina Bovee 1985
Test proteinaceous, with calcified inner layer, or completely chitinoid with recycled mineral or
organic particles; pseudopodia conical, pointed, consist solely of the hyaloplasm, sometimes
branched and may anastomose. Cryptodifflugia, Meisterfeldia*, Phryganella, Wailesella*.
●●●Euamoebida Lepşi 1960 sensu Smirnov et al. 2011
Naked amoebae with tubular, subcylindrical pseudopodia (or the entire cell is monopodial
and subcylindrical); no alteration of the locomotive form; no adhesive uroidal structures;
sorocarpic development in some species. Amoeba, Cashia*, Chaos, Copromyxa,
Copromyxella*, Deuteramoeba, Glaeseria, Hartmannella, Hydramoeba*, Nolandella,
Parachaos*, Polychaos*, Ptolemeba, Saccamoeba, Trichamoeba*.
●Evosea Kang et al. 2017 (R)
Representatives of this clade can vary across almost the entire range of morphologies seen
in Amoebozoa. Many members have complex life cycles12 that include amoeboid, ciliated
and fruiting stages. Some species appear to be exclusively ciliated with no amoeboid
features. Most taxa with only a subset of these life cycle stages. The least inclusive clade
containing Physarum polycephalum (Eumycetozoa), Protostelium nocturnum (Variosea),
Squamamoeba japonica (Cutosea), and Entamoeba histolytica (Archamoebea).
12
In the most complete version spores from a sporocarp germinate as ciliated amoebae,
cells that reversibly are amoeboid or ciliate, that then go on to develop into an obligate
amoeboid stage that cannot produce cilia with the obligate amoeba differentiating into one or
more sporocarps. However, some members are obligate ciliates or obligate amoebae. The
kinetid structures of ciliated stages are diagrammed in Spiegel et al. (2017), Mikrjukov and
Mylnikov (1998), Hibberd (1983), and Pánek et al. (2016).
●●Variosea Cavalier-Smith et al. 2004 (R) 13
Amoebae elongated or flabellate during locomotion and sometimes branched to reticulate,
with long, pointed, often branching and occasionally anastomosing subpseudopodia; ciliated
cells may be the sole state, or present as ciliated amoebaes, or be one state in a life cycle
that also includes obligate amoebae; the kinetid of ciliates bikont or unikont, associated at
least with one cone of microtubules; several taxa contain a sporocarp state. The least
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Accepted Article
inclusive clade containing Flamella balnearia, Protostelium nocturnum, Acramoeba
dendroida and Phalansterium solitaruium.
13
Recent papers with relatively broad taxon sampling, based on SSU phylogeny (Berney et
al. 2015) and multigene phylogeny (Kang et al. 2017) suggest grouping of some variosean
genera into higher rank clades. However, SSU phylogeny shows little or no statistical
support for many of these groupings, while many important variosean taxa are not yet
represented in the multigene trees. Therefore, we prefer to be cautious about including
certain higher level taxa proposed in these studies at this time. Hence we list most variosean
clades under the similarly high level regardless of the traditional ranks until more robust
groups are established.
●●●Flamellidae Cavalier-Smith 2016 (R)
Flattened amoebae capable of forming fan-shaped or semicircular locomotive form with
numerous fine, tapering hyaline subpseudopodia, directed anteriorly; ciliated stages
unknown. The least inclusive clade containing Flamella aegyptia and Telaepolella
tubasferens. Flamella, Telaepolella.
●●●Filamoeba Page 1967 (R)
Flattened amoebae, fan-shaped, triangular or crescent-shaped in locomotion, with numerous
spine-like hyaline subpseudopodia, directed anteriorly; ciliated stages unknown. The least
inclusive clade containing Filamoeba nolandi and F. sinensis. Filamoeba.
●●●Heliamoeba Berney, Bass & Geisen 2015 (R) (M)
Binucleate amoebae with filose-like pseudopodia; with clearly distinct cell body always
present, the pronounced pseudopodia making up most of the total cell dimension; cell body
rarely branching; never reticulate; pseudopodia often branching and present mostly in the
anterior and posterior parts of fully extended cells, or all around the cell body in more
condensed forms; cell movement slow; ciliated stages unknown. Heliamoeba mirabilis.
●●●Protosteliida Olive & Stoianovitch 1966 sensu Shadwick et Spiegel in Adl et al. 2012
Sporocarpic amoebae with acutely pointed subpseudopodia and usually orange
pigmentation contained in lipid droplets visible en masse; one taxon ciliated amoebae with
1–9 unikont kinetids not associated with nucleus; taxa without cilia with ring-shaped
component in a nucleus-associated MTOC; sporocarps of variable morphology, with long,
delicate stalk supporting single spore. The least inclusive clade containing Protostelium
nocturnum and Protostelium mycophaga. Protostelium14.
14
The genus Planoprotostelium is subsumed into Protostelium (Shadwick et al. 2017).
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●●●Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017 (R)15
Accepted Article
Uninucleate, flabellate to branching amoebae; several members sporocarpic, one species
with ciliated amoebaes and obligate amoebae. The least inclusive clade containing
Soliformovum irregularis, Nematostelium gracile, and Acramoeba dendroida. Acramoebidae,
Schizoplasmodiidae, Soliformoviidae.
15
This is the only group revealed in the paper by Lahr et al. (2011) which we suggest to
apply because it is fully supported in a phylogenomic study by Kang et al. (2017) and
combines several monotypic lineages; many of them group with each other in SSU trees as
well.
●●●●Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008 (R) (M)
Uninucleate amoebae, flattened highly branched, with very slender, pointed, sometimes
branched hyaline subpseudopodia never forming a network; ciliated stages unknown.
Acramoeba dendroida.
●●●●Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012
Exclusively sporocarpic group with multinucleate, highly branching and reticulate amoebae,
or plasmodia; plasmodia without directional streaming and a beaded appearance during
mitosis; prespore cells developing from multinucleate fragments of plasmodia; sporocarp
stalk with cup-like apophysis that fits into annular hilum on spore; spores always
multinucleate; one taxon (Ceratiomyxella) with scale-covered ciliated amoebaes that can
develop from zoocysts derived from the plasmodium that germinates from the spore or from
a fragment of a feeding plasmodium; kinetids bikont. The least inclusive clade containing
Ceratiomyxella tahitiensis, Nematostelium ovatum, Schizoplasmodium cavostelioides.
Ceratiomyxella, Nematostelium, Schizoplasmodium.
●●●●Soliformoviidae Lahr & Katz 2011(R)
Uninucleate amoebae, thin, flabellate, fan-shaped to irregularly triangular with numerous
finely pointed hyaline subpseudopodia often heavily concentrated at the leading edge during
locomotion; lobed nucleoli present in at least one stage of the life cycle; multiple small
contractile vacuoles; some species more branched than others; MTOC absent; ciliated
stages unknown; two species sporocarpic; sporocarps deciduous in one species and
ballistosporous in another. The least inclusive clade containing Soliformovum irregularis and
Grellamoeba robusta. Grellamoeba, Soliformovum.
●●●Angulamoeba Berney, Bass & Geisen 2015 (R)
Uninucleate, branching amoebae with slender, pointed and/or filose-like, sometimes
branched pseudopodia; trophozoites moving slowly; main cell body elongated, consisting of
several main branches often with smaller lateral branches, never forming a network;
numerous fine pseudopodia concentrated mostly at the extremities of the lateral and terminal
branches, but can be formed anywhere around the cell body; multiple contractile vacuoles;
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Accepted Article
some species with ciliated amoebae stages. The least inclusive clade containing
Angulamoeba microcystivorans and A. fungorum. Angulamoeba.
●●●Cavosteliida Shadwick & Spiegel in Adl et al. 2012 (R)
Sporocarpic group with various types of amoebae, from uninucleate amoebae to
multinucleate reticulate plasmodia, all characterized by producing long, filose,
subspeudopodia, anastomosing in some taxa; one taxon with ciliated amoebae and obligate
amoeba with possible sex in the life cycle; ciliated amoebae possesses one to several,
reduced unikont kinetids per cell, not associated with the nucleus; species without ciliated
amoebae have akinetid amoebae that germinate from spores; sporocarps in all species with
single, nondeciduous spores; morphology variable and taxon specific; spores of all species
displaying some type of sculpturing; cysts of some species displaying sculpturing as well.
Cavostelium, Schizoplasmodiopsis, Tychosporium.
●●●Ischnamoeba Berney, Bass & Geisen 2015 (R)
Uninucleate, branching naked amoebae, cells usually thin, extended and flat, showing no
well-defined cell body, except often a slight broadening in the area containing the nucleus;
never reticulate, with whole cells often bent, but not extensively branched; branching more
pronounced in condensed cells or in condensed parts of individual cells; very thin
pseudopodia produced almost exclusively at distal parts of cells and more pronounced in
condensed organisms, often branching; movement too slow to be directly observable;
ciliated stages unknown. The least inclusive clade containing Ischnamoeba montana and
Ischnamoeba sp. isolate F4 (Genbank: KP864094). Ischnamoeba.
●●●Darbyshirella Berney, Bass & Geisen 2015
Multinucleate, highly branching and reticulate amoebae with slender, pointed, sometimes
branched and anastomosing pseudopodia; the whole cell body is strongly branching and
narrow, especially in the most extended parts, while more condensed parts are wider;
posterior end usually pointed with no or few pseudopodia and no branching; many
contractile vacuoles present; movement very slow; ciliated stages unknown. The least
inclusive clade containing Darbyshirella terrestris and Darbyshirella sp. (Genbank
KP864088). Darbyshirella.
●●●Holomastigida Lauterborn 1895
Rounded cells with multiple radiating projections, which may be cilia arising from the solitary
kinetosomes. Artodiscus*, Multicilia.
●●●Dictyamoeba Berney, Bass & Geisen 2015 (M)
Multinucleate, highly branching and reticulate naked amoebae with slender, pointed,
sometimes branched pseudopodia; movement of entire cells very slow; the main cell body is
multiply branched and anastomosing, and can grow into giant networks (up to several mm)
with intersecting segments of varying width and numerous terminal branching areas;
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Accepted Article
abundant fine pseudopodia are concentrated mostly at the extremity of lateral and terminal
branches, especially in complex networks, but can be formed anywhere around the cell body
in simpler forms; ciliated stages unknown. Dictyamoeba vorax.
●●●Arboramoeba Berney, Bass & Geisen 2015 (M)
Multinucleate, highly branching and reticulate amoebae; cell body indistinct; nuclei and other
cytoplasmic contents are distributed across the whole network, with network significantly
more complex at the anterior front, forming a wide, very densely reticulate, non-permeable
front where phagocytosis occurs; posterior part of the cells is much less reticulate and
branching; branching, filose-like, pseudopodia are mostly present at the anterior front of the
cell; very strong vacuolar activity across the whole network; movement very slow; ciliated
stages unknown. Arboramoeba reticulata.
●●●Phalansterium Cienkowski 1870
Uniciliate sedentary cells, colonial or solitary; cilium arises from the apical part of the cell;
one centriole per kinetid; ciliary pocket usually surrounded by a collar; some species form
short tapering cytoplasmic projections and move over the substratum using the conformation
of their body or producing cytoplasmic eruptions. The least inclusive clade containing
Phalansterium solitarium and P. filosum. Phalansterium.
●●Eumycetozoa Zopf 1884 sensu Kang et al. 2017 (R)
All known members fruit, either sorocarpically (Dictyostelia), or sporocarpically (Myxogastria,
Protosporangiida); with a life cycle having a single haploid amoeboid state (Dictyostelia); or
a life cycle with a bikont ciliated amoebae state that gives rise to a nonciliate obligate
amoeboid state from which sporocarps develop (Myxogastria and Protosporangiida); ciliated
amoebae of myxogastrids and protosporangiids and amoebae of dictyostelids flat and form
wide pseudopodia with acutely pointed subpseudopodia and no pronounced streaming of
the granular cytoplasm; where sex is well studied, the zygote cannibalizes haploid amoebae.
The least inclusive clade containing Dictyostelium discoideum, Physarum polycephalum, and
Ceratiomyxa fruticulosa.
●●●Dictyostelia Lister 1909, sensu Sheikh et al. 2018 (R)
Sorocarpic amoebae, also known as cellular slime molds or social amoebae, with stalked
fruiting bodies developing from aggregation of amoebae; sorocarps consisting of stalks with
terminal sori of haploid spores; stalks (sorophores) acellular (acytosteloid), cellular and
unbranched or sparsely branched (dictyosteloid), or cellular and regularly branched with
whorls of lateral branches (polysphondyloid); cells of stalks dead, consisting of walls, only, at
maturity; spores usually ellipsoid, spherical in some species; cysts present in some species;
sex, when present associated with a zygote that causes haploid amoebae to aggregate
toward it such that the aggregate lays down a common cyst wall to form a macrocyst in
which the haploid cells are ingested and digested by the zygote and meiosis occurring in the
zygote prior to germination of the macrocyst; amoebae aciliate, haploid, with nucleus with
peripheral reticulate nucleolus; upon starvation, amoebae aggregating, often in streams,
toward an aggregation center that signals with a chemical attractant (an acrasin) with
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Accepted Article
aggregate developing into a slug-shaped, multicellular mass that can migrate then fruit or
fruit directly; anterior cells becoming stalk cells in dictyosteloid and polyspondyloid species
and bulk of the remaining cells becoming spores. Acytostelium, Cavenderia,
Coremiostelium, Dictyostelium, Hagiwaria, Heterostelium, Polysphodylium, Raperiostelium,
Rostrostelium, Speliostelium, Synstelium, Tieghemostelium, probably – Coenonia*16.
16
Coenonia was seen only once by Van Tieghem (1884) who described but never illustrated
it. On the basis of his description, it seems reasonable to conclude it was a dictyostelid.
●●●Myxogastria Macbride 1899 [Myxomycetes Link 1833, sensu Haeckel 1866] (R)
Sporocarpic amoebae where a multinucleate obligate amoeba - the plasmodium differentiates into one or more multinucleate spore-forming masses where the cell cleaves
into individual, uninucleate spores that undergo meiosis after spore wall development in
sexual species; sporocarps can be individual sporangia (with or without stalks), clustered
sporangia, aethalia (massive fruiting derived from a whole plasmodium), or plasmodiumshaped plasmodiocarps; fruiting bodies initially covered by an extracellular peridium and
may contain thread-like spore-suspending capillitium; spores germinating as bikont ciliated
amoebaes with rootlets as with Eumycetozoa with rootlet 3 consisting of a band of several
microtubules; ciliated amoebae developing into plasmodia (involving plasmogamy and
karyogamy of gametic ciliated amoebaes in sexual species); plasmodia usually tubular in
cross section with streaming of central granular cytoplasm. One species known to lack
plasmodial state and one species known to lack ciliated amoebae.
●●●●Lucisporidia Cavalier-Smith 2013 (R)
Containing taxa with light- or bright-colored spores, in mass. Alwisia, Arcyria, Calomyxa,
Cornuvia, Cribraria, Dianema, Dictydiaethalium, Hemitrichia, Licea, Lindbladia, Lycogala,
Metatrichia, Minakatella*, Oligonema, Perichaena, Prototrichia, Reticularia, Trichia,
Tubifera.17
●●●●Columellidia Cavalier-Smith 2015. (R)
Containing taxa predominantly with dark colored spores, in mass. Amaurochaete, Badhamia,
Barbeyella, Brefeldia, Clastoderma, Collaria, Colloderma, Comatricha, Craterium,
Diachaeopsis, Diachea, Diderma, Didymium, Echinosteliopsis, Echinostelium, Elaeomyxa,
Enerthenema, Fuligo, Kelleromyxa, Lamproderma, Leocarpus, Lepidoderma, Leptoderma,
Macbrideola, Meriderma, Mucilago, Paradiachea*, Paradiachaeopsis, Physarella, Physarina,
Physarum, Protophysarum, Stemonaria, Stemonitis, Stemonitopsis, Symphytocarpus,
Willkommlangea.17
17
Many taxa in need of revision because of rampant paraphyly.
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●●●Protosporangiida Shadwick & Spiegel in Adl et al. 2012 (R)
Accepted Article
Exclusively fruiting, with microscopic (protosteloid) sporocarps with a microscopic stalk with
one to four, sometimes more, spores; life cycle with ciliated amoebae stage with rootlets as
Eumycetozoa with rootlet 3 consisting of a band of only two microtubules; giving rise to a
uninucleate to plurinucleate obligate amoeba that develops into one or more sporocarps;
prespore cells site of meiotic prophase and meiosis completed in spore complement.
●●●●Protosporangiidae Spiegel in Adl et al. 2012
With ciliated amoebae as Protosporangiida; obligate amoeba uninucleate to plurinucleate,
often resembling very early developmental stages of myxogastrid plasmodia; individually
developing into a single two to four-spored sporocarp. Clastostelium, Protosporangium.
●●●●Ceratiomyxa Schroeter 1889
With ciliated amoebaes developing from cleavage of germling from a tetranucleate spore;
obligate amoeba is multinucleate plasmodium secreting an extracellular slime mound or
columns upon which it cleaves into single uninucleate prespore cells that individually
develop into a stalked sporocarp bearing a single, tetranucleate spore. Ceratiomyxa.
●●Cutosea Cavalier-Smith et al. 2016
Amoebae bounded by a continuous thin, somewhat flexible, envelope separated from the
plasma membrane and having oval scale-like substructure within a denser matrix; small
pores penetrate the envelope, allowing subpseudopodia to protrude for very slow,
occasional locomotion; locomotive cells flattened, oval, rounded or irregularly triangular.
Armaparvus, Sapocribrum, Squamamoeba.
●●Archamoebea Cavalier-Smith 1983 sensu Cavalier-Smith et al. 2004
Amoebae or ciliated amoebae, anaerobic or microaerophilic, free-living or endobionts of
different invertebrate or vertebrate hosts; ciliated amoebae usually with hyaline lateral
pseudopodia; unikont, with single kinetosome at the base of cilia, connected to the
microtubular cone, in some cases both the kinetosome and the axoneme have atypical
complements of microtubules; without typical mitochondria, in several cases mitochondrial
derivates, i.e. mitosomes, have been demonstrated.
●●●Mastigamoebida Frenzel 1897 sensu Cavalier-Smith 2013
Ciliated amoebaes or amoeboid organisms without cilia. The single motile anterior cilium,
when present, associated with microtubular cone connected to the nucleus. Ciliated
amoebaes with hyaline lateral pseudopodia. Endamoeba*, Endolimax, Iodamoeba,
Mastigamoeba, Mastigina*.
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●●●Pelobiontida Page 1976 sensu Cavalier-Smith 2013
Accepted Article
Anaerobic or microaerophilic ciliated amoebae with slow-beating monokinetid or immobile
polykinetids; ciliated amoebae often with hyaline lateral pseudopodia. Pelomyxa, Mastigella.
●●●Tricholimax Frenzel 1897
Ciliated amoebaes with single immobile cilium, microtubular cone associated with nucleus,
when several nuclei present, each nucleus is connected to its own microtubular cone; with
rhizostyle, derived from the lateral microtubular root. Tricholimax*.
●●●Entamoeba Casagrandi & Barbagallo 1895
Cilia and kinetosomes absent; with mitosomes instead of classical mitochondria;
peroxisomes absent; mitosis closed with endonuclear centrosome and spindle; reduced
Golgi dictyosome. Entamoeba.
●●●Rhizomastix Alexeieff 1911
Ciliates possessing a rhizostyle arising from the basal body of the cilium and probably
derived from the microtubular cone. Rhizomastix.
●Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011
Flattened naked amoebae, never producing tubular, subcylindrical pseudopodia and never
altering the locomotive form to the tubular, subcylindrical one; cytoplasmic flow polyaxial or
without a pronounced axis; ciliated stages unknown; several taxa sporocarpic.
●●Flabellinia Smirnov et al. 2005
Flattened generally fan-shaped, oblong or irregularly triangular cells, never with pointed
subpseudopodia.
●●●Thecamoebida Schaeffer 1926 sensu Smirnov et al. 2011
Flattened amoebae, oblong, lingulate, or irregularly triangular amoebae, usually with dorsal
folds and/or ridges; anterior hyaloplasm often forms an antero-lateral crescent and rarely
occupies more than half of the body length; never produce discrete pseudopodia or
subpseudopodia. Sappinia, Stenamoeba, Stratorugosa, Thecamoeba.
●●●Dermamoebida Cavalier-Smith 2004
Oblong, lancet-shaped or irregularly triangular cells; with a smooth cell surface or with few
wide ridges, never wrinkled; short, wide triangular pseudopodia and, in some,
subpseudopodia of dactylopodial type; thick cell coat, multilayered or consisting of tightly
packed helical structures. Dermamoeba, Mayorella, Paradermamoeba.
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●●●Mycamoeba Blandenier et al. 201718 (M)
Accepted Article
Flattened lingulate amoebae without differentiated glycocalyx; with complex life cycle where
active cells transform into coccoid stages, which undergo subsequent buddings, eventually
turning into ramified structures (pseudomycelia) with spherical cysts in a terminal position on
the ramifications; these pseudomycelia disappear and cysts are released prior to
germinating into active trophozoites. Mycamoeba gemmipara.
18
The species Mycamoeba gemmipara in Blandenier et al. (2017) groups with
Dermamoeba, however the phylogenetic analysis in this paper uses a limited number of taxa
and does not show Dermamoebida as a clade, so we list this genus as a separate branch
until it position is better resolved.
●●●Dactylopodida Smirnov et al. 2005 sensu Kang et al. 2017
Locomotive form mostly has a shape of an irregular triangle with basement directed forward;
wide anterior hyaloplasm; fibrous axial cores both in dactylopodia and in the floating
pseudopodia. Cunea, Janickina*19, Korotnevella, Neoparamoeba, Paramoeba,
Pseudoparamoeba, Vexillifera.
19
Two known species of this genus – J. chaetognathi (Grassi, 1881) and J. pigmentifera
(Grassi, 1881) are not triangular but monopodial in locomotion which may be a consequence
of their parasitic life style. No molecular data on this genus are available, so it is left among
the Dactylopodida provisionally, basing on the presence of a kinetoplastid intracellular
symbiont (PLO), which appeares to have originated only once in the evolution of
paramoebids (Sibbald et al. 2017).
●●●Vannellida Smirnov et al. 2005
Locomotive form fan-shaped to spatulate; cells do not form discrete pseudopodia or
subpseudopodia; wide anterior hyaloplasm up to a half of the cell; posterior granuloplasm
concentrated in a “hump”, often raised over the substratum; one species of Vannella (V.
fimicola) with protosteloid sporocarps. Clydonella, Lingulamoeba, Paravannella,
Pessonella*20, Ripella, Vannella.
20
This genus may be a junior synonym of Vannella, being a life form of some Vannella
species.
●●Stygamoebida Smirnov et al. 2011 (P)21
Flattened, elongate amoebae resembling tooth-picks or splinters, temporarily acquiring
forked or branched form; elongate, expanded area of anterior hyaloplasm; mitochondrial
cristae flattened, ribbon-like; MTOC known in one species. Stygamoeba, Vermistella.
This article is protected by copyright. All rights reserved.
21
Accepted Article
These genera group together in some SSU phylogenetic trees, but usually they appear as
separate branches in phylogenetic studies. In the phylogenomic study of Kang et al. (2017)
they do not form a clade, but this is the only region of the tree that is not fully supported.
Taking into account the superficial similarity of the ultrastructure, including the unique shape
of the mitochondrial cristae, in these two genera we suggest keeping this assemblage as a
potential branch in the tree unless the opposite is proven with increased taxon sampling.
●●Centramoebia Cavalier-Smith et al. 2016 (R)
MTOC located near the dictyosome; several taxa with protosteloid sporocarpy. The least
inclusive clade containing Pellita catalonica, Gocevia fonbrunei, Endostelium zonatum,
Acanthamoeba castellanii.
●●●Acanthopodida Page 1976
Flattened with prominent subpseudopodia, flexible and tapering to a fine tip and sometimes
furcated near their base (acanthopodia); without adhesive uroid; trilaminate MTOC; some
species in culture appear as a branched, flattened sheet; at least two taxa, Acanthamoeba
and Luapeleamoeba, contain species with protosteloid sporocarpy. Acanthamoeba,
Balamuthia, Dracoamoeba, Luapeleamoeba, Protacanthamoeba, Vacuolamoeba.
●●●Pellitida Smirnov & Cavalier-Smith 2011 sensu Kang et al. 2017
Thick cell coat envelops the entire cell with the exception of subpseudopodial tips and is
integrated with plasma membrane, or is located on the dorsal surface only, and is loosely
attached to the plasma membrane; MTOC, when known, trilaminate. One genus,
Endostelium, with several protosteloid sporocarpic species. Endostelium, Gocevia,
Paragocevia*, Pellita.
●●●Himatismenida Page 1987
Dorsal surface covered with a flexible coat without defined aperture; ventral surface entirely
or partly naked; can form ventral flattened sheet of hyaloplasm used for adhesion to the
substratum; MTOC, when known, bar-like. Cochliopodium, Ovalopodium, Parvamoeba.
Opisthokonta Cavalier-Smith 1987, emend. Adl et al. 2005
Single posterior cilium without mastigonemes, present in at least one life cycle stage or
secondarily lost; with a pair of kinetosomes or centrioles, sometimes modified; flat (rarely
tubular) mitochondrial cristae in the unicellular stage.
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● Holozoa Lang et al. 2002 (R)
Accepted Article
The most inclusive clade containing Homo sapiens Linnaeus 1758 (Metazoa), but not
Neurospora crassa Shear and Dodge 1927 (Fungi). This is a branch-based definition in
which all the specifiers are extant.
The apparent composition of Holozoa is Filasterea (Ministeria, Capsaspora, Pigoraptor),
Ichthyosporea, Corallochytrium, Syssomonas, Choanoflagellata, and Metazoa,. The primary
reference phylogenies are Carr et al. (2017, Fig. 2), Hehenberger et al. (2017, Fig. 2),
Torruella et al. (2015, Fig. 1), Simion et al. (2017, Fig. 3), Whelan et al. (2017, Fig. 2).
Incertae sedis Holozoa:
Corallochytrium 22 limacisporum Raghu-Kumar 1987 (M)
Spherical single cells 4.5–20 µm in diameter; binary fissions releasing numerous elongated
amoeboid cells; marine saprotrophic, usually recovered from coral reefs in the Indian Ocean;
free-living cells grow as osmotrophic chitin cell-walled schizont as ichthyosporeans; a ciliary
apparatus has been observed in culture conditions and further demosntrated by molecular
means (conserved ciliary toolkit expressed in transcriptome).
Syssomonas 22 Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017 (M)
Predominantly unicellular, roundish uniciliated motile swimming cells; cilium emerges from
the middle-lateral point of the cell, ended by short acroneme and directs backward; cells
naked; cells can form clusters of multiple cells; predatory phagotroph of heterotrophic
chrysomonads and bodonids; life cycle includes unicilaited roundish motile swimming cells,
ciliated amoeboid cells, amoeboid aciliated cells with filopodia, and spherical cysts; known
from freshwater. Syssomonas multiforma.
●● Ichthyosporea 22 Cavalier-Smith 1998 [Mesomycetozoea Mendoza et al. 2002]
Single-celled trophic organisms, Ichthyophonus with hyphal multinucleated filaments; flat
mitochondrial cristae but some may have tubular mitochondrial cristae; if present, single
cilium; without collar or cortical alveoli; some species form only elongate amoeboid cells;
most animal parasites, some free-living and saprotrophic (Sphaeroforma, LKM51 isolate);
chitin reported in cell wall (proven by staining with wheat germ agglutinin and molecular
phylogeny of chitin synthases); both marine and freshwater.
22
Teretosporea Torruella et al. 2015 (R) is a monophyletic clade consisting of at least
Corallochytrium and Ichthyosporea; Pluriformea Hehenberger et al. 2017 (R) is a
monophyletic clade consisting of at least Corallochytrium and Syssomonas. These are two
competing phylogenetic hypotheses.
●●● Dermocystida Cavalier-Smith 1998 [Rhinosporidaceae Mendoza et al. 2001]
Zoospore with posterior cilium; flat mitochondrial cristae; when parasite of animals, spherical
phenotypes with several 2–20 µm endospores that are eventually released and become
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Accepted Article
mature cells with endospores to continue the parasitic cycle. Amphibiocystidium ranae,
Amphibiothecum penneri, Chromosphaera perkinsii, Dermocystidium, Rhinosporidium
seeberi, Sphaerothecum destruens.
●●● Ichthyophonida Cavalier-Smith 1998 [Ichthyophonae Mendoza et al. 2001;
Amoebidiidae Reeves 2003] (R)
Parasites of fish, arthropods, and insects, or free-living and saprotrophic; usually with flat
mitochondrial cristae but Ichthyophonus with tubular mitochondrial cristae; some
characteristic amoeboid cells, but in others, amoeboid cells absent or unreported.
Abeoforma whisleri, Amoebidium parasiticum, Anurofeca richardsi, Astreptonema, Caullerya
mesnili, Creolimax fragrantissima, Eccrinidus flexilis, Enterobryus oxidi, Enteropogon
sexuale, Ichthyophonus, Palavascia patagonica, Pseudoperkinsus tapetis, Psorospermium
haeckeli, Sphaeroforma arctica; S. tapetis.
●● Filasterea Shalchian-Tabrizi et al. 2008
Trophic cells naked, unicellular; uninucleate; aerobic with flat mitochondrial cristae; long
nontapering tentacles supported by microfilaments, unlike collar in choanoflagellates;
phagotrophic. Capsaspora, filose amoeba with cystic and aggregative stages; Ministeria and
Pigoraptor with cilium, Ministeria is not motile but uses a stalk attached to the substrate;
Pigoraptor, ciliated amoeba and predator, as Capsaspora it can present pluricellular clusters.
Capsaspora, Ministeria, Pigoraptor.
●● Choanoflagellata Kent 1880-1882 [Craspedomonadina Stein 1878;
Craspedomonadaceae Senn 1900; Craspedophyceae Chadefaud 1960;
Craspédomonadophycidées Bourrelly 1968; Craspedomonadophyceae Hibberd 1976;
Choanomonadea Krylov et al. 1980; Choanoflagelliida Lee, Hutner, and Bovee 1985;
Choanoflagellatea Cavalier‐Smith 1997 emend. Cavalier-Smith 1998; Choanomonada23 Adl
et al. 2005] 24
Phagotrophic with collar of actin-supported microvilli around a single cilium; radial symmetry;
solitary or colonial; flat mitochondrial cristae; ciliated basal body associated with ring or
multiple arcs of cytoskeletal (cortical) microtubules, with second aciliated basal body located
at an angle; fibrillar root if present minor and without obvious banding; central filament in
kinetosome transition zone.
23
Choanomonada was an unfortunate error in spelling that was corrected in an erratum,
Journal of Eukaryotic Microbiology 60 (3): 321, published online March 11, 2013.
24
The clade that comprises the Metazoa and Choanoflagellata is called Choanozoa Brunet
and King 2017 [Choanozoa Cavalier-Smith et al. 1991]
This is a branch-based definition including the most recent common ancestor of animals and
choanoflagellates (the Urchoanozoan), along with all of its descendants, including Homo
sapiens Linnaeus 1758 and Monosiga brevicollis Ruinen 1938. The Greek root “choanē” (or
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Accepted Article
funnel) refers to the collar, which in the current state of knowledge is a synapomorphy of the
clade. Although “Choanozoa” was used previously to refer to an assemblage of protists that
later proved paraphyletic, that usage was not adopted, and the name is more appropriately
applied as defined here. The informal term “choanimal” and the formal term Apoikozoa have
both been previously proposed for the clade containing choanoflagellates and animals, but
neither has been formally described nor adopted. In particular, the term “Apoikozoa” is
incorrect as the root “apoiko-” refers to colony formation, which is neither universally present
in choanozoans, nor exclusive to them.
●●●Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011
Extracellular glycocalyx or theca that is entirely organic and does not project above the
anterior end of the extended feeding cell; vegetative stage usually sedentary and stalked;
brief motile stage for dispersal.
●●●●Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011
Vegetative cells with glycocalyx or theca that is entirely organic; glycocalyx is flexible,
nonrestrictive and fibrous; theca is rigid and microfibril-based; sedentary cells adhere to a
surface by a peduncle extending from the base of the glycocalyx or theca; cell division with
nonrestricting glycocalyx is longitudinal in situ, with restricting theca it is emergent and
involves cell becoming amoeboid and dividing outside the theca; juvenile daughter cells
disperse as naked; under certain conditions colonies of cells may develop. Type genus:
Salpingoeca James-Clark 1867. Recognized genera: Astrosiga, Aulomonas, Choanoeca,
Cladospongia, Codonocladium, Codonosigopsis, Codosiga (junior synonym Codonosiga),
Desmarella (junior synonyms Codonodesmus and Kentrosiga), Dicraspedella, Diploeca,
Diplosiga, Diplosigopsis, Hartaetosiga, Kentia, Lagenoeca, Microstomoeca, Monosiga,
Mylnosiga, Pachysoeca, Salpingoeca*, Salpingorhiza, Sphaeroeca, Stagondoeca,
Stelexomonas, Stylochromonas.
●●●Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
Cells surrounded by a basket-like lorica of siliceous costae comprising rod-shaped costal
strips and a partial or entire organic matrix on inner surface.
●●●●Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011
Lorica with costae arranged in two layers, outer longitudinal and inner helical; occasionally
only one layer around cell body, in which case costae are helical; adult loricate cells
sedentary; cell cycle, and lorica production accord to nudiform condition; cell division is
diagonal resulting in both daughter cells facing forwards; upper daughter cell (juvenile) is
naked with cilium for dispersal; juvenile attaches to surface, withdraws cilium, and deposits
costal strips in correct orientation; strips are accumulated in vertical bundles on the surface
of the spindle-shaped cell body; costal strips destined for longitudinal costae are deposited
first followed by those for the inner layer of costae; lorica assembly is achieved by a forwards
and clockwise rotation which extends costal strips to form mature pattern of costae. Type
genus: Acanthoeca Ellis 1929. Recognized genera: Acanthoeca, Helgoeca, Polyoeca,
Savillea.
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●●●●Stephanoecidae Leadbeater 2011
Accepted Article
Costae arranged in two layers with longitudinal costae outermost; internal costal layer is
helical in posterior chamber of some species, but usually comprises transverse costae
(rings) in the anterior chamber of lorica and some species only possess transverse rings; cell
cycle and lorica production accords to tectiform condition; costal strips are deposited in
inverted orientation; strips destined for the inner layer of costae are deposited first followed
by those for the outer layer of longitudinal costae; costal strips are exocytosed through
anterior end of cell and accumulated in bundles at the top of the inner surface of the collar;
cell division is inverted with juvenile daughter cell being turned upside down and pushed into
accumulated strips and emerging from parent lorica backwards; costal strips destined for
longitudinal and helical costae are located vertically on juvenile cell, costal strips destined for
transverse costae are located horizontally; once free of parent lorica, juvenile cell constructs
new lorica immediately and there is no swimming dispersal stage. Type genus: Stephanoeca
Ellis 1929. Recognized genera: Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta,
Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina,
Crucispina, Diaphanoeca, Didymoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula,
Platypleura, Pleurasiga, Polyfibula, Saepicula, Saroeca, Spinoeca, Spiraloecion,
Stephanacantha, Stephanoeca*, Syndetophyllum.
●●Metazoa Haeckel 1874, emend. Adl et al. 2005 [Animalia Linnaeus 1758; Eumetazoa
Bütschli 1910]
Reproduction sexual through an egg cell, fertilized usually by a monociliated sperm cell with
acrosome; embryonic development with blastula followed by gastrulation that begins the
differentiation into endoderm, ectoderm, mesoderm, and neuroderm; tissues organized into
organs that share tasks for the individual, unless secondarily lost; some secondarily reduced
to small number of cells (e.g. Myxozoa Grassé 1970); coordination of cells and tissues by
membrane receptors that respond to ligands through elaborate signal transduction;
characteristic cell–cell junctions with belt desmosomes or zonulae adherentes; basal lamina
and extracellular matrix with collagen and other fibrous proteins (laminin, nidogen, perlecan);
heterotrophic nutrition with secretion of digestive enzymes and osmotrophy through a
digestive tract; without cell wall; ectoderm completely surrounding body, and endoderm
surrounding a digestive tract; sensory cells in epithelium; nervous tissue in organized
network; epithelial actin-myosin based contractile cells between endoderm-ectoderm; some
tissues with phagotrophic cells. Subdivisions beyond Porifera and Trichoplax not shown.
●●● Porifera 25 Grant 1836 [Parazoa Sollas 1884]
Flat mitochondrial cristae; sexual species, zygotes forming larva (nine known larval types) or
juveniles; asexual reproduction by gemmules, budding or fragmentation; sessile adult;
differentiation of larva to a variety of cell types, including choanocytes, amoeboid cells, and
cells with granular inclusions; cell types transformable into other types as necessary; cells
more or less independent; without mesoderm, nervous tissue, desmosomes, localized
gonad, or glandular digestive cells.
25
The clade comprising the Porifera, Trichoplax, Cnidaria, Ctenophora, and Bilateria is
called Metazoa, Metazoa Haeckel 1874.
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●●●● Hexactinellida Schmidt 1870
Accepted Article
Exclusively marine, and especially in the deep-sea; siliceous spicules triaxonic, hexactinic;
square axial proteinaceous filament in spicules, whole sponge formed by a single continuous
multinucleate syncytium, with some differentiated cells; electrical conductance across body;
reproduction when known is viviparous with a trichimella larvae.
●●●●● Amphidoscophora Schulze 1886
Amphidisc spicules. Amphidoscosida.
●●●●● Hexasterophora Schmidt, 1870
Hexaster spicules. Lychniscosida Schrammen, 1903; Lyssacinosida Zittel, 1877;
Sceptrulophora Mehl, 1992; Hexasterophora incertae sedis.
●●●● Demospongiae Sollas 1885
Verongimorpha and Keratosa do not have (for the most part) siliceous spicules,
Heteroscleromorpha have a high diversity of siliceous spicules; spicules differentiated in
meglascleres and microscleres, triangular axial proteinaceous filament in spicules; larva with
outer ciliated cells; one family (Cladorhizidae) with extracellular digestion, by amoeboid cell
aggregation of captured crustacean prey; one order Spongillida living in freshwater.
●●●●●Verongimorpha Erpenbeck, Sutcliffe, De Cook, Dietzel, Maldonado, van Soest,
Hooper and Wörheide 2012.
Mostly with spongin skeleton, otherwise with siliceous spicules (Chondrilla),or no skeleton at
all. Synapomorphies include the following ultrastructure characters: orientation of accessory
centriole, the nuclear apex, the Golgi apparatus and similarities in embryonic development.
Chondrillida Redmond, Morrow, Thacker, Diaz, Boury-Esnault, Cárdenas, Hajdu, LoboHajdu, Picton, Pomponi, Kayal and Collins, 2013; Chondrosiida Boury-Esnault and Lopes,
1985; Verongiida Bergquist, 1978.
●●●●●Keratosa Grant 1861
Demospongiae with a skeleton made of spongin fibre; spongin fibres are either homogenous
or pithed and strongly laminated with pith grading into bark. One genus has a hypercalcified
basal skeleton (Vaceletia). Dendroceratida Minchin, 1900; Dictyoceratida Minchin, 1900.
●●●●●Heteroscleromorpha Cárdenas, Pérez and Boury-Esnault, 2012
Demospongiae with a skeleton composed of siliceous spicules which can be monaxones
and/or tetraxones and when they are present, microscleres are highly diversified. Agelasida
Hartman, 1980; Axinellida Lévi, 1953; Biemnida Morrow and Cárdenas, 2015; Bubarida
Morrow and Cárdenas, 2015 Clionaida Morrow and Cárdenas, 2015; Desmacellida Morrow
and Cárdenas, 2015; Haplosclerida Topsent, 1928; Merliida Vacelet, 1979; Poecilosclerida
This article is protected by copyright. All rights reserved.
Accepted Article
Topsent, 1928; Polymastiida Morrow and Cárdenas, 2015; Scopalinida Morrow and
Cárdenas, 2015; Sphaerocladina Schrammen, 1924; Spongillida Manconi and Pronzato,
2002; Suberitida Chombard and Boury-Esnault, 1999; Tethyida Morrow and Cárdenas,
2015; Tetractinellida Marshall 1876; Trachycladida Morrow and Cárdenas, 2015.
●●●● Homoscleromorpha Bergquist 1978
Exclusively marine, from shallow depths to the deep-sea; siliceous spicules or no spicules at
all, tetraxonic, not differentiated between megascleres and microscleres, without defined
axial proteinaceous filament in spicules (only observed in one species); true epithelium;
hermaphroditic; viviparous cinctoblastula larva. Homosclerophorida Dendy, 1905.
●●●● Calcarea Bowerbank 1862 [Calcispongia Johnston 1842]
Exclusively marine, from shallow depths to the deep-sea; calcium carbonate spicules;
viviparous, hermaphrodites.
●●●●● Calcinea Bidder 1898
Unambiguous characters congruent with molecular phylogenies unclear. Larva
amphiblastula. Clathrinida Hartman, 1958; Murrayonida Vacelet, 1981.
●●●●● Calcaronea Bidder, 1898
Unambiguous characters congruent with molecular phylogenies unclear. Larva calciblastula;
hermaphroditic. Leucosolenida Hartman, 1958, Lithonida Vacelet, 1981.
●●● Trichoplax 26 von Schulze 1883 [Placozoa Grell 1971] (M)
Two layers of epithelial cells, with a middle layer of syncytial contractile fibrous cells, and
undifferentiated cells; with digestive glandular cells; belt desmosomes or zonulae adherentes
connecting adjacent cells; without extracellular matrix; collagen fibres absent; without
endoderm, ectoderm, mesoderm or nerve cells; ventral cells having ated kinetosomes with 2
horizontal fibrillar rootlets and one vertical rootlet; egg cell and aciliate sperm in mid-layer;
asexual binary division of body possible. Trichoplax adhaerens.
26
Although monotypic, genetic diversity of isolates indicate there are probably multiple
genera, and it is probably a sister clade to Cnidaria (Srivastava 2008, and Schierwater and
DeSalle 2018).
● Nucletmycea Brown et al. 2009 [syn. Holomycota Liu et al. 2009] (R) 27, 28
The most inclusive clade containing Neurospora crassa Shear and Dodge 1927 (Fungi) and
not Homo sapiens Linnaeus 1758 (Metazoa). The composition of Nucletmycea is Fungi,
Opisthosporidia, Nucleariida, and Fonticula. The primary reference is Brown et al. (2009).
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Accepted Article
Additional phylogenies are Brown et al. (2009, Fig. 3, 4).This is a branch-based definition in
which all the specifiers are extant.
Incertae sedis Nucletmycea: Sanchytriaceae Karpov and Aleoshin 2017
Thallus monocentric, epibiotic, penetrates host wall with rhizoid in parasitic species;
amoeboid zoospores with posterior pseudocilium; sporangia as in Rhizophydiales
(Chytridiomycetes); sexual reproduction not observed. Amoeboradix.
27
Nucletmycea and Holomycota were proposed at about the same period and they are to be
considered synonymous, but Nucletmycea has nomenclatural priority having been published
first. Since, Holomycota has come into more usage in favour of the symmetry with Holozoa.
28
There is no agreement on the definition, thus placement, of a clade named Fungi.
Variations differ from the historical understanding of Fungi that included social amoebae,
now dispersed across protists, and several other clades also dispersed across protists.
●● Rotosphaerida Rainer 1968 [junior syn. Cristidiscoidida Page 1987, Cavalier-Smith 1993,
1998, Nucleariidae Patterson 1983, 1999]
Aciliate predominantly spherical or flattened amoebae from which elongated actin-based
filopodia extend; with flat discoid mitochondrial cristae; uninucleate or polynucleate (with few
nuclei); free-living phagotrophs that feed on bacteria, cyanobacteria and algae. Some
sorocarpic eg. F. alba; some have symbionts eg N. thermophila. Fonticula, Nuclearia,
Parvularia.
Incertae sedis Rotosphaerida: Pompholyxophrys, Lithocolla, Vampyrellidium, Pinaciophora,
Rabdiophrys, Rabdiaster.
●●Fungi 29 R.T. Moore 1980
This is a minimum-crown clade definition:the smallest crown clade containing Rozella
allomycis F.K. Faust 1937, Batrachochytrium dendrobatidis Longcore, Pessier and D.K.
Nichols 1999, Allomyces arbusculus E.J. Butler 1911, Entomophthora muscae (Cohn)
Fresen1856, Coemansia reversa Tiegh. and G. Le Monn1873, Rhizophagus intraradices
(N.C. Schenck and G.S. Sm.) C. Walker and A. Schüßler 2010, Rhizopus oryzae Went and
Prins. Geerl. 1895, Saccharomyces cerevisiae Meyen 1838, and Coprinopsis cinerea
(Schaeff.) Redhead, Vilgalys and Moncalvo 2001. The primary reference phylogeny is
James et al. (2006: Fig. 1); see also James et al. (2013: Fig. 2), Karpov et al. (2013: Fig. 3),
Paps et al. (2013: Fig. 1), Chang et al. (2015: Fig. 1), Torruella et al. (2015: Fig. 1), and
Spatafora et al. (2016: Fig. 1). Its composition is Rozella, Microsporidia, Aphelida,
Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Mucoromycota,
Zoopagomycota, Ascomycota and Basidiomycota (Hibbett et al. 2007, Karpov et al. 2014,
Spatafora et al. 2016). There are no unambiguous morphological, subcellular, or biochemical
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Accepted Article
synapomorphies of Fungi. Most Fungi are filamentous, have chitinous cell walls, lack cilia,
and have intranuclear mitosis with spindle pole bodies instead of centrioles.
29
Holomycota is the sister lineage to Holozoa and is comprised of Fungi and the group
Rotosphaerida containing nucleariids. In this classification we include Opisthosporidia
(Karpov et al. 2014), comprising the endoparasitic lineages Cryptomycota, Aphelida, and
Microsporidia, in the Fungi, noting that this is an ongoing point of contention. New genomic
and transcriptomic data provide modest support for the monophyly of an Opisthosporidia
clade (Toruella et al. 2018), but multiple molecular studies nonetheless support the
placement of all three lineages at the base of the Fungi (Quandt et al. 2017; Toruella et al.
2018). A major point of contention has been the fact that Opisthosporidia all have a
vegetative phase that is unbounded by a cell wall, unlike most Fungi, and that Aphelida and
Rozella have an intracellular (parasitic) phagotrophic feeding mode (Karpov et al. 2014;
Powell et al. 2017). On the other hand, all of the Opisthosporidia share with other Fungi a
chitinous cell wall at some stage in their life cycle. Recent analysis of an aphelid
transcriptome (the lineage that has most retained ancestral characters within
opisthosporidians) suggests a genomic composition and metabolism more aligned with the
free-living chytrid fungi with degradative enzymes, than other Opisthosporidia (Toruella et al.
2018). But an alternative interpretation places empahsis on Opisthosporida cell biology
which is more similar to other Opisthokonta than to Fungi, because of the phagotrophic
nature of their nutrition. Ultimately, additional cell biology and genomic sequencing is needed
for these poorly known organisms. Because there is no synapomorphy for the Fungi
regardless of whether the Opisthosporidia are included (Richards et al. 2017), determining
the constituency of the Fungi will rely on which traits are deemed most relevant (presence of
chitinous cell wall or osmoheterotrophy) as both traits have been convergently derived
across the eukaryote tree. A similar debate is ongoing about the distinction between
Cryptomycota (Rozellida) and Microsporidia (Bass et al. 2018) as some rozellids have a
spore structure very similar to Microsporidia but a genomic content less reduced than core
microsporidia, and more like other Fungi. The stance taken in this classification is to follow
the majority opinion of the mycological community to include Opisthosporidia in the Fungi,
noting that this consensus may change with the discovery of new taxa and improved
phylogenies.
●●● Opisthosporidia Karpov, Aleoshin & Mikhailov 2014.
Opisthokont intracellular parasites/parasitoids with amoeboid vegetative stage. Invasive
spores/cysts with chitin cell wall and specialized apparatus for penetration into host cell
(penetration tube; posterior vacuole); if present, zoospores with filopodia and/or a posteriorly
directed whiplash cilium (functional or rudimental); phagotrophic or osmotrophic.
●●●● Aphelidea Gromov 2000 [=Aphelidida Gromov 2000; =Aphelidiomyceta Tedersoo et
al. 2018; =Aphelidiomycota Tedersoo et al. 2018; =Aphelidiomycotina Tedersoo et al. 2018;
=Aphelidiomycetes Tedersoo et al. 2018;=Aphelidiaceae Tedersoo et al. 2018] 30
Intracellular parasitoids of algae with phagotrophic amoeboid vegetative stage and complex
life cycle; invasive cyst with short infective tube of penetration apparatus; zoospore with
filose pseudopodia and/or lamellipodium; zoospores attach to host cell wall and encyst, then
cyst penetrates host wall with chitin tube, its contents migrates into the host becoming the
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Accepted Article
phagotrophic amoeba which engulfs host cell contents; this results in a characteristic central
food vacuole with red-brownish excretory body; parasite growth and subsequent nuclear
divisions lead to multinucleate plasmodium which consequently produces either a resting
spore rounded to oval with a thick smooth cell wall, or zoospores released from host wall;
mitochondrial cristae from tubular to lamellar. Amoeboaphelidium, Aphelidium,
Pseudoaphelidium, Paraphelidium.
30
The placement of Aphelidea in the Opisthosporidia is unstable and may change.
●●●● Cryptomycota M. D. M. Jones & T. A. Richards 2011 [=Rozellida Lara et al. 2010,
emend Karpov and Aleoshin 2014, =Rozellomycota Doweld 2013; =Rozellosporidia Karpov
et al. 2017; =Rozellomycotina Tedersoo et al. 2018] (R)
Unicellular, holocarpic, zoospores single-celled with a single posterior cilium; cysts with
chitin cell wall; endobiotic (intracellular or intranuclear) parasites; known to be parasites on,
at least, Chytridiomycota, Blastocladiomycota, Peronosporomycetes, Basidiomycota, and
the green alga Coleochaete. Chitin or cell wall may be secondarily lost due to parasitic habit.
Rozella.
●●●● Microsporidia Balbiani 1882
Obligate intracellular parasites, usually of animals but also protists such as Amoebozoa,
Ciliophora, or Apicomplexa; without mitochondria and peroxisomes, with mitosomes; spores
with inner chitin wall and outer proteinaceous wall; without kinetosomes, centrioles or cilia;
centrosomal plaque; extrusive specialized polar tube for host penetration; sexual, asexual or
both. Contains numerous diverse lineages currently poorly defined by morphology, found
ubiquitously in soil, marine, and fresh water. Subdivisions uncertain. Amblyospora,
Amphiacantha, Buxtehudia, Caudospora, Chytridiopsis, Desportesia, Encephalitozoon,
Enterocytozoon, Glugea, Hessea, Metchnikovella, Mitosporidium, Nosema, Nucleophaga,
Paramicrosporidium, Spraguea, Vairimorpha.
●●● Blastocladiales Petersen 1909 [= Blastocladiineae Petersen 1909, Blastocladiomycota
T. Y. James 2007, Blastocladiomycetes T. Y. James 2007]
Thallus monocentric or polycentric; aerobic to facultatively anaerobic, found in aquatic and
terrestrial environments, saprobic and/or parasitic; uniciliated motile cells with microtubules
radiating anteriorly from the proximal end of the kinetosome and continuing on to wrap
around a cone-shaped nucleus that also terminates near the kinetosome and is capped by a
mass of membrane-bound ribosomes; no electron-opaque plug in kinetosome transition
zone; one side-body complex (= microbody lipid globule complex); reproduces asexually by
unciliated cells, while sexual reproduction occurs through fusion of planogametes with a
sporic type of meiosis. Allomyces, Blastocladia, Blastocladiella, Blastocladiopsis,
Catenomyces, Catenophlyctis, Caternaria, Coelomomyces, Coelomomycidium,
Paraphysoderma, Physoderma, Polycaryum, Sorochytrium, Urophlyctis.
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●●●Chytridiomycota Doweld 2001, emend. M. J. Powell in Hibbett et al. 2007
Accepted Article
Thallus monocentric, polycentric, or filamentous; uniciliated zoospores with a posteriorly
directed cilium, nine ciliary props, microbody-lipid globule complex (MLC) consisting of a
cisterna which may be simple or fenestrated (=rumposome), microbodies, and mitochondria
associated with lipid globules; Golgi apparatus with stacked cisternae; nuclear envelope
fenestrated at poles during mitosis; reproduction asexual by uniciliated zoospores and where
known sexually by zygotic meiosis; found in soil and water as saprotrophs but also parasitic
on animals, plants, protists, and other fungi.
●●●●Chytridiomycetes de Bary 1863, emend. Cavalier‐Smith 1998, emend. M. J. Powell in
Hibbett et al. 2007
Thallus monocentric or rhizomycelial polycentric, endobiotic or epibiotic; aerobic. Zoospore
ciliary apparatus posterior and includes a non-ciliated centriole and a ciliated kinetosome,
typically with kinetosome-associated structures; the MLC cisterna is adjacent to the lipid
globule; asexual reproduction by posteriorly uniciliated zoospores, sexual reproduction not
oogamous.
Incertae sedis Chytridiomycetes: Blyttiomyces, Zygorhizidium, Dangeardia.
●●●●● Caulochytriales Doweld 2014
Thallus monocentric, eucarpic with endogenous development; parasitic, penetrating host
with haustorium; sporangium inoperculate, sessile or aerial at tip of hollow-stalk. Zoospore
with posteriorly directed, laterally inserted cilium; non-ciliated centriole at 45° angle to
kinetosome and joined by uniformly dense material; pulsating vacuole; scattered ribosomes;
striated rhizoplast joining kinetosome and nuclear envelope; MLC with one to numerous lipid
globules, branched microbody, simple membrane cisternae and spherical mitochondria.
Caulochytrium.
●●●●●Chytridiales Cohn 1879, emend. Schröter 1892, emend. D. J. S. Barr 1980, emend.
D. J. S. Barr 2001, emend. Letcher and Powell 2006, emend. Mozl.-Standr. 2009, emend.
Vélez et al. 2011
Thallus monocentric or polycentric rhizomycelial, sporangia operculate or inoperculate.
Zoospores covered by cell coat over body; containing a MLC composed of microbodies,
mitochondria and fenestrated or simple cisterna adjacent to lipid globules, paracrystalline
inclusion, an electron‐opaque plug at base of cilium; microtubule root when present a bundle
of parallel microtubules extending from the side of kinetosome to MLC cisterna; kinetosomeassociated structure a shield, saddle, globule, wing , stacked plates or combination;
ribosomes aggregated around or near the nucleus; non-ciliated centriole parallel to ciliated
kinetosome and connected to it by fibrous material; nucleus not associated with kinetosome;
Avachytrium, Chytridium, Chytriomyces, Delfinachytrium, Dendrochytrium, Dinochytrium,
Fayochytriomyces, Irineochytrium, Obelidium, Odontochytrium, Pendulichytrium,
Physocladia, Podochytrium, Pseudorhizidium, Siphonaria, Rhizidium, Rhizoclosmatium.
This article is protected by copyright. All rights reserved.
●●●●●Cladochytriales Mozl.-Standr. 2009
Accepted Article
Thallus epibiotic or endobiotic; eucarpic, monocentric or polycentric with intercalary
swellings; sporangium operculate or inoperculate; rhizoidal axis apophysate or
nonapophysate, and rhizoids can be catenulate, isodiametric or tapering; zoospores with
ribosomal aggregation; MLC with fenestrated cisterna; non-ciliated centriole parallel to
ciliated kinetosome and joined by fibrillar bridge, ciliary plug at base of cilium, up to 25 crosslinked microtubules in a cord‐like microtubular root situated between the kinetosome and the
fenestrated cisterna; lacking paracrystalline inclusions and kinetosome-associated structure.
Allochytridium, Catenochytridium, Cladochytrium, Cylindrochytridium, Endochytrium,
Nephrochytrium, Nowakowskiella, Septochytrium.
●●●●● Gromochytriales Karpov & Aleoshin 2014
Thallus monocentric, eucarpic with endogenous development and inoperculate sporangium;
parasite of green algae; penetrates host with a single, weakly branched rhizoid. Zoospore
spherical to oval; ribosomes clustered, posterior to the nucleus, covering anterior ends of
kinetosome and centriole, and lacking associated endoplasmic reticulum; MLC anterior with
fenestrated cisterna and microbody associated with lipid globule and microbody sandwiched
between lipid globule and nucleus, mitochondria scattered; non-ciliated centriole at a 30°
angle to kinetosome and connected by a dense band over their anterior ends; kinetosomeassociated structure a short, straight spur. Gromochytrium.
●●●●●Lobulomycetales D. R. Simmons 2009, emend. D. R. Simmons 2012
Thallus monocentric, eucarpic with endogenous development; sporangium operculate or
inoperculate; rhizoids isodiametric ranging from 0.5–1.5 μm wide. Zoospore contains a
ribosomal aggregation surrounded by endoplasmic reticulum, an opaque ciliar plug with
anterior or posterior plug extensions, non-ciliated centriole and kinetosome parallel and
joined with a dense amorphous bridge, one to three lipid globules in the MLC; MLC cisterna
absent, simple or irregularly fenestrated; microtubules, kinetosome-associated structures,
and Golgi apparatus absent. Algomyces, Alogomyces, Cyclopsomyces, Clydaea,
Lobulomyces, Maunachytrium.
Incertae sedis Lobulomycetales: Algochytrops.
●●●●● Mesochytriales Doweld 2013
Thallus monocentric, eucarpic with endogenous development and inoperculate sporangium;
parasite of green algae; penetrates host with peg-like haustorium. Zoospore spherical to
oval; ribosomes dispersed; MLC posterior to nucleus with a single lipid globule, large
mitochondrion, lobed microbody, and fenestrated cisterna proximal to kinetosome; rough
endoplasmic reticulum encircles MLC; non-ciliated centriole with a veil and at 30° angle to
kinetosome and connected along their sides by a broad, dense fibrillar bridge; ciliar plug
absent. Mesochytrium.
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●●●●●Polychytriales Longcore & D.R. Simmons 2012
Accepted Article
Thallus monocentric or polycentric lacking intercalary swellings; monocentric species with
multiple rhizoidal axes; sporangia operculate or inoperculate. Zoospore with ribosomal
aggregation; non-ciliated centriole parallel or at slight angle (14-24°) to kinetosome and
connected by dense material throughout their lengths, length of non-ciliated centriole equal
to or longer than its diameter; one to many lipid globules in MLC; may or may not possess
each of the following: a ciliary plug, a kinetosome-associated structure as a spur, a
fenestrated cisterna, and if present 1-3 microtubular roots. Arkaya, Karlingiomyces,
Lacustromyces, Neokarlingia, Polychytrium.
●●●●● Polyphagales Doweld 2014
Thallus interbiotic with multiple rhizoids, functions as a prosporangium; Zoospore with
posteriorly located MLC with fenestrated cisterna and single lipid globule; ribosomes
aggregated with layers of endoplasmic reticulum; disc-like striated rootlet; resting spores
sexually formed. Polyphagus.
●●●●●Rhizophydiales Letcher 2006, emend. Letcher 2008
Thallus monocentric, eucarpic, inoperculate or operculate. Zoospore with one or more of the
following characters: microtubular root with one or more stacked microtubules extending
from one side of the kinetosome to a MLC cisterna on the lipid globule; ribosomes
aggregated with endoplasmic reticulum binding or ramifying through; mitochondria;
microbodies, and fenestrated or simple cisterna associated with lipid globule (MLC); nonciliated centriole either parallel or slightly angled to kinetosome and connected by a fibrillar
bridge; fibrillar bridge either perpendicular to or diagonal between kinetosome and nonciliated centriole; kinetosome‐associated structure when present a solid spur, laminated spur
or shield; no electron‐dense ciliary plug. Alphamyces, Angulomyces, Aquamyces,
Batrachochytrium, Betamyces, Boothiomyces, Collimyces, Coralloidiomyces, Dinomyces,
Gammamyces, Globomyces, Gorgonomyces, Halomyces, Kappamyces, Paranamyces,
Operculomyces, Paranamyces, Pateramyces, Paludomyces, Protrudomyces,
Staurastromyces, Terramyces, Rhizophydium, Uebelmesseromyces, Ulkenomyces,
Urceomyces.
Incertae sedis Rhizophydiales: Homolaphlyctis.
●●●●●Rhizophlyctidales Letcher 2008
Thallus monocentric or polycentric, eucarpic; interbiotic sporangium that is either
inoperculate or endo‐operculate with one to several discharge short tubes; multiple rhizoidial
axes. Zoospore possesses a nonciliated centriole that is at an acute angle (<40°) to the
kinetosome and attached by a fibrillar bridge along the length of the nonciliated centriole;
multiple mitochondria; ribosomes either dispersed or aggregated in the cytoplasm; MLC with
one to many lipid globules, simple MLC cisterna when present; without microtubules.
Arizonaphlyctis, Borealophlyctis, Rhizophlyctis, Sonoraphlyctis.
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●●●●●Spizellomycetales D. J. S. Barr 1980, emend. D. J. S. Barr 1983
Accepted Article
Thallus monocentric, sporangia epibiotic or interbiotic. Zoospore with nucleus either closely
associated with the kinetosome or connected by its root; ribosomes dispersed in the
cytoplasm; MLC cisterna simple; non-ciliated centriole typically at an angle to the ciliated
kinetosome; without electron‐opaque material in the kinetosome transition zone.
Barromyces, Brevicalcar, Bulbosomyces, Fimicolochytrium, Gaertneriomyces, Gallinipes,
Geranomyces, Kochiomyces, Powellomyces, Spizellomyces, Thoreauomyces, Triparticalcar.
Incertae sedis Polyphagales: Endocoenobium.
●●●●● Synchytriales Doweld 2014, emend. Longcore, DR Simmons & Letcher 2016
The least inclusive clade of the Chytridiomycetes that includes Synchytrium taraxaci and
Synchytrium species included in James et al. 2006, Smith et al. 2014, Longcore et al. 2016.
Synchytrium.
Incertae sedis Synchytriales: Micromyces.
●●● Dikarya Hibbett et al. 2007 emend. Hibbett et al. 2018
Unicellular or filamentous Fungi, lacking cilia, often with a dikaryotic state. The leastinclusive clade that contains Ascomycota and Basidiomycota and Entorrhizomycete.
Incertae sedis Dikarya: Entorrhizomycetes Begerow et al., 2007 [=Entorrhizaceae R. Bauer
and Oberw. 1997; =Entorrhizales R. Bauer and Oberwinkler 1997; =Entorrhizomycetes
Begerow et al. 2007; =Entorrhizomycota R. Bauer et al. 2015; =Entorrhizomycotina
Tedersoo et al. 2018] (M)
Phytoparasitic fungi infecting roots with regularly septate coiled hyphae; septal pores without
Woronin bodies or membrane caps. Includes Entorrhizales (Entorrhiza), Talbotiomycetales.
●●●● Ascomycota Cavalier-Smith 1998
Sexual reproduction within asci (saccate structures); meiosis usually followed by mitosis to
produce from one to over 1,000 ascospores, but usually eight; ascospore walls form inside
ascus; mating types heterothallic, homothallic (selfing) or both; may reproduce sexually
(teleomorph) or asexually (anamorph) only, or both sexually and asexually (holomorph); asci
cylindrical, fusiform, clavate or globose, persistent or evanescent, with or without a fruiting
structure (ascoma, -ata); asci developing directly from ascogenous hyphae, from a crozier or
from a single cell; asexual reproduction by conidiospores (mitospores) formed by
fragmentation of vegetative hyphae (thallic), blastically from single cells, hyphae, or
conidiophores; vegetative body of single cells or tubular, septate filaments (hyphae); septa
with simple pores, except for those associated with ascogenous hyphae and asci; cell walls
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Accepted Article
lamellate with a thin electron-dense outer layer and a relatively thick electrontransparent
inner layer, consisting of varying proportions of chitin and glucans; saprobes, endophytes,
parasites (especially on plants) or lichen forming.
●●●●● Taphrinomycotina O. E. Eriksson and Winka 1997
Mycelium present or absent; asci produced from binucleate cells; do not form croziers or
interascal tissue.
●●●●●● Archaeorhizomyces Rosling and T. James 2011 [=Archaeorhizomycetes Rosling
and T. James 2011; =Archaeorhizomycetales Rosling and T. James 2011]
Phylogenetically placed among Taphrinomycotina, differing by mycelial growth on MMN agar
together with an association with roots of living plants. Distinctive molecular characters
(nuclear large subunit rRNA). Synonymous to "Soil Clone Group 1 (SCG1)".
Archaeorhizomyces finlayi.
●●●●●● Neolecta Spegazzini 1881 [=Neolectomycetes Eriksson and Winka 1997;
=Neolectales Landvik et al. 1997; =Neolectaceae Redhead 1977] (M)
Mycelium present, multinucleate; ascomata apothecial, stalked, fleshy; interascal tissue
absent; cylindrical asci formed from binucleate cells undergo karyogamy, meiosis, and one
mitotic division to produce eight cylindrical ascospores, thin-walled, walls blueing in iodine;
ascus apex truncate, slightly thickened below ascus wall, with wide apical slit, persistent;
ascospores ellipsoidal to globose, hyaline, aseptate; anamorph unknown; saprobic; found in
wet mixed woodlands. Neolecta flavovirescens.
●●●●●● Pneumocystis P. Delanoë and Delanoë 1912 [=Pneumocystidales O. E. Eriksson
1994; =Pneumocystidomycetes Eriksson and Winka 1997; =Pneumocystidaceae] (M)
Mycelium and ascomata absent; vegetative cells thin-walled, irregularly shaped, uninucleate,
dividing by fission; sexual reproduction initiated by fusion of two vegetative cells followed by
karyogamy, cyst wall formation, meiosis, and in some, one mitotic division, to produce four to
eight nuclei that are delimited by the cyst (ascus) vesicle; ascospore walls are deposited
between the delimiting membranes; cyst walls rupture to release ascospores; extracellular
parasite of mammalian lungs. Pneumocystis carinii.
●●●●●● Schizosaccharomyces Lindner, 1893 [=Schizosaccharomycetaceae Beij. ex Klöcker
1905; Schizosaccharomycetales O. E. Eriksson et al. 1993; =Schizosaccharomycetes O. E.
Eriksson and Winka 1997] (M)
Mycelium absent or poorly developed; ascomata absent; vegetative cells cylindrical,
proliferating by mitosis followed by cell division to produce two daughter cells; cell wall
composition differs from that of species of Saccharomycetes; sexual reproduction initiated by
fusion of two vegetative cells to form an ascus; karyogamy and meiosis occur within the
ascus to produce four nuclei, which may or may not divide once again mitotically;
ascospores aseptate, delimited by enveloping membrane system (EMS), wall formed within
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Accepted Article
bilayers of EMS, wall blueing in iodine, hyaline or pigmented; saprophytes in sugary plant
exudates; fermentation positive. Schizosaccharomyces pombe.
●●●●●● Taphrinales Gäumann and C. W. Dodge 1928 [=Taphrinomycetes O. E. Eriksson
and Winka 1997]
Vegetative mycelium mostly absent; ascomata absent; interascal tissue absent; dikaryotic
mycelium infects host and proliferates through host tissue; dikaryotic cells or mycelium
develop directly into asci, often forming a palisade layer on the host; asci globose or
ellipsoidal, eightspored; ascospores hyaline, aseptate; biotrophic on angiosperms forming
galls or lesions; cells bud from ascospores to form a yeast-like, monokaryotic, saprobic
anamorph. Protomyces, Taphrina.
●●●●● Saccharomycetales Kudryavtsev 1960 [=Saccharomycetes O.E. Eriksson and
Winka, 1997; =Saccharomycotina O.E. Eriksson and Winka 1997]
Mycelium mostly absent or poorly developed; hyphae, when present, septate, with septa
having numerous pores rather than a single septal pore; vegetative cells proliferating by
budding or fission; walls usually lacking chitin except around bud scars; ascomata absent;
sexual reproduction by fusion of two vegetative haploid cells or fusion of two haploid nuclei
in a single cell or within diploid cells, followed by meiosis and, in some cases, one mitotic
division to produce either four or eight nuclei; cells undergoing meiosis become asci,
ascospores delimited by an enveloping membrane system (EMS); ascospore wall formed
within bilayers of EMS; ascospores aseptate, colourless or pigmented, often with wall
thickenings of various types; most osmotrophic, some species parasitic on animals.
Ascoidea, Candida, Cephaloascus, Dipodascus, Endomyces, Lipomyces, Metschnikowia,
Pichia, Saccharomyces, Scheffersomyces, Trichomonascus, Wickerhamomyces, Yarrowia.
●●●●● Pezizomycotina O.E. Eriksson and Winka 1997
Mycelium present; hyphae filamentous, septate; septa with simple pores and Woronin
bodies; life cycle haploid with a dikaryotic stage immediately prior to sexual reproduction;
ascomata discoid, perithecial, cleistothecial or occasionally lacking; antheridium present or
absent; ascogonium, ascogenous hyphae, and crosiers present; the penultimate cell of the
crozier, in which meiosis and usually one mitotic division occur, becomes the ascus; asci
fissitunicate or not fissitunicate, cylindrical, clavate or saccate; asci frequently with
ascospore discharge mechanism; usually eight ascospores surrounded by enveloping
membrane system; ascospore morphology and pigmentation varied; asexual state present
or absent, produced from vegetative hyphae in a thallic or blastic manner; mitospores
(conidiospores) varied in morphology and pigmentation.
●●●●●● Arthoniales Henssen and Jahns ex D. Hawksw. and O. E. Eriksson 1986
[=Arthoniomycetes O. E. Eriksson and Winka 1997]
Ascomata usually apothecial, occasionally closed with an elongated poroid opening;
peridium thin- or thick-walled; interascal tissue of branched paraphysoids in a gel matrix;
asci thick-walled, fissitunicate, blueing in iodine, with or without a large apical dome;
ascospores aseptate or septate, sometimes becoming brown and ornamented; anamorphs
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Accepted Article
pycnidial; forming crustose lichens with green algae, lichenicolous or saprobic on plants.
Arthonia, Chrysothrix, Melaspilea, Opegrapha, Roccella, Roccellographa.
●●●●●● Dothideomycetes O. E. Eriksson and Winka 1997
Ascomata variable (apothecial, perithecial, cleistothecial), formed lysigenously from
stromatic tissue (ascolocular); interascal tissue present or absent, of branched paraphysoids
or pseudoparaphyses; asci cylindrical to saccate, thick-walled, fissitunicate, rarely with apical
structures; ascospores mostly septate or muriform, colorless to dark brown; anamorphs
hyphomycetous or coelomycetous; saprobes, plant parasites, coprophilous or lichen forming.
Note that this group partially includes loculoascomycetes. Containing Dothideomycetidae
(Capnodiales, Dothideales, Myriangiales), Pleosporomycetidae (Hysteriales, Jahnulales,
Mytilinidiales, Pleosporales).
Incertae sedis Dothideomycetes: Containing Abrothallales (Abrothallus), Acrospermales
(Acrospermum, Oomyces), Asterinales (Asterina), Asterotexiales (Asterotexis),
Botryosphaeriales (Botryosphaeria, Guignardia, Saccharata), Eremithallales
(Encephalographa), Microthyriales (Microthyrium), Minutisphaerales (Minutisphaera),
Monoblastiales (Monoblastia, Anisomeridium), Natipusillales (Natipusilla), Patellariales
(Baggea, Patellaria), Phaeotrichales (Phaeotrichum), Stigmatodiscales (Stigmatodiscus),
Strigulales (Strigulales), Superstratomycetales (Superstratomyces), Trypetheliales (Laurera,
Trypethelium), Tubeufiales (Tubeufia, Bezerromyces, Wiesneriomyces), Valsariales
(Valsaria), Venturiales (Apiosporina, Sympoventuria, Venturia).
●●●●●● Eurotiomycetes O. E. Eriksson and Winka 1997, emend. Geiser et al. 2006 (R)
Morphologically heterogeneous, circumscribed using phylogenetic re-delimitation to contain
Chaetothyriomycetidae, Eurotiomycetidae, Mycocaliciomycetidae and
Sclerococcomycetidae. Important industrially and medically; saprobic, pathogenic on
animals and rarely on plants, some lineages lichenized. Chaetothyriomycetidae
(Chaetothyriales, Pyrenulales, Verrucariales), Coryneliomycetidae (Coryneliales),
Eurotiomycetidae (Eurotiales, Onygenales), Mycocaliciomycetidae (Mycocaliciales),
Sclerococcomycetidae (Sclerococcales).
●●●●●● Geoglossaceae Corda 1838, emend. Schoch et al. 2009 [=Geoglossales Zheng
Wang et al. 2009; Geoglossomycetes Zheng Wang et al. 2009]
Ascomata scattered to gregarious, capitate, stipitate; stipe cylindrical, black, smooth to
furfuraceous; ascigerous portion capitate, club-shaped to pileate, indistinguishable from
stipe; hymenium surface black, continues with stipe at early development stage; asci
clavate, inoperculate, thin-walled, J+, usually 8-spored; ascospores elongate, dark- brown,
blackish to hyaline, septate when mature; paraphyses filiform, blackish to hyaline; global
distribution, terrestrial, habitat usually boggy and mossy. Geoglossum, Trichoglossum.
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●●●●●● Laboulbeniomycetes Engler 1898
Accepted Article
Mycelium absent except in Pyxidiophorales; cellular thallus hyaline to dark, with basal
haustorium present; ascomata perithecial, surrounded by complex appendages, translucent,
ovoid, thin-walled; interascal tissue absent; asci few and basal, not fissitunicate, clavate,
thin-walled, evanescent, maturing sequentially, usually with four ascospores; ascospores
two-celled, hyaline, elongate, one end modified as attachment to host; anamorphs
hyphomycetous, spermatial; ectoparasitic on insects, some may be coprophilous.
Containing Laboulbeniales, Pyxidiophorales.
●●●●●● Lecanoromycetes O. E. Eriksson and Winka 2001
Ascomata apothecial, discoid, perithecial or elongated, sometimes stalked or immersed,
occasionally evanescent; interascal tissue of simple or branched paraphyses swollen at the
apices, often with a pigmented or iodine-staining epithecium; hymenial gel often present;
asci not fissitunicate, but thick-walled, with a thickened, cap-like apex, often with an internal
apical ocular chamber; ascus walls and thickened apex often stains blue with iodine;
ascospores one to several septate, occasionally, multiseptate, rarely plurilocular, hyaline or
pigmented; anamorphs pycnidial where known; mostly lichen forming with protococcoid
algae, with thallus foliose, fructicose, crustose or occasionally absent; some lichenicolous,
some saprobic. Containing Acarosporomycetidae (Acarosporales), Lecanoromycetidae
(Caliciales, Lecanorales, Lecideales, Leprocaulales, Peltigerales, Rhizocarpales,
Teloschistales), Ostropomycetidae (Arctomiales, Baeomycetales, Hymeneliales, Ostropales,
Pertusariales, Sarrameanales), Umbilicariomycetidae (Umbilicariales).
Incertae sedis Lecanoromycetes: Candelariales (Candelaria, Candelariella)
●●●●●● Leotiomycetes O. E. Eriksson andWinka 1997
Ascomata apothecial, discoid, cleistothecial, elongated or rarely absent; apothecia stalked or
sessile, frequently fleshy, sometimes hairy or with appendages, occasionally stromatic or
sclerotioid; interascal tissue of simple paraphyses or absent; peridium thin- walled; asci
typically inoperculate, cylindrical, thin-walled, not fissitunicate, occasionally with apical pore;
apical apparatus variable; ascospores aseptate or transversely septate, hyaline or
pigmented and longitudinally slightly asymmetrical; anamorphs occasionally present,
hyphomycetous or coelomycetous; saprobes or plant parasites, some lichenized or
lichenicolous. Containing Cyttariales (Cyttaria), Erysiphales (Blumeria, Erysiphe,
Microsphaera, Oidium, Podosphaera), Helotiales (Botryotinia, Bulgaria, Dermea,
Hyaloscypha, Lachnum, Leotia, Sclerotinia, Vibrissea), Rhytismatales (Ascodichaena,
Cudonia, Rhytisma), and Thelebolales (Thelebolus, Antarctomyces).
●●●●●● Lichinales Henssen and Büdel 1986 [=Lichinomycetes Reeb et al. 2004]
Ascomata apothecial, discoid, sometimes immersed, occasionally clavate, stalked, setose,
and fleshy; peridium often not well-defined; interascal tissue varied; hymenium often stains
blue with iodine; asci thin-walled or apically thickened, not fissitunicate, without well-defined
apical structures, usually with an iodine-staining outer gelatinized layer; ascospores oneseptate or occasionally multiseptate, ellipsoidal to fusiform, hyaline or pigmented;
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Accepted Article
anamorphs pycnidial; lichenized with cyanobacteria forming crustose, fruticose or foliose
often gelatinized thalli. Gloeoheppia, Heppia, Lichina, Peltula.
●●●●●● Orbiliaceae Nannfeldt 1932 [=Orbiliales Baral et al. 2003; =Orbiliomycetes Eriksson
and Baral 2003]
Ascomata apothecial, small, waxy, translucent or lightly pigmented; interascal tissue of
simple paraphyses, usually with knob-like apices, united by a matrix; asci minute, not
fissitunicate, apex truncate, with J apical rings, often forked at the base; ascospores minute,
cylindrical, hyaline, often aseptate; anamorphs hyphomycetous where known; saprobic,
often on wet wood. Halorbilia, Orbilia.
●●●●●● Pezizales J. Schröter 1894 [=Pezizomycetes O. E. Eriksson and Winka 1997]
Ascomata apothecial or cleistothecial, usually visible with unaided eye, leathery or fleshy;
carotenoids as bright colours to dark, sometimes present; interascal tissue present
(paraphyses); asci not fissitunicate, usually elongated, cylindrical but more or less globose in
cleistothecial species, thin-walled, lacking obvious apical wall thickening or apical apparatus,
with operculum or vertical slit except in cleistothecial species, forcibly discharging
ascospores except in cleistothecial species; ascospores usually ellipsoidal or globose,
aseptate, hyaline to darkly pigmented, smooth or ornamented; anamorphs hyphomycetous,
where known; saprobes on soil, dead wood or dung; some species hypogeous and
mycorrhizal. Ascobolus, Ascodesmis, Caloscypha, Carbomyces, Chorioactis, Discina,
Glaziella Helvella, Karstenella, Morchella, Peziza, Pyronema, Rhizina, Sarcoscypha,
Sarcosoma, Tuber.
●●●●●● Sordariomycetes O. E. Eriksson and Winka 1997 (R)
Defined using molecular phylogenetic methods, by a parsimony comparison of small subunit
rRNA sequences, containing Boliniales (Bolinia, Camarops), Calosphaeriales (Calosphaeria,
Pleurostoma), Chaetosphaeriales (Chaetosphaeria, Melanochaeta), Coniochaetales
(Barrina, Coniochaeta), Diaporthales (Cryphonectria, Diaporthe, Gnomonia, Melanconis,
Phyllachorales (Phaeochora, Phyllachora), Pseudovalsa, Schizoparme, Sydowiella, Valsa,
Vialaea), Magnaporthales (Gaeumannomyces, Magnaporthe, Ophioceras), Ophiostomatales
(Kathistes, Ophiostoma), Sordariales (Annulatascus, Cephalotheca, Chaetomium,
Lasiosphaeria, Neurospora, Sordaria).
Incertae sedis Sordariomycetes: Koralionastetales (Koralionastes, Pontogeneia),
Lulworthiales (Lindra, Lulworthia, Spathulospora), Meliolales (Armatella, Meliola),
Pisorisporiales (Pisorisporium), Trichosphaeriales (Trichosphaeria).
●●●●●● Xanthopyreniaceae Zahlbr. 1926 [=Collemopsidiales Pérez-Ortega et al. 2016;
Collemopsidiomycetes Tedersoo et al. 2018]
Thallus comprised of fine hyphae loosely associated with Cyanobacteria and developing
ascomata; ascomata perithecioid, solitary, unilocular, with a carbonized to hyaline exciple;
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Accepted Article
branched and anastomosing, often irregularly thick, net-like physes; asci bitunicate,
fissitunicate, with ocular chamber, ovoid to subcylindrical, usually stalked; ascospores
hyaline (rarely brownish in mature specimens), oblong to ovoid-fusiform, 1-septate, with
gelatinous perispore usually present; conidiomata pycnidial; conidiogenous cells cylindrical;
conidiogenesis phialidic; conidia bacilliform to ellipsoid; lichenized and lichenicolous fungi
with crustose, epilithic or endolithic, or lichenicolous forms and Cyanobacteria as
photobionts. Collemopsidium, Xanthopyrenia
●●●●●● Xylonomycetes R. Gazis and P. Chaverri 2012
Strongly supported as a separate class within the Pezizomycotina (BS: 100%; PP: 1) and
contained by the superclass ‘Leotiomyceta’ (BS: 100%; PP: 1) sensu Schoch et al. (2009);
based on 6 loci phylogeny (nucSSU, nucLSU, mitSSU, 5.8S, RBP1, and RPB2). Xylona.
Contains Symbiotaphrinales, Xylonales.
●●●● Basidiomycota R. T. Moore 1980
Mycelium present, but some with a yeast state primarily in the Tremellomycetes; basidia
produced in a fertile layer with or without fleshy sporocarp; basidia whole or divided
longitudinally, typically with four spores per basidium but ranging from one to eight; fusion of
compatible mycelia of opposite mating types results in a dikaryotic mycelium in which nuclei
of the parent mycelia remain paired but not fused; karyogamy quickly followed by meiosis,
one or more mitotic divisions and migration of the nuclei into the developing basidiospores;
asexual reproduction may occur through production of conidiospores or via spores produced
on basidia from nuclei that have not undergone karyogamy and meiosis (secondary
homothallism); cell wall with xylose; septa with swelling near pore; septal pore caps
(parenthesomes- multilayered endoplasmic reticulum) usually present, elaborate in
Tremellomycetes; clamp connections present in hyphae or at base of basidia in some
groups; mycelial or yeast states; karyogamy typically in probasidium or teliospore, followed
by meiosis in a separate compartment (metabasidia), but in some it occurs in the same
compartment (holobasidia); holobasidia remain whole or fragment at septation after meiosis
(phragmobasidia); metabasidia typically transversely septate with basidiospore borne
laterally; cell wall with xylose; parenthesome pore caps absent but with microbodies at septal
pores; septal pores occluded by a plug; centrosome multilayered; many are plant pathogens
(rusts), animal pathogens, non-pathogenic endophytes, and rhizosphere species.
●●●●● Agaricomycotina Doweld 2001
With a type B secondary structure of the 5S RNA; a cell wall carbohydrate composition with
dominance of glucose and presence of xylose.
●●●●●● Agaricomycetes Doweld 2001
Fruiting bodies hymenomycetous or gasteroid; basidia two- to eight-spored; parenthesomes
perforate or imperforate. The least-inclusive clade containing Agaricomycetidae (Agaricales,
Amylocorticiales, Atheliales, Boletales, Jaapiales, Lepidostromatales), Phallomycetidae
(Geastrales, Gomphales, Hysterangiales, Phallales).
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Accepted Article
Incertae sedis Agaricomycetes: Auriculariales (Auricularia, Exidia, Hyaloria), Cantharellales
(Botryobasidium, Cantharellus, Ceratobasidium, Clavulina, Hydnum, Tulasnella), Corticiales
(Corticium, Punctularia), Gloeophyllales (Gloeophyllum), Hymenochaetales
(Hymenochaete), Polyporales (Antrodia, Coriolopsis, Donkiopora, Ganoderma, Lentinus,
Phanerochaete, Phlebia, Polyporus, Sparassis, Trametes), Russulales (Heterobasidion,
Lactarius, Peniophora, Russula), Sebacinales (Piriformospora, Sebacina), Thelephorales
(Hydnellum, Sarcodon), Trechisporales (Trechispora) and Tremellodendropsidales
(Tremellodendropsis).
●●●●●● Dacrymycetales Hennings 1898 [=Dacrymycetes Doweld 2001]
Fruiting bodies gelatinous; basidia furcate, rarely unisporous; parenthesomes imperforate.
Cerinomyces, Dacrymyces.
●●●●●● Tremellomycetes Doweld 2001
Dimorphic fungi; fruiting bodies gelatinous or absent; basidia septate or nonseptate;
parenthesomes sacculate or absent. Containing Cystofilobasidiales (Cystofilobasidium,
Mrakia), Filobasidiales (Filobasidium), Holtermanniales (Holtermannia), and Tremellales
(Sirobasidium, Syzygospora, Tremella).
●●●●● Pucciniomycotina R. Bauer et al. 2006 [=Urediniomycetes Swann and Taylor 1995]
Mycelial or yeast states; karyogamy typically in probasidium or teliospore, followed by
meiosis in a separate compartment (metabasidia), but in some it occurs in the same
compartment (holobasidia); holobasidia remain whole or fragment at septation after meiosis
(phragmobasidia); metabasidia typically transversely septate with basidiospore borne
laterally; cell wall with xylose; parenthesome pore caps absent but with microbodies at septal
pores; septal pores occluded by a plug; centrosome multilayered; many are plant pathogens
(rusts), animal pathogens, non-pathogenic endophytes, and rhizosphere species.
●●●●●● Agaricostilbomycetes R. Bauer et al. 2006
Dimorphic, nonphytoparasitic, with fucose as cell wall carbohydrate component, septal pores
without associated microbodies, aseptate basidiospores during germination and no
colacosomes, teliospores, curved holobasidia, and radiate conidia; septal pores without
microbodies, nucleoplasmic spindle-pole body (SPB) separation, metaphasic SPB
intranuclear. Containing Agaricostilbales (Agaricostilbum, Chionosphaera) and
Spiculogloeales (Mycogloea, Spiculogloea).
●●●●●● Atractiellales Oberwinkler and Bandoni 1982 [=Atractiellomycetes R. Bauer et al.
2006]
With symplechosomes. Atractiella, Phleogena, Saccoblastia.
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●●●●●● Classiculales R. Bauer et al. 2003 [=Classiculomycetes R. Bauer et al. 2006]
Accepted Article
With septal pores associated with microbodies and tremelloid haustorial cells. Classicula,
Jaculispora.
●●●●●● Cryptomycocolax Oberwinkler and R. Bauer 1990 [=Cryptomycocolacaceae Oberw.
and R. Bauer 1990; =Cryptomycocolacales Oberwinkler and R. Bauer 1990;
=Cryptomycocolacomycetes R. Bauer et al. 2006] (M)
With microbodies. Cryptomycocolax abnormis.
●●●●●● Cystobasidiomycetes R. Bauer et al. 2006
With cell wall carbohydrate composition without fucose; cytoplasmic SPB separation;
metaphasic SPBs intranuclear. Containing Cystobasidiales (Cystobasidium),
Erythrobasidiales (Bannoa, Erythrobasidium), and Naohideales (Naohidea).
●●●●●● Microbotryomycetes R. Bauer et al. 2006
With colacosomes and septal pores without microbodies; with colacosomes and taxa derived
from colacosome fungi; metaphasic SPBs intranuclear. Containing Heterogastridiales
(Heterogastridium), Leucosporidiales (Leucosporidiella, Mastigobasidium), Microbotryales
(Microbotryum, Ustilentyloma), and Sporidiobolales (Rhodosporidium, Sporidiobolus).
●●●●●● Mixia Kramer 1959 [=Mixiaceae C.L. Kramer 1987; =Mixiales R. Bauer et al. 2006;
Mixiomycetes R. Bauer et al. 2006] (M)
With multinucleate hyphae and multiple spores produced simultaneously on sporogenous
cells. Mixia osmundae.
●●●●●● Pucciniomycetes R. Bauer et al. 2006
With a metaphasic intermeiotic SPB duplication. Containing Helicobasidiales
(Helicobasidium), Pachnocybales (Pachnocybe), Platygloeales (Eocronartium, Platygloea),
Pucciniales (Coleosporium, Cronartium, Dasyspora, Diorchidium, Melampsora,
Mikronegeria, Nyssopsora, Ochropsora, Phakopsora, Phragmidium, Pileolaria, Puccinia,
Pucciniastrum, Pucciniosira), and Septobasidiales (Auriculoscypha, Septobasidium).
●●●●●● Spiculogloeaceae Denchev 2009 [=Spiculogloeales R. Bauer et al. 2006;
=Spiculogloeomycetes Q.M. Wang et al. 2015]
Characterised by teleomorphic members that may form tremelloid haustorial cells
(nanometer-fusion mycoparasitism). Spiculogloea.
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●●●●●● Tritirachium Limber 1940 [=Tritirachiaceae Aime and Schell 2011; =Tritirachiales
Aime and Schell 2011; =Tritirachiomycetes Aime and Schell 2011] (M)
Accepted Article
With multinucleate hyphae, simple pore septa, conidiophores that are subhyaline to
dematiaceous and subhyaline to dematiaceous sympodial conidiogenous cells that occur in
whorls and bear conidia on an elongated rachis; teleomorph not known. Tritirachium
dependens
●●●●● Ustilaginomycotina R. Bauer et al. 2006
Mycelial in the parasitic phase, and many with saprobic yeast or ballisticonidial states; plant
parasites causing rusts and smuts; meiospores produced on septate or aseptate basidia; cell
wall carbohydrates dominated by glucose; xylose absent; parenthesomes absent at septal
pores; swellings absent at septal pores except in Tilletia; centrosomes globose, unlayered.
●●●●●● Exobasidiomycetes Begerow et al. 2007
With local interaction zones and no intracellular hyphal coils. Containing Ceraceosorales
(Ceraceosorus),Doassansiales (Doassansia, Melaniella, Rhamphospora), Entylomatales
(Entyloma), Exobasidiales (Kordyana, Laurobasidium, Exobasidium, Graphiola),
Georgefischereriales (Eballistra, Georgefischereria, Gjaerumia, Tilletiaria), Golubeviales
(Golubevia), Microstromatales (Microstroma, Quambalaria, Volvocisporium) Robbauerales
(Robbauera), Tilletiales (Tilletia).
●●●●●● Malassezia Baill. 1889 [=Malasseziales R.T. Moore 1980; =Malasseziaceae
Denchev and R.T. Moore 2009; =Malasseziomycetes Boekhout et al. 2014] (M)
Cells globose, ovoid or cylindrical; budding typically monopolar on a more or less broad
base, enteroblastic and percurrent; cell wall multi-lamellate, and the inner layer of the cell
wall corrugated with a groove spiralling from the bud site; lipid dependent or lipophilic;
sugars are not fermented, urease and diazonium blue B (DBB) reactions are positive;
coenzyme Q-9 is formed; xylose absent in whole-cell hydrolysates; sexual morph unknown.
Malassezia furfur.
●●●●●● Moniliella Stolk and Dakin, 1966 [=Moniliellaceae Q.M. Wang et al. 2014;
=Moniliellales Q.M. Wang, et al. 2014; =Monilielliomycetes Q.M. Wang et al. 2014] (M)
Colonies are smooth or velvety, greyish to olivaceous black; budding cells are ellipsoidal and
form terminally on true hyphae that disarticulate with artroconidia; pseudohyphae and
chlamydospores may be present; cell walls are multi-lamellar; hyphal septa typically possess
dolipores with an arch of endoplasmic reticulum, but ‘micropore’-like structures may also be
present; sugars are fermented by most species; nitrate is assimilated; urease and diazonium
blue B (DBB) reactions are positive; coenzyme Q-9 is present; xylose and fucose absent
from whole-cell hydrolysates; sexual morph unknown. Moniliella acetoabutans.
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●●●●●● Ustilaginomycetes R. Bauer et al. 1997
Accepted Article
With enlarged interaction zones. Containing Urocystales (Doassansiopsis, Floromyces,
Thecaphora, Melanotaenium, Urocystis) and Ustilaginales (Anthracoidea, Ustanciosporium,
Sporisorium, Ustilago).
●●●●● Wallemiomycotina Doweld 2014
Conidia arthrospore-like, verruculose, short cylindrical, becoming spherical; conidiophores
unbranched or sympodially proliferating, continuous with conidiogenous cells, smooth;
conidiogenesis basauxic; hyphal septa with a single pore, flaring out near the periphery of
the pore, barrel-shaped, dolipore-like.
●●●●●● Wallemia Johan-Olsen 1887 [=Wallemiaceae R.T. Moore 1996; =Wallemiales Zalar
et al. 2005; =Wallemiomycetes Zalar et al. 2005] (M)
Xerophilic; produce basauxic anamorphs and do not produce basidiomata in culture; with
dolipore septa with adseptal tubular extensions that arise from sheets of endoplasmic
reticulum that form the septal pore cap; septal pore cap sometimes absent; septal pore has
an electron-dense non-membranous septal pore occlusion and striations that are oriented
vertically. Wallemia ichthyophaga.
●●●●●● Geminibasidiaceae H.D.T. Nguyen et al. 2013 [=Geminibasidiales H.D.T. Nguyen et
al. 2013; =Geminibasidiomycetes H.D.T. Nguyen and Seifert 2015]
Xerotolerant; basidiomata not produced in culture; basidia arising from somatic hyphae or
from swollen basidium-bearing cells (primary cells) with a basal lateral projection occurring
either on the basidium or the swollen primary cell; basidiospores symmetrical on sterigma,
not forcibly discharged, and brown at maturity; arthroconidial and/or yeast-like asexual
morphs sometimes produced; species have a dolipore septum that is electron-dense at the
pore swelling with an electron-dense membranous septal pore occlusion; some species are
heat resistant. Geminibasidium.
●●●Monoblepharidomycetes J.H. Schaffn. 1909
Thallus epibiotic, filamentous (hyphal or rhizomycelial), either extensive or a simple
unbranched thallus, often with a basal holdfast. Zoospores oval possessing a non-ciliated
centriole parallel to the ciliated kinetosome with a striated disc partially extending around the
kinetosome; microtubules radiating anteriorly from the striated disc; ribosomal aggregation
around the nucleus; fenestrated cisterna (=rumposome) adjacent to the microbody in the
MLC; Golgi apparatus with stacked cisternae; nuclear envelope fenestrated at poles during
mitosis; aerobic and anaerobic; asexual reproduction occurs via production of posteriorly
uniciliated cells or autospores while sexual reproduction is oogamous via fusion of uniciliated
antherozoids produced in antheridia and nonciliated female gametes produced within
oogonia. Gonapodya, Harpochytrium, Hyaloraphidium, Monoblepharella, Monoblepharis,
Oedogoniomyces, Telasphaerula.
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●●● Mucoromycota Doweld 2001 emend. Spatafora and Stajich 2016 [Zygomycota F.
Moreau 1954, pro parte] (R)
Accepted Article
The least inclusive clade containing Mucoromycotina, Mortierellomycotina, and
Glomeromycotina. Characters associated with sexual reproductive states, where known,
include zygospore production by gametangial conjugation. Asexual reproductive states can
involve chlamydospores and spores produced in sporangia and sporangioles.
●●●● Glomeromycotina (C. Walker and A. Schüßler) 2016
Filamentous; primarily endomycorrhizal, forming arbuscules in roots, sometimes with
vesicles; without cilium; presumed asexual spores outside or within roots of host; some
complex spores with multiple wall groupings, others simple (blastic chlamydospores); without
centrioles, conidia, and airborne spores.
●●●●● Archaeosporales C. Walker and A. Schüßler 2001 [=Archaeosporomycetes
Sieverding et al. 2011]
Known to form symbiosis with plant roots or thalli, or with cyanobacteria; if symbiosis occurs
between plants and fungi, fungal spores may have two morphs, but often only one is known;
species form vesicular arbuscular or arbuscular mycorrhiza. Archaeospora, Ambispora,
Geosiphon.
●●●●● Glomeromycetes Cavalier-Smith 1998, emend. Oehl et al. 2011
Glomoid chlamydospores formed terminally, subterminally or intercalarily in hyphae, either in
or on the surface of soils or sometimes in roots, either singly, in spore clusters or multiplespored loose to compact sporocarps, on subtending hyphae: complex multi- walled spores
on sporogenous structures, or laterally or centrally within a sporiferous saccule or
intrahyphally in the stalk of sporiferous saccules, forming arbuscular or vesicular-arbuscular
mycorrhiza.
●●●●●● Diversisporales C. Walker and A. Schüßler 2001
Spore formation by blastic expansion of hypha (chlamydosporic), or sometimes with complex
spores with up to three walls or wall groups: multiple layered outer wall, and hyaline middle
and inner walls that may be of several components or layers; spores with subtending
hyphae, sometimes with a conspicuous colour change distant to the septum most proximal
to the spore base; spores with 1-3 wall layers; pore rarely open. Acaulospora, Diversispora,
Gigaspora, Pacispora, Racocetra, Scutellospora.
●●●●●● Glomerales J. B. Morton and Benny 1990
Spores by blastic expansion of the hyphal tip or intercalarily formed in hyphae, either in soils
or occasionally in roots, or other subterranean structures such as rhizomes, either singly, in
spore clusters or multiple-spored; sporocarps loose to compact, with a mono- to-multiple
layered spore wall; wall of subtending hyphae continuous with the spore wall and coloured
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Accepted Article
the same as or slightly lighter than it or hyaline to subhyaline; subtending hyphae funnelshaped, cylindrical or constricted; forming arbuscular mycorrhiza. Claroideoglomus,
Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus.
●●●●●● Paraglomus J.B. Morton and D. Redecker 2001 [=Paraglomeraceae J. B. Morton
and D. Redecker 2001; =Paraglomerales C. Walker and A. Schüßler 2001;
=Paraglomeromycetes Oehl et al. 2011] (M)
Endomycorrhizal, forming arbuscular mycorrhiza; asexual spores (chlamydospores) usually
formed in soil, sometimes within roots or other host tissue, sometimes with vesicles; without
cilium; without centrioles, conidia, and aerial spores. Paraglomus occultum.
●●●● Mortierellaceae A. Fischer 1892 [Mortierellales Cavalier-Smith 1998;
=Mortierellomycotina Kerst et al. 2011; =Mortierellomycetes Doweld 2014;
=Mortierellomycota Tedersoo et al. 2018]
Mycelium with anastomosing hyphae, dichotomously branching, bearing stylospores; hyphae
sporangiferous, sporangiophores basally inflated and elongating towards the
sporangiophore apex, erect, coenocytic initially, but irregularily septated at maturity; asexual
reproduction via sporangia and sporangiola; sporangia spherical, multi-spored; columella
absent; ramifications gracilous, primarily horizontally expanding, erecting hyphae sometimes
terminate with sporangiola; spores globose to ellipsoid or irregular, smooth or ornamented;
rhizoids only occasional; giant cells absent; zygospores naked. Mortierella.
●●●● Mucoromycotina Benny 2007
Saprobes, or rarely gall-forming, non-haustorial, facultative mycoparasites, or forming
ectomycorrhiza; mycelium branched, coenocytic when young, sometimes producing septa
that contain micropores at maturity; asexual reproduction by sporangia, sporangiola, or
merosporangia, or rarely by chlamydospores, arthrospores, or blastospores; sexual
reproduction by more or less globose zygospores formed on opposed or apposed
suspensors.
●●●●● Endogonales Moreau ex R. K. Benjamin 1979 [=Endogonomycetes Doweld 2014]
Filamentous, hyphae coenocytic; saprobic and ectomycorrhizal; zygospores with apposed
suspensors produced in a subterranean sporocarp. Endogone, Sphaerocreas.
●●●●● Mucorales Fritz 1832, emend. Schröter 1897 [=Mucoromycetes Doweld 2014] (P)
Filamentous, generally saprotrophic, with exceptions; septa absent except in older hyphae;
with plasmodesmata at septal pores; asexual reproduction with one to many spores in
merosporangia, sporangiola, or sporangium; reproduction by zygospore, typically with
opposed suspensors. Traditional subdivisions artificial. Backusella, Chaetocladium,
Choanephora, Cunninghamella, Lentamyces, Lichtheimia, Mucor, Mycotypha, Phycomyces,
Pilobolus, Radiomyces, Saksenaea, Syncephalestrum.
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Accepted Article
●●●●● Umbelopsidales Spatafora, Stajich and Bonito 2016 [=Umbelopsidomycetes
Tedersoo et al. 2018]
The least inclusive clade containing the genus Umbelopsis. Asexual reproduction by
sporangia and chlamydospores. Sporangiophores may be branched in a cymose or
verticillate fashion. Sporangia are typically pigmented red or ochre, multi- or single-spored
and with or without conspicuous columella. Sporangiospores are globose, ellipsoidal, or
polyhedral and pigmented like sporangia. Chlamydospores are filled with oil globules and
often abundant in culture. Sexual reproduction is unknown. Umbelopsis.
●●● Neocallimastigaceae Heath 1983, emend. Barr 1989 [;=Neocallimastigales J. L. Li et al.
1993, =Neocallymastigacetes M. J. Powell 2007, = Neocallimastigomycota M. J. Powell
2007]
Thallus monocentric or polycentric; anaerobic fermentative, found in digestive system of
larger herbivorous mammals and possibly in other terrestrial and aquatic anaerobic
environments; asexual reproduction; mitochondria absent; hydrogenosomes of mitochondrial
origin; uni- and multiciliated zoospores with a kinetosome-associated complex that includes
a skirt, strut, spur, and circumary ring, microtubules stretching from the spur and radiating
around the nucleus, forming a posterior fan; unikont kinetid and without props; nuclear
envelope is retained during mitosis. Anaeromyces, Buwchfawromyces, Caecomyces,
Cyllamyces, Feramyces, Neocallimastix, Oontomyces, Orpinomyces, Pecoramyces,
Piromyces.
●●● Olpidium (A. Braun) Rabenh. 1868 [=Olpidiaceae J. Schröt. 1889; =Olpidiales CavalierSmith 2013; Olpidiomycota Doweld 2013; =Olpidiomycotina Doweld 2013; =Olpidiomyceta
Tedersoo et al. 2018] (M)
Thallus monocentric, holocarpic or eucarpic, with no hyphae; zoospores posterior, uniciliate,
generally with a single globule, cone-shaped striated rhizoplast fused to both the functional
and vestigial kinetosomes, gamma-like particles and rough endoplasmic reticulum;
sporangium single, endobiotic; nucleus associated with the basal body, no nuclear cap; two
parallel centrioles linked to nucleus by shared, tapering, striated rhizoplast; no root
microtubules or dictyosome; side-body complex lacking; pathogens of terrestrial plants.
Olpidium brassicae.
●●● Zoopagomycota Gryganskyi, M.E. Smith, Spatafora and Stajich 2016 [Zygomycota F.
Moreau 1954, pro parte]
The least inclusive clade containing Entomophthoromycotina, Kickxellomycotina, and
Zoopagales. Sexual reproduction, where known, involves the production of zygospores by
gametangial conjugation. Morphologies associated with asexual reproductive states include
sporangia, merosporangia, conidia, and chlamydospores.
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●●●● Entomophthoromycotina Humber 2007
Accepted Article
Obligate pathogens of animals (primarily arthropods), cryptogamic plants, or saprobes;
occasionally facultative parasites of vertebrates. Somatic state consisting of a well-defined
mycelium, coenocytic or septate, walled or protoplastic, which may fragment to form
multinucleate hyphal bodies; protoplasts either hyphoid or amoeboid and changeable in
shape; cystidia or rhizoids formed by some taxa. Conidiophores branched or unbranched.
Primary spores true conidia, uni-, pluri-, or multinucleate, forcibly discharged by diverse
possible means or passively dispersed; secondary conidia often produced. Resting spores
with thick bi-layered walls form as zygospores after conjugations of undifferentiated
gametangia from different or the same hyphal bodies or hypha or as azygospores arising
without prior gametangial conjugations.
●●●●● Basidiobolus Eidam 1886 [=Basidiobolomycetes Doweld 2001 emend. Humber 2012]
(M)
Differs from Entomophthoromycetes and Neozygitomycetes by unusually large nuclei (often
≥10 μm long) with a large central nucleolus that is the major feature of uninucleate cells.
Mitoses involve barrel-shaped spindles, mitotic organelles incorporating microtubules (but
not centrioles) but not always located at the spindle poles, and the nuclear content isolated
from the cytoplasm by a layer of nuclear and cytoplasmic membrane fragments.
Basidiobolus ranarum.
●●●●● Entomophthorales G. Winter 1880 [=Entomophthoromycetes Humber 2012]
Filamentous, primarily without septa; mostly parasites of insects, mites, and spiders; sexual
reproduction by thick-walled zygospore, strictly homothallic, where known; asexual
reproduction by conidia formed by blastosporogenesis; conidia forcibly discharged and often
form secondary conidia. Ancylistes, Completoria, Entomophthora, Meristacrum.
●●●●● Neozygitaceae Ben-Ze’ev, R.G. Kenneth and Uziel 1987 [=Neozygitomycetes
Humber 2012;= Neozygitales Humber 2012]
Differs from Basidiobolomycetes and Entomophthoromycetes by vermiform, moderately
sized chromosomes that condense during mitosis on a central metaphase plate but uncoil
during interphase. Nuclear numbers in vegetative cells and conidia are low and apparently
controlled at (3)-4-(5). Neozygites.
●●●● Zoopagales Bessey ex R.K. Benjamin 1979 [=Zoopagomycotina Benny 2007]
Filamentous, hyphae coenocytic or septate; parasites of soil fungi, invertebrates, and
amoebae; asexual reproduction by conidia or merosporangia; sexual reproduction by
globose zygospores with apposed suspensors. Amoebophilus, Piptocephalis,
Rhopalomyces, Sigmoideomyces, Stylopage.
●●●● Kickxellomycotina Benny 2007
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Accepted Article
Saprobes, mycoparasites, or obligate symbionts; thallus arising from a holdfast on other
fungi as a haustorial parasite, or branched, septate, subaerial hyphae; mycelium branched
or unbranched, regularly septate; septa with median, disciform cavities containing plugs;
asexual production by 1- or 2-spored merosporangia, trichospores, or arthrospores; sexual
reproduction by zygospores that are globose, biconical, or allantoid and coiled.
●●●●● Asellariales Manier ex Manier and Lichtwardt 1978 [=Asellariaceae Manier ex Manier
and Lichtw. 1968]
Kickxellomycotina with filamentous, branched thalli; asexual reproduction by arthrospore-like
cells that disarticulate from the corresponding thallus; in the digestive tracts of terrestrial,
aquatic, and marine isopods, as well as springtails. Asellaria, Baltomyces, Orchesellaria.
●●●●● Dimargaritaceae R.K. Benjamin 1959 [=Dimargaritales R. K. Benjamin 1979]
Hyphae regularly septate; septa containing a lenticular cavity; asexual reproduction by
bisporous merosporangia; sexual reproduction by a zygospore, often ornamented; obligate
haustorial parasites of fungi, especially Mucorales. Dimargaris, Dispira, Spinalia,
Tieghemiomyces.
●●●●● Harpellales Lichtwardt and Manier 1978
Endosymbionts of freshwater arthropods with basal cell attached to the host, from which a
filamentous thallus develops; hyphae septate, with or without branching; septa contain a
lenticular cavity; asexual reproduction occurs by lateral elongate monosporous trichospores;
sexual reproduction by conical or biconical zygospores. Note that this group includes taxa
previously referred to as trichomycetes. Harpella, Orphella, Smittium, Zygopolaris.
●●●●● Kickxellaceae Linder 1943 [=Kickxellales Kreisel ex R. K. Benjamin 1979]
Filamentous; hyphae possessing septa with a lenticular cavity; asexual reproduction by
unispored sporangiola (merosporangia) produced on a sporocladium; saprobic or
mycoparasitic, isolated from soil and dung. Coemansia, Dipsacomyes, Kickxella, Linderina,
Martensella, Martensiomyces, Spirodactylon, Spiromyces.
DIAPHORETICKES Adl et al. 2012
Incertae sedis Diaphoretickes:
Microheliella Cavalier-Smith 2012 (M)
Aciliated, central centrosome with two concentric shells of dense material and a dense
central core; axopodia supported by triads of microtubules, bearing ellipsoid extrusomes;
single nucleus eccentric, with internal channels where microtubular triads pass;
mitochondrial cristae tubular; cortical filogranular network. Microheliella maris.
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Ancoracysta Janouskovec et al. 2017 (M)
Accepted Article
Small ovoid marinecytotrophic predators on small protists; cell covered by a theca and
dense glycocalyx; one pair of heterodynamic cilia; anterior cilium with mastigonemes at its
anterior; posterior cilium with short vane, and traverses cell along a groove; mitochondria
with lamellar cristae; characteristic extrusome (ancoracyst). Ancoracysta twista.
Rappemonads Kim et al. 2011
Marine and fresh water 5–7 µm cells with 2–4 plastids containing chlorophyll a. Poorly
characterized, rare low abundance organisms, known only from environmental samples, and
no species or genera described.
Telonemia Shalchian-Tabrizi 2006
Biciliated cells with a proboscis-like structure located at the ciliary pole and a complex
cytoskeleton composed of layers of microtubules and microfilaments; tripartite tubular hairs
on the long cilium; mitochondria with tubular cristae; peripheral vacuoles located just
beneath the cell membrane; chloroplasts not observed. Telonema Griessmann 1913, may
consist of several genera.
Picozoa Seenivasan et al. 2013 [Picobiliphytes Not et al. 2007] (M)
Oblong cell separated in two by a cleft; of picoplanktonic size; marine; without plastid;
cytotrophic; two cilia inserted laterally; mitochondrion with tubular cristate; heterotrophic,
possibly feeding on small viruses or colloidal particles. Picomonas judraskeda.
Archaeplastida Adl et al. 2005
Photosynthetic plastid with chlorophyll type-a from an ancestral primary endosymbiosis with
a cyanobacterium; plastid with two membranes without periplastid endoplasmic reticulum;
plastid reduced in some; usually with cell wall or other extracellular covering; flat
mitochondrial cristae; starch storage product.
● Glaucophyta Skuja 1954 [Glaucocystaceae West 1904 Glaucocystophyta Kies and Kremer
1986]
Unicellular or colonial algae; plastid in the form of a cyanelle, which is distinct from the
chloroplasts of other organisms in that, like cyanobacteria, it has a conspicuous
peptidoglycan wall between its two membranes; chlorophyll type-a only, with
phycobiliproteins and other pigments; ated and nonated species or life cycle stages; without
cellulosic cell wall except Glaucocystis. Reported only in freshwater. Cyanophora,
Cyanoptyche, Glaucocystis, Gloeochaete.
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● Rhodophyceae Thuret 1855, emend. Rabenhorst 1863 [Rhodophyta Wettstein 1901,
Rhodoplantae Saunders and Hommersand 2004] emend. Adl et al. 2005
Accepted Article
Red algae without ciliated stages, and without centrioles, or basal bodies, or other 9 + 2
microtubular structures – presence of polar rings instead; two-membraned simple
chloroplasts, unstacked thylakoids with phycobilisomes, and chlorophyll-a only, lacking
external endoplasmic reticulum; cytoplasmic carbohydrate reserve floridean starch;
chromosomal and interzonal microtubules not converging towards polar rings, so spindle
poles very broad; telophase spindle and nuclear envelope persisting with closed mitosis
surrounded by perinuclear endoplasmic reticulum; cell wall of cellulose; cells in filamentous
forms linked by pit plugs, formed between cells after incomplete cell division; sexual
reproduction typically oogamous; triphasic life history common.
●● Cyanidiales T. Christensen 1962 [Cyanidiophyceae Merola et al. 1981, Cyanidiophyta
Moehn ex Doweld 2001]
Unicellular, spherical or elliptical in shape; thick cell wall or lack of cell wall; facultative
heterotrophs or obligate photoautotrophs; cell division or endospore formation; inhabiting
acidic and high temperature environments. Cyanidioschyzon, Cyanidium, Galdieria.
●● Proteorhodophytina Muñoz-Gómez et al. 2017 (R)
Clade consisting of Compsopogonales, Porphyridiophyceae, Rhodellophyceae,
Stylonematales, based on phylogenetic analysis.
●●● Compsopogonales Skuja 1939 [Compsopogonophyceae G. W. Saunders and
Hommersand 2004]
Pluricellular with monosporangia and spermatangia usually cut out by curved walls from
ordinary vegetative cells; Golgi–ER association; encircling thylakoids in the plastid; life
history biphasic if known; inhabiting freshwater or marine environment. Boldia,
Compsopogon, Erythrotrichia, Rhodochaete.
●●● Porphyridiophyceae H. S. Yoon et al. 2006
Unicellular with a single branched or stellate plastid, with or without pyrenoid; Golgi
association with mitochondria and ER; cells with floridoside as a low molecular-weight
carbohydrate; reproduction by cell division; inhabiting marine, freshwater and even moist
terrestrial areas. Erythrolobus, Flintiella, Porphyridium.
●●● Rhodellophyceae Cavalier-Smith 1998 [Rhodellophytina Cavalier-Smith 1998]
Unicellular; single highly lobed plastid with eccentric or centric pyrenoid; Golgi association
with nucleus and ER; contains mannitol; reproduction by cell division; inhabiting marine and
freshwater habitats. Dixoniella, Glaucosphaera, Rhodella.
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●●● Stylonematales K. Drew 1956 [Stylonematophyceae H.S. Yoon et al. 2006]
Accepted Article
Unicellular or pseudofilamentous or filamentous; various plastid morphologies with or without
pyrenoid; Golgi association with mitochondria and ER; reproduction by cell division or
monospores; inhabiting freshwater, brackish and marine environment. Bangiopsis,
Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, Rufusia, Stylonema.
●● Eurhodophytina G.W.Saunders & Hommersand 2004 (R)
Clade containing Bangiales and Florideophycidae, based on phylogenetic analysis.
●●● Bangiales Nägeli 1847 [Bangiophyceae A. Wettstein 1901]
Pluricellular with Golgi–ER/mitochondrion association; life history biphasic, heteromorphic,
gametophyte macroscopic, initially uniseriate, becoming pluriseriate or foliose by diffuse
growth; carposporangia and spermatangia produced in packets by successive perpendicular
divisions; sporophyte filamentous, with pit plugs with a single cap layer, but lacking
membranes; typically forming conchospores in fertile cell rows; inhabiting mostly marine
environment. Bangia, Bangiomorpha, Boreophyllum, Dione, Minerva, Porphyra, Pyropia,
Pseudobangia.
●●● Florideophycidae Cronquist 1960
Pluricellular with Golgi–ER/mitochondrion; growth by means of apical cells and lateral initials
forming branched filaments in which the cells are linked throughout by pit connections; life
history fundamentally triphasic consisting of gametophytic, carposporophytic, and
tetrasporophytic phases; reproductive cells (monosporangia, spermatangia, carposporangia,
tetrasporangia) generally terminal or lateral on the filaments; carpogonia terminal or lateral,
bearing an apical extension, the trichogyne, to which the spermatangia attach;
carposporophyte developing directly from the carpogonium or its derivative; inhabiting mostly
marine environment.
●●●● Hildenbrandia Nardo 1834 [Hildenbrandiophycidae G. W. Saunders and Hommersand
2004]
Pluricellular that are crustose and smooth to tubercular or with erect branches; composed of
a basal layer of laterally adhering branched filaments and laterally adhering simple or
branched erect filaments; pit plugs with a single cap layer and membrane; tetrasporangia
zonately or irregularly divided, apomeiotic, borne in ostiolate conceptacles; sexual
reproduction unknown. Hildenbrandia.
●●●● Nemaliophycidae Christensen 1978
Pluricellular; pit plugs characterized by two cap layers. Acrochaetium, Balbiania, Ballia,
Batrachospermum, Colaconema, Entwisleia, Nemalion, Palmaria, Rhodychlya, Thorea.
This article is protected by copyright. All rights reserved.
●●●● Corallinophycidae L. Le Gall & G. W. Saunders 2007
Accepted Article
Pluricellular; carpogonial branches two-celled; tetrasporangia zonate or cruciate in division;
pit plug with two cap layers at cytoplasmic faces, outer dome shaped, membrane absent;
calcification in the form of calcite. Corallina, Harveylithon, Hydrolithon, Lithophyllum,
Mastophora, Melobesia, Metagoniolithon, Neogoniolithon, Porolithon, Rhodogorgon,
Sporolithon.
●●●● Ahnfeltiophycidae G. W. Saunders & Hommersand 2004
Pluricellular; carpogonia terminal and sessile; carposporophyte developing outward; pit plugs
naked, lacking caps and membranes. Ahnfeltia, Pihiella.
●●●● Rhodymeniophycidae G. W. Saunders & Hommersand 2004
Pluricellular with sexual life histories generally triphasic; carposporophyte developing directly
from the carpogonium or carpogonial fusion cell, or indirectly from an auxiliary cell that has
received the postfertilization diploid nucleus; pit plugs with membranes only (single inner cap
in Gelidiales). Acrosymphytum, Bonnemaisonia, Ceramium, Gelidium, Gigartina, Gracilaria,
Halymenia, Nemastoma, Peyssonnelia, Plocamium, Rhodymenia, Sebdenia.
● Chloroplastida Adl et al. 2005 [Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey
1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and
Crane 1997]
Plastid with two membranes without periplastid endoplasmic reticulum; plastid with
chlorophyll a and b; starch inside plastid; cell wall often with cellulose, or scaly extracellular
covering; swimming cells with cilia in multiples of two, or rarely single cilium, with stellate
structure linking 9 pairs of microtubules at basal body transition zone; with centrioles;
Rubisco small subunits encoded in the nuclear genome.
●● Chlorophyta Pascher 1914, emend. Lewis and McCourt 2004
Plastid thylakoids single or stacked; glycolate dehydrogenase present; cell division without
phragmoplast.
●●● Ulvophyceae Mattox & Stewart 1984 (P)
Swimming cells with one or two pairs of cilia, without mastigonemes; basal bodies with 4
microtubular rootlets in cruciate arrangement, and smaller roots of two sizes, alternating
between 2 or more microtubules; cilia with scales and rhizoplasts; cell wall more or less
calcified; cell division by furrowing with mitotic spindle closed, centric and persistent;
phycoplast absent; thallus can be branched or unbranched, mono- or distromatic sheet
(phyllose), or cushiony forms of compacted tubes; thallus often multinucleate and siphonous;
free-living diplobiontic life cycle, iso- or heteromorphic. Acetabularia, Caulerpa, Chladophora,
Codium, Pithophora, Pseudonochloris, Rhizoclonium. Note: The inclusion of
This article is protected by copyright. All rights reserved.
Accepted Article
Oltmannsiellopsis in Ulvophyceae causes instability in phylogenies, and the monophyly is
questioned.
●●● Trebouxiophyceae Friedl 1995 [Pleurastrophyceae Mattox et al. 1984, Microthamniales
Melkonian 1990] (P?)
Swimming cells with one or two pairs of cilia, without mastigonemes; basal bodies with4
microtubular rootlets in cruciate arrangement, including a multilayered structure, and
asmaller root, alternating between 2 or more microtubules; basal bodies with
prominentrhizoplast, cruciate, displaced counter-clockwise and counter-clockwise basal
bodyorientation; closed mitosis with metacentric spindle, semi-closed mitosis; cytokinesis
with phycoplast; asexual reproduction by autospores or zoospores; sexual reproduction
reported but not observed; lichenose and free-living forms; most with cell walls; osmotrophy
and autotrophy. Botryococcus, Chlorella, Choricystis, Coccomyxa, Microthamnion,
Nannochloris, Oocystis, Pabia, Prasiola, Prototheca, Trebouxia (P).
●●● Chlorophyceae Christensen 1994.
Swimming cells with one to hundreds of cilia, without mastigonemes; when 2 or 4 cilia,basal
bodies with 4 microtubular rootlets in cruciate arrangement, alternating between 2 and more
microtubules; basal bodies displaced clockwise or directly opposed; rhizoplast connects
basal bodies and extends to nucleus; in colonial forms, basal bodies reoriented to face
outside of colony; closed mitosis; cytokinesis has phycoplast withmicrotubules, sometimes
with furrowing, with formation of plasmodesmata cell-cellconnections; haplobiontic life cycle;
sexual reproduction by isogamy, anisogamy, or oogamy; asexual reproduction by
aplanospores, akinetes, or autosporic; osmotrophyand autotrophy. Bracteacoccus,
Chlamydomonas (P), Desmodesmus, Floydiella, Hydrodictyon, Oedegonium, Pediastrum,
Scenedesmus, Volvox.
Incertae sedis Chlorophyceae: Carteria, Cylindrocapsa, Hafniomonas, Mychanastes,
Treubaria, Trochiscia.
●●● Chlorodendrophyceae Fritsch 1917
Cells with a pair of cilia, inserted in a ciliary pit; cilia beat in breast-stroke pattern; basal body
rootlets structure in X2X2 configuration; with organic extracellular scales, outerlayer of
scales fused to form a theca; metacentric spindle collapses at telophase; nutrition by
autotrophy and osmotrophy. Treated as prasinophyte clade IV (Nakayamaet al. 1998).
Scherffelia, Tetraselmis.
●●● Pedinophyceae Moestrup 1991, emend. Fawley et al. in Adl et al. 2012
Unicellular, with single cilium; closed mitosis with persistent spindle; phycoplast absent;
counterclockwise basal body orientation; a covered with rigid or thin, hair-like appendages;
single parietal chloroplast. Marsupiomonas, Pedinomonas.
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●●● Chloropicophyceae Lopes dos Santos & Eikrem 2017
Accepted Article
Small coccoid cells with a diameter of 1.5–4 μm; pyrenoid absent; without cilium; with
layered cell wall; marine. Treated as prasinophyte clade VII A & B (Santos et al. 2017).
Chloroparvula, Chloropicon.
●●● Picocystophyceae Lopes dos Santos & Eikrem 2017
Coccoid, but ovoid or tri-lobed forms observed in old cultures; layered cell wall containing
polyarabinose, mannose, galactose and glucose. Treated as prasinophyte clade VII C
(Santos et al. 2017). Picocystis.
●●● Pyramimonadales Chadefaud 1950
Swimming cells with 4–16 cillia; helical structure in the cilliary transitional region; trailing cells
bearing a single cillum observed in some, which may represent gametes;chloroplast cupshaped; pyrenoid present; some with eyespot(s); several layers of body and cilliary scales;
some producing conspicuous cyst (called phycoma); with one or morelarge vacuoles and
associated duct system; phagotrophy in some. Treated asprasinophyte clade I (Nakayama
et al. 1998). Cymbomonas, Halosphaera, Pterosperma, Pyramimonas.
●●● Mamiellophyceae Marin & Melkonian 2010 [
Cells typically solitary, with single chloroplast, sometimes two; prasinoxanthin
commonlypresent; 2 cilia, single or no cilium present; cilia equal or unequal in length;
eyespotposterior if present; cells and/or cilia with 1-2 layers of flattened, rounded or elliptical
scales, or scales absent; scales ornamented with spider web-like or uniformly reticulate
pattern; mostly marine, some freshwater. Treated as prasinophyte clade II (Nakayamaet al.
1998). Bathycoccus, Crustomastix, Dolichomastix, Mamiella, Monomastix, Mantoniella.
●●● Nephroselmis [Nephroselmidophyceae Cavalier-Smith 1993, emend.Yamaguchi 2011]
Cells laterally compressed; two cilia inserted laterally; square- or diamond-shapedscales
cover cell body and a, except in at least one species – Nephroselmis pyriformis; single, cupshaped chloroplast with pyrenoid and eyespot; contractile vacuole near arybases in
freshwater species; sexual reproduction by hologamy; mostly marine, somefreshwater.
Treated as prasinophyte clade III (Nakayama et al. 1998). Nephroselmis.
●●● Pycnococcaceae Guillard 1991 emend. Fawley 1999 [Pseudoscourfieldiales and
Pseudoscourfieldiaceae Melkonian 1990]
Plastid with prasinoxanthin; with or without scaly covering; vegetative cells with two cilia or
no cilia; trailing cells bearing a single cilium rarely observed in Pycnococcus culture;
pyrenoid in the plastid; intrusion of mitochondrial membranes into the pyrenoid. Treated as
prasinophyte clade V (Fawley et al. 2000). Pycnococcus, Pseudoscourfieldia.
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●●● Palmophyllophyceae Leliaert et al. 2016
Accepted Article
Marine; solitary, in loose colonies, or cells grouped in gelatinous matrix; strongly supported
in plastid multi-gene and nuclear ribosomal DNA phylogenies.
●●●● Palmophyllales Zechman et al. 2010
Thallus macroscopic, crustose or erect; subspherical cells in gelatinous matrix make up
thallus; cell diameter 6–10 μm; each cell with single cup-shaped chloroplast lacking
pyrenoids; benthic marine. Palmophyllum, Palmoclathrus, Verdigellas.
●●●● Prasinococcales Guillou et al. 2004, as in Leliaert et al. 2016
Marine; planktonic; solitary or forming loose colonies; no cilium; without scaly covering; with
cell wall; chloroplast cup-shaped and with pyrenoid; cell division by unequal binary fission in
which one of the daughter cells retains the parent wall, while the other is released with a
newly produced cell wall. Treated as prasinophyte clade VI (Fawley et al. 2000).
Prasinococcus, Prasinoderma.
●● Streptophyta Bremer & Wanntorp 1981 [Charophyta Migula 1897, emend. Karol et al.
2009; Charophyceae Smith 1938, Jeffrey 1967 Streptophyta, Mattox and Stewart 1984]
Asymmetric motile cells, when present, with pair of cilia without mastigonemes; basal bodies
with distinctive multilayered structure of microtubular rootlet and cytoskeletal anchor;
thylakoids stacked; open mitosis; usually with phycoplast,but some with phragmoplast and
cell plate; with primary plasmodesmata between adjacent cells in filamentous forms;
filaments branching or nonbranching; with non-motile vegetative phase; some with
multinucleate cells; with or without sexual reproduction; sexual species with haplobiontic life
cycle; with desiccation-resistant cysts (zygospores); glycolate oxidase in peroxisomes;
Cu/Zn superoxide dismutase; ciliary peroxisome.
●●● Chlorokybus Geitler 1942 [Chlorokybophyceae Lewis and McCourt 2004] (M)
Sarcinoid packets of cells; subaerial; biciliated zoospores; cilia with hairs; multi-layered
structure (MLS) at ciliary root. Chlorokybus atmophyticus.
●●● Mesostigma Lauterborn 1894 [Mesostigmatophyceae Marin and Melkonian 1999,
emend. Lewis and McCourt 2004; Mesostigmata Turmel et al. 2002] (M)
Asymmetrical cell with pair of lateral cilia without mastigonemes, emerging from a pit;
presence of multilayered structures adjacent to the ciliary basal bodies; with
glycolateoxidase; ciliary peroxisome present; cell wall of cellulose; organic scales cover cell
wall and cilia. Mesostigma viride.
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●●● Klebsormidiophyceae van den Hoek et al. 1995
Accepted Article
Coccoid or unbranched filaments; one or two chloroplasts with one pyrenoid; most
chloroplasts parietal; cleavage furrow during cell division but no cell plate or phragmoplast;
sexual reproduction unknown. Entransia, Interfilum, Klebsormidium.
●●● Phragmoplastophyta Lecointre & Guyander 2006
Cell division by way of some form of phragmoplast; some oogamous, others anisogamous
with nonmotile female gamete and motile male gamete.
●●●● Zygnematophyceae van den Hoek et al. 1995, emend. Hall et al. 2009
Without ciliated stages; sexual reproduction via conjugation; thalli unicellular or filamentous;
no centrioles. Spirogyra, Staurastrum.
●●●● Coleochaetophyceae Jeffrey 1982
Thalli discs of cells or branched filaments; sheathed hairs as extensions of the cell wall.
Coleochaete, Chaetosphaeridium.
●●●● Charophyceae Smith 1938, emend. Karol et al. 2009 [Charales Lindley 1836;
Charophytae Engler 1887]
Thallus attached to substrate with rhizoids; thallus a central axis of multinucleate internodal
cells, with whorls of branchlets radiating from mononucleate cells at nodes; calcium
carbonate accumulates in cell wall of many species; haplobiontic life cycle; sexual
reproduction oogamous with sperm cells; differentiated sperm and egg producing organs;
antheridium with several shield cells and a manubrium that gives rise to spermatogenous
filaments; primarily in fresh water. Chara, Nitella, Tolypella.
●●●● Embryophyta Engler 1886, emend. Lewis and McCourt 2004 [Cormophyta Endlicher
1836; Plantae Haeckel 1866]
Ciliated basal bodies, when present, with distinctive multilayered structure of microtubules
and cytoskeletal anchor; open mitosis with phragmoplast at cytokinesis; plasmodesmata and
other characteristic cell-cell junctions; diplobiontic life cycle, with vegetative propagation
possible in many; alternation of generations with fertilization of egg by sperm inside
protective test; embryology with tissue differentiation coordinated by hormones;
differentiated sperm and egg cells, may be on different sexual individuals, on different
organs of the same individual, or in the same organ. Subdivisions not shown.
Sar Burki et al. 2008, emend. Adl et al., 2012
The least inclusive clade containing Bigelowiella natans Moestrup and Sengco 2001
(Rhizaria), Tetrahymena thermophila Nanney and McCoy 1976 (Alveolata), and
Thalassiosira pseudonana Cleve 1873 (Stramenopiles). This is a node-based definition in
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Accepted Article
which all of the specifiers are extant; it is intended to apply to a crown clade; qualifying
clause – the name does not apply if any of the following fall within the specified clade –
Homo sapiens Linnaeus 1758 (Opisthokonta), Dictyostelium discoideum Raper 1935
(Amoebozoa), Arabidopsis thaliana (Linnaeus) Heynhold 1842 (Archaeplastida), Euglena
gracilis Klebs 1883 (Excavata), Emiliania huxleyi (Lohmann) Hay and Mohler in Hay et al.
1967 (Haptophyta). The name is derived from the acronym of the three groups united in this
clade. The apparent composition of Sar is: Alveolata, Rhizaria, and Stramenopiles, as
defined in Adl et al., 2012. The primary reference phylogeny is Burki et al. (2008, Fig. 1).
● Stramenopiles Patterson 1989, emend. Adl et al. 2005
Motile cells typically biciliate, typically with heterokont ciliation – anterior cilium with tripartite
mastigonemes in two opposite rows and a posterior usually smooth cilium; tubular
mitochondrial cristae; typically, 4 microtubular kinetosomal roots.
Incertae sedis Stramenopiles: Environmental lineages MAST-21, MAST-25 Massana et al.
2014
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes. These clades are mostly detected in the analysis of small size fractions (pico and
nano-eukaryotes).
Incertae sedis Stramenopiles: Platysulcus. Marine bacterivorous heterokont cell with short
anterior cilium and long posterior cilium; cell with wide, shallow ventral furrow.
●●Bigyra Cavalier-Smith 1998 emend. 2006 (R)
Heterotrophs, mostly phagotrophs, without vegetative cell walls.
●●●Opalozoa Cavalier Smith 1991 emend. 2006
Cilia without tubular hairs or absent; without plastids, typically without vegetative cell walls;
most of them phagotrophic but often osmotrophic saprotrophs in vertebrate guts.
Incertae sedis Opalozoa: Spherical or D-shaped cells with two heterokont cilia;
microaerophilic, in marine sediments. Cantina, Rictus.
Incerta sedis Opalozoa: Environmental lineage MAST-12 Massana et al. 2014 (R)
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes, detected mostly in the analysis of small size fractions (pico and nanoeukaryotes).
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●●●● Nanomonadea Cavalier-Smith 2012 (clade MAST-3)
Accepted Article
Phagotrophic and non-photosynthetic free-living ciliated cells. Includes the uniciliated
Solenicola and Incisomonas, and their related environmental 18S rDNA sequences.
Incisomonas, Solenicola.
●●●● Opalinata Wenyon 1926, emend. Cavalier-Smith 1997 [Slopalinida Patterson 1985]
Pluriciliated with double-stranded transitional helix at the transitional region between
kinetosome and cilium; cilia without tubular hairs evenly spaced cortical ridges underlain by
microtubules, ranging from singlets to ribbons; cyst-forming; many are osmotrophic in
vertebrate guts.
●●●●● Proteromonadea Grasse 1952 (P?)
One or two anterior pairs of anisokont cilia; uninucleate; endobionts in intestinal tract of
amphibians, reptiles, and mammals. Karotomorpha, Proteromonas.
●●●●●Opalinea Wenyon 1926
Multiciliated with cilia originating from an anterior morphogenetic centre, the falx, and
forming oblique longitudinal rows or files; microtubular ribbons supporting longitudinal
pellicular ridges between ciliary rows; two to many monomorphic nuclei; endobionts in
amphibians and some fish; life cycle complex, with sexual processes induced by hormones
of host and linked to the host’s life cycle. Cepedea, Opalina, Protoopalina, Protozelleriella,
Zelleriella.
●●●●●Blastocystis Alexeev 1911
Rounded aciliated yeast-like cells, anaerobic commensals/parasites of intestinal tracts; cilia
secondarily lost. Environmental samples form 17 genetically distinct clades called sub-types,
without specific host. Blastocystis.
●●●● Placidida Moriya et al. 2002
Biciliate cells without plastids; described species have mastigonemes on anterior cilium,
attach to substrates by posterior cilium during feeding; double-stranded transitional helix.
Placidia, Suigetsumonas, Wobblia.
●●●● Bicosoecida Grasse 1926, emend. Karpov 1998
Biciliate with or without tripartite mastigonemes, typically lacking transitional helix; without
plastids; phagotrophic with cytostome, supported by broad microtubular rootlet No. 2 of
posterior cilium; predominantly sedentary, often attach to substrate with posterior cilium; with
or without lorica; solitary and colonial. Adriamonas, Anoeca, Bicosoeca, Caecitellus,
Cafeteria, Cyathobodo, Filos, Halocafeteria, Nanum, Paramonas, Pseudobodo,
Pseudodendromonas.
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Accepted Article
Incerta sedis Bicosoecida environmental lineages MAST-16, MAST-22, MAST-24 Massana
et al. 2014 (R).
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes, detected mostly in the analysis of small size fractions (pico and nanoeukaryotes).
●●● Sagenista Cavalier-Smith 1995
Heterotrophic phagotrophs and in some cases osmotrophs, biciliated cells present in some
stages of their life cycle in most species.
Incertae sedis Sagenista environmental lineages MAST-4, MAST-7, MAST-8, MAST-9,
MAST-10, MAST-11, MAST-20Massana et al. 2014 (R)
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes. These clades are mostly detected in the analysis of small size fractions (pico and
nanoeukaryotes). The majority of these clades form a sister group to Labyrinthulomycetes
●●●● Labyrinthulomycetes Dick 2001
Producing an ectoplasmic network of anastomosing branched wall-less filaments with an
organelle called bothrosome; Golgi-derived scales; biciliate zoospores with lateral insertion
in many species.
●●●●● Amphitremida Poche 1913 emend. Gomaa et al. 2003
Phagotrophs or mixotrophs; planktonic or benthic; aerobic, freshwater and marine, and
anaerobic/micro-aerophilic environments. Amphitrema, Archerella, Diplophrys,
Paramphitrema.
●●●●● Amphifilida Cavalier-Smith 2012
Pseudostomes instead of true bothrosomes, ectoplasmic elements in the form of
pseudopodia. Amphifila, Fibrophrys, Sorodiplophrys.
●●●●● Oblongichytrida Bennett et al. 2017
Slender oblong zoospores. Oblongichytrium
●●●●● Labyrinthulida Doffein 1901
Spindle-shaped vegetative cells distributed in an extensive ectoplasmic net; zoospores with
eyespots; sexual reproduction. Aplanochytrium, Labyrinthula Stellarchytrium.
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●●●●● Thraustochytrida Sparrow 1943
Accepted Article
Cells producing a small ectoplasmic net; presence of interphase centrioles in vegetative
cells; no eye- spots; no sexual reproduction. Althornia, Aurantiochytrium, Botryochytrium,
Japanochytrium, Monorhizochytrium, Parietichytrium, Schizochytrium, Sicyoidochytrium
Thraustochytrium, Ulkenia
●●●● Pseudophyllomitidae Shiratori et al 2016 (MAST-6)
Free-living phagotrophic biciliates, anterior cilium with tubular mastigonemes; mitochondria
with tubular cristae; ciliary transitional region with transitional helix. Pseudophyllomitus (P).
●● Gyrista Cavalier-Smith 1998
Cells with helical or double helix/ring system ciliary transition zone.
Incertae sedis Gyrista: Environmental lineages MAST-1, MAST-2, MAST-23 Massana et al.
2014
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes. These clades are mostly detected in the analysis of small size fractions (pico and
nanoeukaryotes).
●●● Developea Karpov et Aleoshin 2016
Free swimming, naked, heterotrophic, bearing two cilia, anterior cilium with mastigonemes.
Developayella, Develorapax.
●●● Hyphochytriales Sparrow 1960
Single anteriorly directed cilium.
●●●● Anisolpidiaceae Karling 1943, emend. Dick 2001
Thallus holocarpic. Anisolpidium, Canteriomyces.
●●●● Hyphochytrium Karling 1939 [Hyphochytridiomycetaceae Fischer 1892, emend.
Karling 1939]
Thallus eucarpic and polycentric. Hyphochytrium.
●●●● Rhizidiomycetaceae Karling 1943
Thallus eucarpic and monocentric. Latrostium, Rhizidiomyces, Rhizidiomycopsis.
This article is protected by copyright. All rights reserved.
●●● Peronosporomycetes Dick 2001 [Oomycetes Winter 1897, emend. Dick 1976]
Accepted Article
Thallus mainly aseptate; cell wall of glucan-cellulose, may have minor amount of chitin;
haplomictic-B nuclear cycle; lysine synthesized via the diaminopimelate (DAP) pathway;
lanosterol directly from squalene oxide; zoospores biciliate and heterokont but rarely
uniciliate; cilia anteriorly inserted; anteriorly directed cilium shorter; transitional plate of
kinetosome sitting above the plasma membrane with a central bead; kinetid base structure
with six parts, including four roots; oogamous reproduction that results in the formation of
thick-walled sexual spores known as oospores, due to contact between male and female
gametangia in the most derived groups.
Incertae sedis Peronosporomycetes: Atkinsiella, Ciliomyces, Crypticola, Ectrogella,
Eurychasma, Halodaphnea, Haliphthoros, Haptoglossa, Lagena, Lagenisma, Olpidiopsis,
Pontisma, Pythiella, Rozellopsis, Sirolpidium.
●●●●Saprolegnialean lineage Lara in Adl et al. 2019
Obligate biotrophs and facultative parasites. Oogamous sexual reproduction. Two, often
morphologically different generations of zoospores, which may have lost cilia secondarily.
Complex kinetosome-associated “K-bodies”. Achlya, Aphanomyces, Aplanopsis,
Apodachlya, Aquastella, Geolegnia, Leptomitus, Newbya, Pythiopsis, Protoachlya,
Salisapilia, Saprolegnia,Thraustotheca.
●●●●Peronosporalean lineage Lara in Adl et al. 2019
Obligate biotrophs and facultative parasites. Oogamous sexual reproduction. Unable to
synethize sterols required for sexual reproduction. Characteristic periplasmic pattern of
oogenesis. Albugo, Bremia, Chlamydomyzium, Halophytopthora,,Hyaloperonospora,
Lagenidium, Myzocytiopsis, Peronospora, Plasmopara, Pythium, Pseudoperonospora, ,
Phytophthora, Phytopythium, Pustula.
●●●Pirsoniales Cavalier-Smith 1998 emend. 2006
Biciliate parasites of diatoms that differentiate into an intracellular feeding part (trophosome)
and external generative part (auxosome). Pirsonia.
●●● Actinophryidae Claus 1874, emend. Hartmann 1926
Axopodia emerging from amorphous centrosome near nuclei; axonemal microtubules in
double interlocking coils; single central nucleus or several peripheral nuclei; tubular
mitochondrial cristae; two types of extrusomes for prey-capture along axopodia; cysts
covered with siliceous elements; autogamy reported within cysts; cell division with semiopen orthomitosis; cilia never formed; freshwater and marine. Actinophrys, Actinosphaerium.
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●●● Ochrophyta Cavalier-Smith 1986 emend. Cavalier-Smith & Chao 1996
Accepted Article
Commonly with chloroplasts, endoplasmic reticulum surround plastids like a membrane;
plastids commonly containing chlorophyll c1, and often c2.
●●●● Chrysista Cavalier-Smith 1986
Unicellular, or filamentous or parentchymatous; ciliary supra-tz helix ancestrally; eyespot
present or absent; transitional helix present or absent; chloroplast usually few in number and
with girdle lamella; chloroplasts endoplasmic reticulum usually attached to the nuclear
envelope.
Incertae sedis Chrysista: Environmental lineages MOCH-3, MOCH-5 Massana et al. 2014
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes. These clades are mostly detected in the analysis of small size fractions (pico and
nanoeukaryotes).
Incertae sedis Chrysista: Environmental lineages Synchromophyceae, Chrysomerophyceae,
Picophagus, Chrysowaernella, Aurearena.
●●●●● Chrysophyceae Pascher 1914
Predominately ciliated cells, but also capsoid, coccoid, filamentous, and parenchymatous
forms; swimming cells biciliated – one anteriorly directed and one laterally directed; tripartite
mastigonemes with short and long lateral hairs on the shaft; kinetosome usually with 4
microtubular kinetosomal roots and one large striated root or rhizoplast; ciliary transitional
helix with 4–6 gyres located above the major transitional plate; no paraciliary rod; cell
coverings, when present, include organic scales, silica scales, organic lorica, and cellulose
cell wall; chloroplast with girdle lamella; outer chloroplast endoplasmic reticulum membrane
with direct membrane connection to the outer nuclear envelope membrane; plastid DNA with
ring-type genophore; eyespots present or absent; plastid pigments include chlorophylls a
and c 1 & 2, fucoxanthin, viola- xanthin, anthaxanthin, and neoxanthin; plastid secondarly
lost in some, as noted below.
Incertae sedis Chrysophyceae: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion,
Phaeoplaca.
●●●●●● Chromulinales Pascher 1910
Swimming cells with only one cilium visible by light microscopy; photosynthetic; four
microtubular kinetosomal roots. Chromulina, Chrysomonas.
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●●●●●● Hibberdiales Andersen 1989
Accepted Article
Swimming cells with only one cilium visible by light microscopy; photosynthetic; three
microtubular kinetosomal roots. Hibberdia.
●●●●●● Ochromonadales Pascher 1910
Swimming cells with two cilia visible by light microscopy; some secondarily lost
photosynthetic ability, and are colourless; heterotrophic species can be phagotrophic.
Spumella, Pedospumella, Ochromonas.
●●●●●● Paraphysomonadida Scoble & Cavalier-Smith 2014
Phagotrophic colorless cells with two visible cilia; scales composed of unperforated base
plate, usually circular, with slender simple spines. Paraphysomonas.
●●●●●● Synurales Andersen 1987
Predominately ciliated photosynthetic cells, some form benthic palmelloid colonies;
swimming cells usually with two anteriorly directed cilia – one bearing tripartite tubular
mastigonemes with short and long lateral hairs on their shafts, two microtubular kinetosomal
roots and one large striated kinetosomal root or rhizoplast. Chrysodidymus, Mallomonas,
Synura, Tesselaria.
●●●●● Eustigmatales Hibberd 1981
Coccoid organisms, single cells or colonies; swimming cells biciliate – one anteriorly directed
and one posteriorly directed; 4 microtubular kinetosomal roots and one large striated
kinetosomal root or rhizoplast; ciliary transitional helix with 6 gyres located above the major
transitional plate; no paraciliary rod; cell walls present; chloroplast without girdle lamella;
outer chloroplast endoplasmic reticulum membrane with direct membrane connection to the
outer nuclear envelope membrane; plastid DNA with ring-type genophore; eyespot present
but located outside of the chloroplast; plastid pigments include chlorophylls a, violaxanthin,
and vaucherioxanthin. Botryochloropsis, Eustigmatos, Monodopsis, Nannochloropsis,
Pseudocharaciopsis, Vischeria.
●●●●● Phaeophyceae Hansgirg 1886 [Kjellman 1891, Pfitzer 1894]
Filamentous, syntagmatic, parenchymatous or ciliated; swimming cells with two cilia usually
inserted laterally – one anteriorly directed and one posteriorly directed; usually 4
microtubular kinetosomal roots but no striated kinetosomal root or rhizoplast; ciliary
transitional helix typically with 6 gyres located above the major transitional plate; no
paraciliary rod; little to no substantial tissue diff erentiation occurring in parenchymatous
forms; cell wall present, containing alginate compounds and cellulose; plasmodesmata or
pores between cells in parenchymatous forms; chloroplasts with girdle lamella; outer
chloroplast endoplasmic reticulum membrane with direct membrane connection to the outer
nuclear envelope membrane; plastid DNA with ring-type genophore; eyespots present or
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Accepted Article
absent; plastid pigments include chlorophylls a and c 1 & 2, fucoxanthin, and violaxanthin.
Note that several subdivisions are separated on the basis of life history and gene sequence
information, but taxonomic classification is still in flux.
●●●●●● Ascoseirales Petrov 1964
Sporophyte parenchymatous, with intercalary growth; several scattered discoid plastids
without pyrenoid; heteromorphic life cycle but gametophyte not free-living; isogamous sexual
reproduction.
Ascoseira.
●●●●●● Desmarestiales Setchell & Gardner 1925
Gametophyte small and filamentous; sporophyte larger and pseudo-parenchymatous;
several scattered discoid plastids with no pyrenoid; trichothallic growth; heteromorphic life
cycle; oogamous sexual reproduction. Arthrocladia, Desmarestia (P), Himantothallus,
Phaeurus.
●●●●●● Dictyotales Bory de Saint-Vincent 1828
Gametophyte and sporophyte parenchymatous, with apical or marginal growth; several
scattered discoid plastids without pyrenoid; isomorphic life cycle; oogamous sexual
reproduction. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
●●●●●● Discosporangiales Kawai et al. 2007
Simple branched filaments with apical growth; plastids multiple, discoid, without pyrenoids;
species lack heterotrichy and phaeophycean hairs. Note that the early divergence of this
group from other brown algae is reflected in their continuous division and elongation of
vegetative cells. Choristocarpus, Discosporangium.
●●●●●● Ectocarpales Bessey 1907, emend. Silva & Reviers 2000
Gametophyte and sporophyte uniseriate filaments, either branched or unbranched, with
diff use growth; one or more ribbon-shaped plastids with pyrenoid; isomorphic life cycle;
isogamous, anisogamous or oogamous sexual reproduction. Adenocystis, Acinetospora,
Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
●●●●●●Fucales Bory de Saint-Vincent 1927
Sporophyte parenchymatous, with apical cell growth; several scattered discoid plastids
without pyrenoid; diploid life stage only with meiosis producing gametes; (mostly) oogamous
sexual reproduction. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira,
Sargassum, Turbinaria.
This article is protected by copyright. All rights reserved.
●●●●●● Ishige Yendo 1907 [Ishigeacea Okamura 1935, Ishigeales Cho et al. 2004]
Accepted Article
Isomorphic alternation of generations, with apical cell growth; scattered discoid plastids
without pyreniods; terminal unilocular sporangia or uniseriate plurilocular sporangia; cortex
pseudoparen- chymatous with assimilatory filaments; phaeophycean hairs in cryptostigmata.
Ishige.
●●●●●● Laminariales Migula 1908
Gametophyte small and filamentous with apical growth; sporophyte large and
parenchymatous, with intercalary growth; several scattered discoid plastids without pyrenoid;
heteromorphic life cycle; oogamous sexual reproduction with eggs sometimes ciliated.
Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
●●●●●● Nemoderma Schousboe ex Bonnet 1892 [Nemodermatales Parente et al. 2008] (M)
Encrusting heterotrichous thalli; numerous discoid plastids per cell without pyrenoids;
isomorphic life cycle; anisogamous gametes; plurilocular reproductive structures are lateral,
whereas unilocular sporangia are intercalary. Nemoderma.
●●●●●● Onslowiales Draisma & Prud’homme van Reine 2008
An irregularly branched oligostichous thallus, both branches and reproductive structures are
the result of lateral divisions from thallus cells; prominent apical cell lacking transverse
division of sub-apical cells; multiple discoid plastids without pyrenoid; isomorphic life cycle;
sexual reproduction can occur by plurilocular or unilocular sporangia, or via vegetative
propagules lacking a central apical cell. Onslowia.
●●●●●● Ralfsiales Nakamura ex Lim & Kawai 2007
Crustose in at least one phase of the life history or via a disc-type germination; plastids
without pyrenoids, from one to many per cell; plurilocular sporangium intercalary and having
one or more terminal sterile cells. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
●●●●●● Scytothamnales Peters & Clayton 1998
Gametophyte large and parenchymatous, with intercalary growth; sporophyte small and
filamentous, with apical growth; one or more stellate or axial plastids with pyrenoid;
heteromorphic alternation of generations; anisogamous sexual reproduction. Scytothamnus,
Splachnidium, Stereocladon.
●●●●●● Sphacelariales Migula 1908
Gametophyte and sporophyte branched multiseriate filaments, with apical growth; several
scattered discoid plastids without pyrenoid; usually an isomorphic alternation of generations;
isogamous, anisogamous or oogamous sexual reproduction. Chaetopteris, Halopteris,
Stypocaulon, Sphacelaria, Verosphacella.
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●●●●●● Sporochnales Sauvageau 1926
Accepted Article
Gametophyte and larger sporophyte pseudoparenchymatous, with trichothallic growth;
several scattered discoid plastids without pyrenoid; heteromorphic alternation of generations;
oogamous sexual reproduction. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
●●●●●● Syringodermatales Henry 1984
Gametophyte 2–4 cells; sporophyte parenchymatous with apical and marginal growth;
several scattered discoid plastids without pyrenoid; heteromorphic alternation of generations
but gametophyte not free-living; isogamous sexual reproduction. Syringoderma.
●●●●●● Tilopteridales Bessey 1907
Polystichous construction of the thallus, which grows by a trichothallic meristem; several
scattered plastids without pyrenoids; isomorphic alternation of generations; oogamous
sexual reproduction. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria,
Tilopteris.
●●●●● Phaeothamniophyceae Andersen & Bailey in Bailey et al. 1998
Filamentous, capsoid, palmelloid, ciliated, or coccoid; swimming cells biciliated – anteriorly
directed cilium bearing tripartite tubular mastigonemes and posteriorly directed cilium without
tripartite hairs; 4 microtubular kinetosomal roots but no striated kinetosomal root or
rhizoplast; ciliary transitional helix with 4–6 gyres located above the major transitional plate;
no paraciliary rod; cells covered with an entire or two-pieced cell wall; chloroplast with girdle
lamella; chloroplast endoplasmic reticulum membrane with direct membrane connection to
the outer nuclear envelope membrane; plastid DNA with ring-type genophore; eye-spots
present; plastid pigments include chlorophylls a and c, fucoxanthin, heteroxanthin,
diatoxanthin, and diadinoxanthin.
●●●●●● Phaeothamniales Bourrelly 1954, emend. Andersen & Bailey in Bailey et al. 1998
(R)
Distinguished from the Pleurochloridales based upon molecular phylogenetic analyses.
Phaeothamnion.
●●●●●●Pleurochloridales Ettl 1956 (R)
Distinguished from the Phaeothamniales based upon molecular phylogenetic analyses.
Pleurochloridella.
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●●●●● Raphidophyceae Chadefaud 1950, emend. Silva 1980
Accepted Article
Naked swimming biciliates with one anteriorly directed cilium bearing tripartite tubular
mastigonemes and one posteriorly directed cilium lacking tripartite mastigonemes;
microtubular kinetosomal roots present but poorly characterized; one large striated
kinetosomal root or rhizoplast present; ciliary transitional helix absent; no paraciliary rod;
chloroplast with or without girdle lamella; outer chloroplast endoplasmic reticulum membrane
with no or very weak direct membrane connection to the outer nuclear envelope membrane;
plastid DNA with scattered granule-type genophore; eyespots absent; plastid pigments
include chlorophylls a and c 1 & 2; carotenoid composition distinctly diff erent between
marine (m) and freshwater (fw) species - fuco-xanthin (m), violaxanthin (m), heteroxanthin
(fw), vaucherioxanthin (fw). Chattonella, Fibrocapsa, Goniostomum, Haramonas,
Heterosigma, Merotricha, Olisthodiscus, Vacuolaria.
●●●●● Schizocladia Henry et al. in Kawai et al. 2003 [Schizocladales Kawai et al. 2003] (M)
Branched filamentous algae with biciliated zoospores – an immature cilium bearing tubular
tripartite hairs; ciliary transitional helix with ~5 gyres located above the transitional plate;
ciliary apparatus and kinetoso- mal roots, if present undescribed; chloroplasts parietal with
girdle lamella; outer chloroplast endoplasmic reticulum membrane with direct membrane
connection to the outer nuclear envelope membrane; plastid DNA with ring-type genophore;
plastids with chlorophylls a and c as well as carotenoids (unverified); cell wall containing
alginates but lacking cellulose and plasmodesmata; eyespot present; major storage product
undescribed. Schizocladia.
●●●●● Xanthophyceae Allorge 1930, emend. Fritsch 1935 [Heterokontae Luther 1899,
Heteromonadea Leedale 1983, Xanthophyta Hibberd 1990]
Predominately coccoid or filamentous, rarely amoeboid, ciliated or capsoid; swimming cells
with two cilia – one anteriorly directed and bearing tripartite tubular hairs and one posteriorly
directed and lacking tripartite hairs; 4 microtubular kinetosomal roots and one large striated
kinetosomeal root or rhizoplast; ciliary transitional helix with 6 apparently double gyres
located above the major transitional plate; no paraciliary rod; cell walls typical, probably of
cellulose and either entire or H-shaped bisectional walls; chloroplast with girdle lamella;
outer chloroplast endoplasmic reticulum membrane with direct membrane connection to the
outer nuclear envelope membrane; plastid DNA with ring-type genophore; eyespots present or absent; plastid pigments include chlorophylls a and c 1 & 2, violaxanthin,
heteroxanthin, and vaucherio- xanthin.
●●●●●● Tribonematales Pascher 1939
Filamentous, coccoid, and capsoid forms, sometimes becoming parenchymatous or
multinucleate with age; cell walls, when present, either with H-shaped overlapping cell wall
pieces or with complete or entire cell walls; elaborate reproductive structures lacking. Botrydium, Bumilleriopsis,
Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus,
Tribonema, Xanthonema.
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●●●●●● Vaucheriales Bohlin 1901
Accepted Article
Siphonous filaments; elaborate sexual reproductive structures as antheridia and oogonia.
Vaucheria.
●●●● Diatomista Derelle et al. 2016 emend. Cavalier-Smith 2017 (R)
Unicellular or aggregative; no cell wall; naked or with silica frustules or scales; without supratz helix
Incertae sedis Diatomista: Environmental lineages MOCH-1, MOCH-2, MOCH-4 Massana et
al. 2014
Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA
genes. These clades are mostly detected in the analysis of small size fractions (pico and
nanoeukaryotes).
●●●●● Bolidophyceae Guillou et al. 1999 [Parmales Booth and Marchant 1987]
Two types of cells known: motile and nonmotile. Swimming cells with two cilia, one anteriorly
directed (with mastigonemes) and one posteriorly directed; no microtubular or fibrillar
kinetosomal roots; ciliary transitional helix absent; no paraciliary rod; chloroplast with girdle
lamella; outer chloroplast endoplasmic reticulum membrane with direct membrane
connection to the outer nuclear envelope membrane; plastid DNA with ring-type genophore;
no eyespot; plastid pigments include chlorophylls a and c 1-3, fucoxanthin, 19’butanoyloxyfucoxanthin, diatoxanthin, and diadinoxanthin. Nonmotile cells possess
chloroplasts like those of swimming cells but are surrounded by complete multipartite walls
comprised of abutting silica plates (circular shield and ventral plates, elongate or triradiate
girdle plates, and triradiate dorsal plates), often bearing ridges and spines and radiating lines
of pores; exclsuively marine. Bolidomonas, Triparma, Tetraparma, Pentalamina.
●●●●●Diatomeae 31 Dumortier 1821 [= Bacillariophyta Haeckel, 1878]
Vegetative cells cylindrical with a circular, elongate or multipolar cross-section, lacking any
trace of cilia except in the sperm of centric lineages; cell wall complete, composed of tightly
integrated silicified elements and comprised of two valves, one at each end of the cell, with
several girdle bands (as hoops or segments) covering the cylindrical ‘girdle’ lying between
the valves; valves penetrated by simple or chambered pores arranged in rows (striae); other
openings often present in the valves (so-called ‘fields’ and ‘processes’, slits), involved in
secretion and motility; chloroplasts usually present, bounded by 4 membranes, and with
lamellae of 3 thylakoids and a ring nucleoid (rarely multiple nucleoids); ciliated sperm cells
bearing a single anterior cilium with a 9 + 0 axoneme and mastigonemes; life cycle diplontic
and of unique pattern – slow size reduction over several years during the vegetative phase,
caused by an unusual internal wall morphogenesis, alternating with rapid size restitution via
a growth phase (auxospore) over several days.
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31
Accepted Article
This revision reflects numerous advances in the phylogeny of the diatoms over the last
decade. Due to our poor taxon sampling outside of the Mediophyceae and pennate diatoms,
and the known and anticipated diversity of all diatoms, many clades appear at a high
classification level (and the higher level classification is rather flat). Nomenclature follows the
botanical code (ICN). Some of the basal nodes will probably become better resolved in the
future, and would permit additional subdivisions. The genera are provided as examples only,
and are far from complete lists.
●●●●●● Leptocylindrophytina D.G. Mann, in Adl et al. 2019
Chain forming or solitary; valves circular, valve pattern radiating from a central circular
annulus; pores simple; girdle bands segmental to strap-like; sexual reproduction oogamous
or apparently absent; chloroplasts several, small; exclusively marine.
●●●●●●● Leptocylindrophyceae D.G. Mann, in Adl et al. 2019
Chain-forming (linked by short spines or secretions), delicate; valves circular, flat-topped or
domed; a single simple process often present near the annulus; girdle bands segmental;
auxospore forming a dormant resting stage (rare in other diatom clades). Leptocylindrus,
Tenuicylindrus.
●●●●●●● Corethrophyceae D.G. Mann, in Adl et al. 2019
Solitary; valves circular, domed; elaborate articulating silica spines secreted from around the
valve margin; rimoportulae and other processes absent; girdle bands segmental. Corethron.
●●●●●● Ellerbeckiophytina D.G. Mann, in Adl et al. 2019
Chain-forming (linked by valve spines), heavily silicified; valves circular, with radially
symmetrical valve pattern; rimoportulae or tube processes small, restricted to the mantle;
girdle bands hoop-like; marine and freshwater; sexual reproduction as yet unknown.
Ellerbeckia.
●●●●●● Probosciophytina D.G. Mann, in Adl et al. 2019
Usually solitary, with a long pervalvar axis; valves circular, extended into an eccentric beak
(proboscis); rimoportulae and other processes absent; girdle bands segmental; exclusively
marine; sexual reproduction oogamous. Proboscia.
●●●●●● Melosirophytina D.G. Mann, in Adl et al. 2019
Usually chain-forming (linked by valve spines or by central secretions); valves circular,
radially symmetrical, pattern radiating from a central annulus (which may occupy the whole
of the cylindrical valve in Aulacoseira and some Melosira); rimoportulae small, scattered on
the valve face or marginal; girdle bands hoop-like or segmental; marine and freshwater;
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Accepted Article
sexual reproduction oogamous. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia,
Endictya.
●●●●●● Coscinodiscophytina Medlin & Kaczmarska 2004, emend.
Solitary, robust; valves generally circular, pattern radiating from a central, subcentral or
submarginal circular annulus; valve structure chambered; rimoportulae central, scattered on
the valve face, or in a submarginal ring, sometimes with slit-like apertures, tubes or cap-like
structures externally; girdle bands hoop-like; sexual reproduction oogamous; mostly marine.
Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
●●●●●● Rhizosoleniophytina D.G. Mann, in Adl et al. 2019
Chain-forming, rarely solitary; valves circular, radially symmetrical or with the annulus
displaced towards one side; valve structure simple; rimoportula single, associated closely
with the annulus, sometimes developed externally into a spine; girdle bands segmental;
sexual reproduction oogamous; marine. Guinardia, Rhizosolenia, Pseudosolenia.
●●●●●● Arachnoidiscophytina D.G. Mann, in Adl et al. 2019
Solitary, heterovalvar; valves circular, radially symmetrical; valve structure chambered,
complex; valve center with radial slits (apparently modified rimoportulae); girdle bands hooplike; sexual reproduction incompletely known, marine. Arachnoidiscus.
●●●●●● Bacillariophytina Medlin & Kaczmarska 2004, emend.
Chain-forming, colonial or solitary; valve outline bipolar or multipolar, rarely circular; valve
pattern radiating from a central circular or elongate annulus or from a longitudinal rib
(sternum); valve structure simple or chambered; areas of special pores or slits often present,
involved in mucilage secretion; rimoportulae present or absent; girdle bands usually hooplike; sexual reproduction oogamous with nonmotile eggs and uniciliate sperm, or isogamous
with amoeboid or nonciliate ‘spinning’ gametes; auxospore usually with band-like elements
(the ‘perizonium’) that facilitate anisometric expansion; chloroplasts many, few or one, very
rarely apochlorotic.
●●●●●●● Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
Chain-forming or solitary; valve outline bipolar or multipolar, sometimes (perhaps
secondarily) circular; valve pattern radiating from a circular or elongate annulus;
rimoportulae central or marginal; sexual reproduction oogamous; auxospore with scales
and/or perizonium; chloroplasts usually many, small.
●●●●●●●● Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend.
Mostly chain-forming (attached by the valve poles and setae, where present, or by pads)
delicate planktonic species; valve outline usually bipolar, usually with projections or horns at
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Accepted Article
the poles, rarely multipolar or circular; pore fields present at the poles, often also long hollow
setae; annulus central or submarginal; rimoportulae central or submarginal; mostly marine,
but with a few large robustly silicified freshwater forms. Chaetoceros, Bacteriastrum,
Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë,
Hydrosera.
●●●●●●●● Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend.
Chain-forming (linked by the valve poles and/or central region) or solitary; valve outline bi-,
tri- or to multipolar; valve structure simple, with valve pattern radiating from a central annulus
or a scatter of pores; valve poles lacking well-defined pore fields; rimoportula present,
central (within the annulus), sometimes extended externally into a long tube. Lithodesmium,
Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
●●●●●●●● Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990
Cells connected into chains by chitin threads, colonial (forming sheets), or solitary; valve
outline almost always circular; valve pattern generally organized radially about a central
annulus; valve structure simple or chambered; generally with one or two submarginal
rimoportulae; almost all members characterized by ‘fultoportulae’ (special processes
involved in chitin thread secretion); auxospores lacking perizonia; marine and freshwater.
Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella,
Bacteriosira, Skeletonema, Detonula.
●●●●●●●● Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990
Generally chain-forming (linked by spines on the valves), very small-celled, delicate forms;
often heterovalvar; valve outline bipolar; valve pattern sometimes organized about a central
annulus but more often with scattered pores; small well-defined pore fields (‘ocelluli’) present
at the apices and some valves often bearing long spines (‘pili’); a single rimoportula near the
center of some valves; exclusively marine. Cymatosira, Minutocellus, Papiliocellulus,
Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella,
Pierrecomperia.
●●●●●●●● Odontellophycidae, D. G. Mann, in Adl et al. 2019
Chain-forming (linked by mucilage pads) or solitary, generally large-celled and sometimes
very robust; valve outline bi- or multipolar, rarely circular; valve pattern organized radially
about a central circular or elongate annulus; valve structure simple or chambered; valve
poles with well-defined pore fields (‘ocelli’) often surrounded by a thick rim; rimoportulae
present (sometimes with long external tubes) or absent; exclusively marine. Odontella,
Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
●●●●●●●● Chrysanthemodiscophycidae, D.G. Mann, in Adl et al. 2019
Chain-forming (linked by mucilage pads) or solitary; valve outline circular, bipolar (and then
sometimes extremely elongate, either isopolar or heteropolar) or multipolar; valve pattern
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Accepted Article
organized radially about a central annulus, which can be circular or extremely elongate (and
then with striae extending inwards from the annulus, which is therefore ‘bifacial’); valve
structure simple or chambered (alveolate); rimoportulae present or absent; pore fields
present at the poles (and then poorly differentiated, i.e. ‘pseudocelli’) or absent; exclusively
marine. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus,
Ardissonea, Climacosphenia, Toxarium.
●●●●●●● Biddulphiophyceae, D. G. Mann, in Adl et al. 2019
Chain-forming or solitary; valve outline bipolar, with elevated projections at the poles; valve
pattern radiating from a circular or elongate annulus; valve structure simple; rimoportulae
present; exclusively marine.
●●●●●●●● Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend.
Chain-forming (linked by mucilage pads), generally large-celled and robust; valve outline
sometimes undulate; polar projections small or large and valve often with additional doming
centrally and sometimes between center and poles; pattern organized radially about a
central circular annulus; pore fields (‘pseudocelli’) present at the poles; rimoportulae central.
Biddulphia.
●●●●●●●● Attheya T. West 1860c
Delicate, solitary; valve outline bipolar, the ends developed into narrow setae; valve pattern
radiating from an elongate annulus; pore fields absent, though the setae may end in
specialized regions with spines; a single off-central rimoportula; sexual reproduction
oogamous; exclusively marine. Attheya.
●●●●●●● Bacillariophyceae Haeckel 1878, emend.
Chain-forming, colonial or solitary;.valve outline almost always bipolar; valve pattern
organized bilaterally about an elongate axial rib (sternum), as in a feather; valve structure
simple or chambered; rimoportulae generally only one or two per valve or none, sometimes
accompanied (or replaced?) by special slits (the ‘raphe’) involved in motility; sexual
reproduction involving gametangiogamy and almost always with gametes of equal size
(although sometimes with behavioral diff erentiation and/or morphological differences);
perizonium generally differentiated into two distinct series, transverse and longitudinal;
chloroplasts usually only 1, 2 or a few and large, less often many and small.
●●●●●●●● Striatellaceae Kützing 1844
Solitary; valve outline bipolar; valve structure simple; a rimmed pore field present at each
pole; rimoportulae present (one at each pole or scattered along the sides of the valve); raphe
absent; sexual reproduction not confirmed;.exclusively marine. Striatella, Pseudostriatella.
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●●●●●●●● Urneidophycidae Medlin 2016 (P?).
Accepted Article
Chain-forming (linked by spines on the valves), colonial (linked by pads) or solitary; valve
outline bi- or multipolar, rarely circular; valve structure simple; pore fields sometimes present
at the poles, rimoportulae present or absent; raphe absent; ‘male’ and ‘female’ gametes of
equal size but ‘male’ gametes with non-cilium projections that generate movement;
exclusively marine. Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis,
Bleakeleya, Asterionellopsis.
●●●●●●●● Fragilariophycidae Round in Round, Crawford & Mann 1990, emend.
Chain-forming or colonial (linked by pads or stalks, less often by valve spines) or solitary;
valve outline bi- or multipolar, very rarely circular (with reduction of the sternum and
secondary evolution of radial symmetry); valve structure usually simple; pore fields (rimmed
or not) often present at the poles; rimoportulae present or absent, very variable in location
but often polar; raphe absent; ‘male’ and ‘female’ gametes of equal or unequal size,
amoeboid, or with ‘male’ gametes with non-cilium projections that generate movement;
marine and freshwater. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia,
Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira,
Thalassionema.
●●●●●●●● Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend.
Usually solitary and motile, less often chain-forming or colonial (linked by stalks or living in
mucilage tubes); valve outline almost always bipolar, frustules sometimes heterovalvar;
rimoportulae usually absent (exception: Eunotiales); valve structure simple or chambered;
pore fields sometimes present at one or both poles; raphe present (rarely infilled during
valve formation); usually 1 or 2 chloroplasts per cell, positioned to avoid the area beneath
the raphe; gametes morphologically similar, amoeboid or fusing through expansion; marine
and freshwater, with many examples of genera or families transgressing the marine–
freshwater interface. The vast majority of diatom species belong here, classified into many
tens of genera. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudo-nitzschia, Cylindrotheca,
Navicula, Seminavis, Haslea, Stauroneis, Pleurosigma, Gyrosigma, Achnanthidium,
Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella,
Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella.
●●●●● Dictyochophyceae Silva 1980
Single cells, colonial ciliated cells or amoebae; swimming cells usually with one cilium,
anteriorly directed and bearing tripartite tubular hairs; kinetosomes adpressed to nucleus; no
microtubular or fibrillar kinetosomal roots; ciliary transitional helix, when present, with 0–2
gyres located below the major transitional plate; paraciliary rod present; cells naked, with
organic scales or with siliceous skeleton; chloroplasts, when present, with girdle lamella;
plastid DNA with scattered granule-type genophore; no eyespot; plastid pigments include
chlorophylls a and c 1 & 2, fucoxanthin, diatoxanthin, and diadinoxanthin.
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●●●●●● Dictyochales Haeckel 1894
Accepted Article
Silica skeleton present on at least one life stage; with chloroplasts. Dictyocha.
●●●●●● Pedinellales Zimmermann et al. 1984
Naked, organically scaled or loricate ciliated cells; with or without chloroplasts. Actinomonas,
Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella,
Pteridomonas.
●●●●●● Rhizochromulinales O’Kelly & Wujek 1994
Vegetative cells amoeboid; zoospore ciliated; with chloroplasts. Rhizochromulina.
●●●●● Pelagophyceae Andersen & Saunders 1993
Ciliated, capsoid, coccoid, sarcinoid or filamentous; swimming cells with 1 or 2 cilia –
anteriorly directed cilium bearing bipartite or tripartite tubular hairs and second cilium, when
present, directed posteriorly; kinetosome(s) adpressed to nucleus; no microtubular or fibrillar
kinetosomal roots on uniciliated cells; four microtubular roots on biciliated cells; ciliary
transitional helix, when present, with 2 gyres located below the major transitional plate;
paraciliary rod present or absent; cells naked or with organic thecae or cell walls;
chloroplasts with girdle lamella; plastid DNA with scattered granule-type genophore; no
eyespot; plastid pigments include chlorophylls a & c 1, 2, fucoxanthin, 19hexanoyloxyfucoxanthin, 19-but-anoyloxyfucoxanthin, diatoxanthin, and diadinoxanthin.
●●●●●● Pelagomonadales Andersen & Saunders 1993
Ciliated or coccoid organisms; when ciliated, a single cilium without a second kinetosome;
no kinetosomal roots. Aureococcus, Aureoumbra, Pelagococcus, Pelagomonas.
●●●●●● Sarcinochrysidales Gayral & Billard 1977
Sarcinoid, capsoid, ciliated or filamentous; cells typically with organic cell wall; ciliated cells
biciliated with four microtubular kinetosomal roots. Ankylochrisis, Nematochrysopsis,
Pulvinaria, Sarcinochrysis.
●●●●● Pinguiophyceae Kawachi et al. 2003
Ciliated or coccoid organisms; swimming cells with one or two cilia; tripartite hairs present or
absent on immature cilium; 3–4 microtubular kinetosomal roots and one large striated
kinetosomal root or rhizoplast; ciliary transitional helix with 2 gyres located below the major
transitional plate; no paraciliary rod; cells naked or enclosed in mineralized lorica; chloroplast
with girdle lamella; outer chloroplast endoplasmic reticulum membrane with direct membrane
connection to the outer nuclear envelope membrane; plastid DNA with scattered granuletype genophore; eyespots absent; plastid pigments include chlorophylls a and c 1 & 2,
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Accepted Article
fucoxanthin, and violaxanthin. Glossomastix, Phaeomonas, Pinguiochrysis, Pinguiococcus,
Polypodochrysis.
● Alveolata Cavalier-Smith 1991
Cortical alveolae, sometimes secondarily lost; with ciliary pit or micropore; mitochondrial
cristae tubular or ampulliform.
●● Colpodellida Cavalier-Smith 1993, emend. Adl et al. 2005, 2019
Photosynthetic, or non-photosynthetic and predatory; complex plastids, when present bound
by four membranes; mitochondrion with tubular cristae; highly flattened cortical alveoli;
microtubules beneath alveolae; conoid-like structure with apical complex and rostrum;
biciliate; micropore present; cysts at least in some species.
●●●Vitrellaceae Oborník & Lukeš 2012
Immotile vegetative cells with laminated cell walls; autosporangia and zoosporangia contain
dozens of immotile autospores and motile biciliate zoospores, respectively; prominent
pyrenoid; sporangia carry an operculum; plastid pigmented by chlorophyll a, violaxanthin,
vaucheriaxanthin and β-carotene; chlorophyll c absent. Vitrella.
●●●Colpodellaceae Adl et al. 2019
Non-photosynthetic ciliated cell predatory on other protists, (found oncein human blood).
Colpodella, Chilovora, Voromonas.
●●●Chromeraceae Oborník & Lukeš 2012
Immotile coccoid cells reproduce by binary division; zoospores with heterodynamic cilia;
pseudoconoid, coccoid wedge and chromerosome present; cells surrounded by thin
sporangium wall; plastid pigmented by chlorophyll a, violaxanthin, isofucoxanthin and βcarotene; chlorophyll c absent. Chromera.
●●●Alphamonaceae Adl et al. 2019
Non-photosynthetic predatory ciliated cells on other protists; carbohydrate reserve granules
absent. Alphamonas.
●● Perkinsidae Levine 1978, emend. Adl et al. 2005 [Perkinsozoa Moestrup & RehnstamHolm, 1999; Perkinsozoa Norén & Moestrup, 1999]
Trophozoites parasitic, dividing by successive binary fissions; released trophozoites (termed
hypnospores) developing outside host to form zoospores via the formation of zoosporangia
or morphologically undifferentiated mononucleate cells via a hypha-like tube; zoospores
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Accepted Article
biciliate; apical organelles including an incomplete conoid (open along one side), rhoptries,
micronemes, and micropores, and a microtubular cytoskeleton with both an anterior and
posterior polar ring. Parvilucifera, Perkinsus, Rastrimonas, X-cell parasites.
Incertae sedis Perkinsidae: Psammosa Okamoto et al. 2012 – morphologically close to
Colpodella and Voromonas, but phylogenetically more related to Perkinsidae.
Incertae sedis Perkinsidae: Phagodinium.
●●Colponemida Cavalier-Smith 1993 emend. Adl et al. 2019 (P?)
Biciliate alveolates, typically cytotrophic predators, found in soil, freshwater, and marine
environments. These described genera are most probably multiple genera as DNA
sequences obtained are divergent and many remain to be described. Poorly sampled due to
cytotrophy, we expect better taxon sampling to improve the resolution of this node.
●●● Colponemidia Tikhonenkov et al. 2014
Biciliate; three-membraned alveolar pellicle; two microtubule bands armour longitudinal
groove; micropore absent; nontubular mastigonemes present; cytotrophic predators and
sometimes on micro- invertebrates. Colponema.
●●● Acavomonidia Tikhonenkov et al. 2014
Biciliate; rigid cells; lack longitudinal grooves and apical complex structures; cytotrophic
predators. Acavomonas.
●●● Palustrimonas Patterson and Simpson, 1996
Deep branching colponemid alveolate; cytotrophic predator; longitudinal feeding groove.
Palustrimonas.
●●● Oxyrrhis Dujardin 1841 [Oxyrrhinaceae Sournia 1984] (M)
Without true cingulum and sulcus; intranuclear mitotic spindle; with amphiesmal vesicles and
trichocysts; cilia inserted laterally; cytotrophic predator. (There may be multiple species).
Oxyrrhis marina.
●●Dinoflagellata Bütschli 1885, emend. Fensome et al. 1993, emend. Adl et al. 2005
Cells with two cilia in the motile stage – typically, one transverse cilium ribbon-like with
multiple waves beating to the cell’s left and longitudinal cilium beating posteriorly with only
one or few waves; nucleus typically a dinokaryon with chromosomes remaining condensed
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Accepted Article
during interphase and lacking typical eukaryotic histones and centrioles; dinoflagellate/viral
nucleoproteins package chromatin; closed dinomitosis with extranuclear spindle.
Incertae sedis Dinoflagellata: Naked and thecate genera with uncertain affiliation. e.g.,
Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis,
Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium,
Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium,
Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium,
Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium,
Pyramidodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium,
Thecadinium,Thecadiniopsis, Togula.
Incertae sedis Dinoflagellata: Parasitic dinoflagellates with dinokaryon during part of the life
cycle only; not highly vacuolated. Fossils unknown. [Blastodiniales Chatton 1906, no longer
valid]. Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon,
Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium,
Stylodinium, Syltodinium, Synchaeta.
●●● Syndiniales Loeblich III 1976
Aplastidic intracellular parasites of marine protists and metazoan, generally surrounded by
an external parasitophorous membrane inside the host; sporogenesis by palintomic
(schizogonous) divisions; motile cells (i.e. dinospores or gametes) with a dinokont-like
arrangement of cilia; lacking well defined cingulum and sulcus; transverse cilium wrapping
loosely around cell. V-shaped chromosomes, attach to the nucleus membrane by the apex
and remain condensed during interphase. Amoebophrya, Duboscquella, Merodinium,
Syndinium.
Incertae sedis Syndiniales: Ichthyodinium (environmental Marine Alveolate (MALV) Group I).
Parasites of the early developmental stages (eggs and larvae) of some species of finfish;
sporogenesis occurs in the yolk sac of embryos.
Incertae sedis Syndiniales: Ellobipsidae: the clade is closely reklated to MALV-I and MALVII. Ellobiopsis, Thalassomyces.
●●●● Euduboscquellidae Coats & Bachvaroff 2012
Parasites of Ciliophora and Radiolaria, with trophont episome bordered by a perinematic ring
and a lamina pharyngea extending into trophont cytoplasm; sporogenesis occurs outside the
host (or outside the central capsule). Euduboscquella (environmental Marine Alveolate
Group I), Dogelodinium, Keppenodinium.
Incertae sedis: RP-parasite, parasite of copepods (environmental Marine Alveolate Group I).
This article is protected by copyright. All rights reserved.
●●●● Amoebophryidae Cachon 1964 (environmental Marine Alveolate Group II)
Accepted Article
Parasites of Dinophyceae, Radiolaria and Ciliophora; feeding through a cytopharynx inside
the host; palintomic schizogonous divisions occur inside the host and produce a swimming
multicellular temporary structure (termed vermiform) after an evagination to leave its host,
then each cell of this structure individualize into dinospore(s). Amoebophrya.
●●●● Syndinidae Chatton 1910 (environmental Marine Alveolate Group IV)
Parasites of crustacean and Radiolaria. Sporogenesis occurs inside the host, and start by
active nucleic divisions into a plasmodium that generally fill the whole body of the host;
sporogenesis occurs inside the host by fragmentation of the plasmodium. Hematodinium,
Syndinium, Solenodinium.
●●●● Sphaeriparaceae Loeblich III 1970
Parasites of Appendicularia and Radiolaria; feeding through a cytopharynx inside the host;
sporogenesis occurs outside the host. Atlanticellodinium, Sphaeripara.
●●●Noctilucales Haeckel 1894 [Noctiluciphyceae Fensome et al. 1993]
Principal life cycle stage comprising a large free-living motile cell inflated by vacuoles;
dinokaryon during part of life cycle only. Fossils unknown. Abedinium, Cachonodinium,
Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium,
Pomatodinium, Scaphodinium, Spatulodinium.
●●●Dinophyceae Pascher 1914
Cell cortex (amphiesma) containing alveolae (amphiesmal vesicles) that may or may not
contain cellulosic thecal plates, the pattern (tabulation) thus formed being a crucial
morphological criterion in recognizing affinities among dinophyceans; with a dinokaryon
through the entire life cycle.
●●●●Gymnodiniphycidae Fensome et al. 1993
With numerous amphiesmal vesicles, arranged nonserially or in more than six latitudinal
series or with the pellicle as the principal amphiesmal element or the amphiesmal structure
uncertain but not comprising a theca divisible into six or fewer latitudinal plates. Few known
fossil representatives.
●●●●●Gymnodinium F. Stein 1878, emend. G. Hansen & Moestrup in Daugbjerg
et al. 2000 sensu stricto
With loop-shaped, anticlockwise apical structure complex. Barrufeta, Chytriodinium,
Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium,
Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Warnowia.
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●●●●●Amphidinium Claparède & Lachmann 1859, emend. Flø Jørgensen et
al. 2004 sensu stricto
Accepted Article
Minute irregular triangular- or crescent-shaped episome deflected to the left; no apical
structure complex. Amphidinium.
●●●●●Gyrodinium Kofoid & Swezy 1921, emend. G. Hansen and Moestrup in
Daugbjerg et al. 2000 sensu stricto
Elliptical apical structure complex, bisected by a ridge; with surface striation/ridges.
Gyrodinium.
●●●●●Kareniaceae Bergholtz et al. 2005
Furrow-like straight or sigmoid apical structure complex; haptophyte-derived chloroplasts.
Brachidinium, Karenia, Karlodinium, Takayama.
●●●●●Ceratoperidiniaceae Loeblich III 1980, emend. Reñé and de Salas 2013
Closed, circular loop-shaped apical structure complex. Ceratoperidinium, Kirithra.
●●●●●Torodiniales Boutrup, Moestrup & Daugbjerg 2016
Hat-like apical projection; counterclockwise spiraling apical structure complex; with
longitudinal surface striation; very large episome. Kapelodinium, Torodinium
●●●●●Levanderina Moestrup et al. 2014
U-shaped apical structure complex. Levanderina.
●●●●●Margalefidinium F. Gómez, Richlen & D.M. Anderson 2017
U-shaped apical structure complex connected to the sulcal extension; sulcus encircles the cell
about once; cingulum encircles the cell about twice; smooth cell surface; eyespot in the
episome. Margalefidinium
●●●●●Cochlodinium F. Schütt emend. F. Gómez, Richlen & D.M. Anderson
2017 sensu stricto
circular apical structure complex connected to the sulcal extension; sulcus invades the episome
as a wide loop; descending cingulum encircles the cell about 1.5 to 2 times; cell surface with
fine striations. Cochlodinium strangulatum.
●●●●●Ptychodiscales Fensome et al. 1993
With wall of the motile cell dominated by a thick pellicle; alveolae, where discernible, usually
devoid of thecal plates, forming a tabulation that is nonserially arranged or is organized into
numerous latitudinal series. Few known fossil representatives. Achradina, Amphitolus,
Balechina, Ptychodiscus, Sclerodinium.
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Accepted Article
●●●●●Borghiellaceae Moestrup, Lindberg, & Daugbjerg 2009
With or without apical pair of elongate vesicles (PEV) with furrow; eyespot type B with
globules inside the chloroplast associated with external brick-like material in vesicles.
Baldinia, Borghiella.
●●●●●Tovelliaceae Moestrup et al. 2005
With alveolae containing light thecal plates with apical line of narrow plates (ALP); eyespot
type C with extraplastidal, nonmembrane bound pigment globules. Bernardinium,
Esopotrodinium, Jadwigia, Tovellia.
●●●●●Suessiaceae Fensome et al. 1993, emend. Moestrup et al. 2009
With alveolae containing light thecal plates and forming a tabulation involving 7--15
latitudinal series, with or without elongate apical vesicle (EAV); eyespot type E with cisternae
containing brick-like material. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis,
Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
●●●●Peridiniphycidae Fensome et al. 1993
With a tabulation that accords with, or derives from, a pattern in which there are five or six
latitudinal plate series; sagittal suture lacking.
●●●●●Gonyaulacales Taylor 1980
Alveolae usually containing thecal plates, forming a tabulation of 5--6 latitudinal series;
distinguished by particular tabulation features that can be recognized generally by a strong
degree of asymmetry in the anterior (apical) and posterior (antapical) areas. This taxon has
fossils extending from the late Triassic period (~210 Ma) to the present day. Alexandrium,
Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma,
Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium,
Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
●●●●●Peridiniales Haeckel 1894
Alveolae containing thecal plates, forming a tabulation of 6 latitudinal series; distinguished by
particular tabulation features that can be recognized generally by a strong degree of
symmetry in the anterior (apical) and posterior (antapical) areas. This taxon has fossils
extending from the early Jurassic Period (~190 Ma) to the present day. Amphidiniopsis,
Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea,
Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium,
Qia, Vulcanodinium.
●●●●●Thoracosphaeraceae Schiller 1930
Calcareous species and non-calcareous relatives. Aduncodinium, Amyloodinium,
Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium,
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Accepted Article
Ensiculifera, Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria,
Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
●●●●●Podolampadaceae Lindemann 1928
No compressed cingulum but homologous plate series. Blepharocysta, Gaarderiella,
Heterobractum, Lissodinium, Mysticella, Podolampas.
●●●●● Kryptoperidiniaceae Lindemann 1925 (= “dinotoms”)
Genera with diatom-derived chloroplasts and reduced peridinin-chloroplast as eyespot;
thecate and athecate taxa. e.g. Blixaea, Durinskia, Galeidinium, Kryptoperidinium,
Unruhdinium.
●●●●●Heterocapsaceae Fensome et al. 1993
Alveolae containing thecal plates, forming a tabulation of 6 latitudinal series; scales.
Heterocapsa.
●●●●●Amphidomataceae Sournia 1984
Alveolae containing thecal plates, forming a tabulation of 5-6 latitudinal series. Amphidoma,
Azadinium.
●●●●●Oxytoxaceae Lindemann 1928
Alveolae containing thecal plates, forming a tabulation of 5-6 latitudinal series; one antapical
plate. Corythodinium, Oxytoxum.
●●●●●Centrodiniaceae Hernández-Becerril 2010
Alveolae containing thecal plates, forming a tabulation of 7 latitudinal series; one antapical
plate. Centrodinium.
●●●●Dinophysales Kofoid 1926
With a cingulum, a sulcus, and a sagittal suture extending the entire length of the cell, one
ciliary pore. Apart from one possible fossil representative, only known from present day
forms. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia,
Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma,
Pseudophalacroma, Sinophysis, Triposolenia.
●●●●Prorocentrales Lemmermann 1910
Without cingulum or sulcus; one ciliary pore; cilia apical – one wavy cilium clearly
homologous with transverse cilium of other dinofagellates and one not wavy; thecal plates.
Fossils unknown. Mesoporus, Prorocentrum.
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●● Apicomplexa Levine 1980, emend. Adl et al. 2005
Accepted Article
At least one stage of the life cycle with flattened sub-pellicular vesicles and an apical
complex consisting of one or more polar rings, rhoptries, micronemes, conoid, and subpellicular microtubules; sexuality, where known, by syngamy followed by immediate meiosis
to produce haploid progeny; asexual reproduction of haploid stages occurring by binary
fission, endodyogeny, endopolyogeny, and/or schizogony/merogony; locomotion by gliding,
body flexion, longitudinal ridges, and/or cilia; mostly parasitic.
Incertae sedis Apicomplexa: Agamococcidiorida Levine 1979
Merogony and gametogony both absent; several families described but position within
Apicomplexa unclear. Gemmocystis*, Rhytidocystis.
Incertae sedis Apicomplexa: Protococcidiorida Kheisin 1956
Merogony absent; extracellular gamogony and sporogony; in some species, gamogony and
fertilization in the host, with oocysts released with sporogony in aqueous environment;
sporozoites exist inside intestinal epithelium briefly, on their way to coelom or vascular
tissues, where development occurs, followed by sporozoite release in the faeces.
Subdivisions uncertain. Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*,
Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
Incertae sedis Apicomplexa: Aggregata Frenzel 1885 – highly divergent 18S rRNA.
Christalloidophora Dehorne, 1934 – Merozoites with 2 to 4 fuchsinophile crystalloids.
Dobellia* Ikeda, 1914 – Life cycle still confused, sporozoites invade intestinal epithelial cells,
two forms of meronts: macromeront with period of intranuclear development, micromeront
epicellular, syzygy of macro- and micromerozoites producing gametocysts, oocyst with 1000
naked sporozoites. Echinococcidium* Porchet 1978 – with single spines and spines
arranged in bundles forming a pyramid on body surface, amylopectin granules, in large
parasitoporous vacuole in intestinal epithelium or free in intestinal lumen. Globidiellum*
Brumpt 1913 – intracellular in mononuclear leukocytes, endothelial cells and erythrocytes,
formation of large number of merozoites. Joyeuxella* Brasil 1902 – Merogony in host
epithelial cells. Rhabdospora* Laguesse 1906 – Meronts in host epithelial cells, merozoites
with rodlets (rhoptries?). Spermatobium* Eisen 1895 – Young stages in sperm sac cells,
later stages free in sperm sac, sporogonia (oocysts?), sporoblasts (sporocysts?) and
residuum described. Spiriopsis* Arvy and Peters 1972 – with micronemes and paraglycon.
Spirogregarina* Wood and Herman 1943 – Elongate, spindle-shaped, cylindrical, with spiral
bands (grooves, epicytic folds?) on surface, bulbous, knob-like terminus at each end.
Toxocystis* Léger and Duboscq 1910 – elongate, falciform with one broader end, nucleus
with two paranuclear bodies opposite each other, not motile. Trophosphaera* Le Calvez
1939 – Spherical cysts with spherical cytomeres, cytomeres form spherical sporocytes
(schizogony), sporocytes form 8 naked spores.
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●●● Aconoidasida Mehlhorn et al. 1980 [= Hematozoa Vivier 1982] (P)
Accepted Article
Apical complex lacking conoid in asexual motile stages; some diploid motile zygotes
(ookinetes) with conoid; macrogametes and microgametes forming independently;
heteroxenous.
●●●● Haemospororida Danilewsky 1885
Zygote motile as ookinete with conoid; ciliated microgametes produced by schizogonous
process; oocyst formed in which sporozoites develop. Dionisia*, Haemocystidium,
Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus,
Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
●●●● Piroplasmorida Wenyon 1926
Piriform, round, rod-shaped or amoeboid; conoid and cilia absent in all stages; polar ring
present; without oocyst; sexuality probably associated with the formation of large
axopodium-like “Strahlen”. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*,
Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
●●●● Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019
Aciliate, motile infective stage (resembling sporozoites); spore-stage with rhoptry- like
inclusions, biciliated stages exist; most of life cycle extracellular; symbionts/parasites of
marine invertebrates (at least tunicates). Nephromyces, Cardiosporidium.
●●● Conoidasida Levine 1988 (P)
Complete apical complex, including a closed conoid in all or most asexual motile stages;
cilia, where present, found exclusively in microgametes (male gametes); with the exception
of microgametes, motility generally via gliding with possibility of body flexion and undulation
of longitudinal pellicular ridges; heteroxenous or homoxenous. This group is not
monophyletic with subdivisions artificial and unclear at this time.
●●●● Coccidia Leuckart 1879 (P)
Mature gametes develop intracellularly; microgamont typically produces numerous
microgametes; syzygy absent; zygote rarely motile; sporocysts usually formed within
oocysts.
●●●●● Adeleorina Léger 1911
Microgamonts produce one to four microgametes, which associate with macrogamete in
syzygy; endodyogony is absent. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*,
Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia,
Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
This article is protected by copyright. All rights reserved.
●●●●● Eimeriorina Léger 1911
Accepted Article
Microgametes and macrogametes develop independenty; syzygy is absent; microgamonts
produce large number of cilated microgametes; zygote is nonmotile; sporozoites always
enclosed in sporocyst within oocyst. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora,
Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*,
Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora,
Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella,
Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*,
Toxoplasma, Tyzzeria*, Wenyonella*.
●●●● Gregarinasina Dufour 1828 (P)
Mature gamonts usually develop extracellularly; syzygy of gamonts generally occurring with
production of gametocyst; similar numbers of macrogametes and microgametes maturing
from paired gamonts in syzygy within the gametocyst; syngamy of mature gametes leading
to gametocyst that contains few to many oocysts, which each contain sporozoites;
sporocysts absent; asexual reproduction (merogony) absent in some species.
Incertae sedis Gregarinasina: Digyalum Koura et al. 1990 - only transverse epicytic folds,
two pouches at anterior end; Exoschizon Hukui 1939 – epicytic folds, schizogony at anterior
end of trophozoite, cytoplasmic buds, 16 merozoites differentiated at anterior end of
trophozoite.
●●●●● Archigregarinorida Grassé 1953 (P)
Trophozoite aseptate; with syzygy; encystment of gamonts; oocysts contain 4–8 or even
more sporozoites. Filipodium, Meroselenidium, Merogregarina, Platyproteum, Selenidium,
Selenocystis, Veloxidium.
●●●●● Eugregarinorida Léger 1900 (P)
Trophozoite with epimerite in gregarines with septum or mucron in gregarines without
septum; syzygy followed by encystment of gamonts; oocysts with 8 sporozoites.
Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola,
Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina,
Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora,
Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis,
Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina,
Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina,
Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia,
Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus,
Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora,
Xiphocephalus, Zygosoma* (examples).
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●●●●● Neogregarinorida Grassé 1953
Accepted Article
Trophozoite with epimerite or mucron; multiple rounds of schizogony/merogony; pairing of
gamonts; oocysts contain 8 sporozoites. Apicystis, Aranciocystis, Caulleryella*,
Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*,
Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
al. 2019
●●●●● Cryptogregarinorida Cavalier-Smith 2014 emend Adl et
Oocysts and meronts with attachment “feeder” organelle; anisogamous, microgametes
aciliate; oocysts without sporocysts containing 4 naked sporozoites; epicellular localization in
host cell. Cryptosporidium.
●●●● Blastogregarinea Chatton and Villeneuve 1936, emend. Simdyanov et al. 2018
Permanent multinuclearity and gametogenesis: nuclear division of merogony and gamogony
proceeds within the same individual (merogamont) throughout its lifespan; merogamonts
motile and sexually differentiated. Female oogamy: continuous budding of macrogametes
from the posterior part of female merogamonts. Male gamogony: budding of multinuclear
microgametocytes or microgametoblasts apparently followed by their dissociation into small
putatively biciliated male gametes. Oocysts with many (10–16) free sporozoites (no
sporocysts). Chattonaria, Siedleckia.
●● Ciliophora Doflein, 1901 [Ciliata Perty, 1852; Infusoria Bütschli, 1887]
Cells with nuclear dimorphism, including a typically polygenomic macronucleus and at least
one diploid micronucleus; somatic kinetids having a postary microtubular ribbon arising from
triplet 9, a kinetodesmal fibril or striated rootlet homologue arising near triplets 5–8, and a
transverse microtubular ribbon arising in the region of triplets 4–6; sexual reproduction, when
present, by conjugation typically with mutual exchange of haploid gametic nuclei that fuse to
form the synkaryon or zygotic nucleus. 32
32
The ordering of the major taxa follows the arrangement of most SSU-rRNA phylogenies
and recent phylogenomic analyses (e.g., Gentekaki et al., 2014). The current classification
contains some polyphyletic or paraphyletic taxa marked by (P) which require further
investigations (morphologic and/or genetic). Families are arranged alphabetically, unless
phylogeny places a family at a higher hierarchical rank.
●●●Postodesmatophora Gerassimova & Seravin, 1976
Somatic dikinetids with postodesmata (overlapping postciliary microtubular ribbons
separated by one or two microtubules).
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●●●● Karyorelictea Corliss, 1974
Accepted Article
Two to many macronuclei containing approximately but sometimes slightly more than the
diploid amount of DNA; macronuclei not dividing but replaced by division of micronuclei;
major postciliary ribbons separated by two groups of microtubules.
●●●●●Kentrophoridae Jankowski, 1980 (Kentrophoros)
●●●●●Loxodida Jankowski, 1980
Non-contractile; somatic cilia as files of dikinetids mainly on the right surface with the left
surface non-ciliated, except for single marginal (‘bristle’?) kinety; extrusomes as somatic
cnidocyst-like organelles in some genera; oral kinetids as two dikinetidal perioral kineties
and one intraoral (intrabuccal) kinety; stomatogenesis monoparakinetal or buccokinetal;
nuclei in clusters, typically two macronuclei and one micronucleus; typically in anoxic
sediments and anoxic waters.
●●●●●●Cryptopharyngidae Jankowski, 1980 (Cryptopharynx)
●●●●●●Loxodidae Bütschli, 1889 (Loxodes)
●●●●●Geleiidae Kahl, 1933 (Geleia)
●●●●Heterotrichea Stein, 1859
Polygenomic macronucleus dividing by extra-macronuclear microtubules; major postciliary
ribbons separated by one microtubule.
●●●●●Blepharismidae Jankowski in Small and Lynn, 1985 (Blepharisma)
●●●●●Climacostomidae Repak, 1972 (Climacostomum)
●●●●●Condylostomatidae Kahl in Doflein & Reichenow, 1929 (Chattonidium,
Condylostoma)
●●●●●Fabreidae Shazib et al., 2014 (Fabrea)
●●●●●Gruberiidae Shazib et al., 2014 (Gruberia)
●●●●●Coliphorina Jankowski, 1967
With a node-based definition: the clade stemming from the most recent common ancestor of
the Maristentoridae and Folliculinidae.
●●●●●●Folliculinidae Dons, 1914 (Folliculina)
●●●●●●Maristentoridae Miao et al., 2005 (Maristentor)
●●●●●Peritromidae Stein, 1867 (Peritromus)
●●●●●Spirostomidae Stein, 1867 (Anigsteinia, Spirostomum)
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●●●●●Stentoridae Carus, 1863 (Stentor)
Accepted Article
●●●Intramacronucleata Lynn, 1996
Polygenomic macronucleus dividing by intramacronuclear microtubules.
Incertae sedis Intramacronucleata: Protocruzia Faria da Cunha and Pinto 1922
[Protocruziidae Jankowski, 1980; Protocruziidia de Puytorac et al., 1987]
Nuclear apparatus a cluster of similar-sized nuclei with paradiploid macronuclei surrounding
one or more micronuclei; each macronucleus possibly organized as a single composite
chromosome. Protocruzia.
●●●●SAL Gentekaki et al., 2014
Group identified by phylogenomics. With a node-based definition: the clade stemming from
the most recent common ancestor of the Spirotrichea (S) and Lamellicorticata (i.e.,
Armophorea (A) and Litostomatea (L)).
Incertae sedis SAL: Cariacothrix Orsi et al., 2012 [Cariacotrichea Orsi et al., 2011]
With archway-shaped kinety around oral opening and extending to posterior body end; with
unique molecular signature ‘GAAACAGUCGGGGGUAUCAGUA’ (spanning nucleotide
positions 283-305 in GenBank accession number GU819615); confirmed only from deep
waters of anoxic Cariaco Basin, Venezuela. At least two adoral organelles; longitudinal
ciliary rows; caudal cilia. Cariacothrix caudata.
Incertae sedis SAL: Mesodiniidae Jankowski, 1980
Somatic cilia bristle-like, of at least two types, arranged in girdles around the body; brosse
kineties absent; extrusomes as oral toxicysts; oral region apical, domed, circular, and
delimited by circumoral dikinetids, but apparently without nematodesmata and bulge
microtubules of rhabdos. Mesodinium.
Incertae sedis SAL: Phacodinium Prowazek, 1900 [Phacodiniidia Small and Lynn, 1985]
Somatic kineties as linear polykinetids; each kinetosome bearing a kinetodesmal fibril, and
sometimes accompanied by a partner kinetosome in some regions of the body, thus
resembling a cirrus. Phacodinium.
●●●●● Spirotrichea Bütschli, 1889
Conspicuous right and left oral and/or preoral ature; left serial oral polykinetids leading,
usually clockwise into the oral cavity, either around a broad anterior end or along anterior
and left margins of the body; DNA replication in the macronucleus accomplished by a
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Accepted Article
complicated migrating structure called replication band; extensive chromosomal
fragmentation.
●●●●●●Euplotia Jankowski, 1979
Adoral zone usually with numerous polykinetids (paramembranelles); body dorsoventrally
flattened; right preoral ature as paroral and/or endoral with diplo- or polystichomonad
structure; somatic ature usually in dikinetidal rows on dorsal side and forming cirri on ventral
side; somatic dikinetids with cilia at anterior basal bodies and retention of kinetodesmal
fibrils; stomatogenesis generally apokinetal, sometimes hypoapokinetal or parakinetal; turnover or replacement of only ventral somatic infraature; typically no resorption of all
kinetosomes in cysts.
●●●●●●●Euplotida Small and Lynn, 1985
Hypoapokinetal stomatogenesis in subsurface tube.
●●●●●●●●Aspidiscidae Ehrenberg, 1830 (Aspidisca)
●●●●●●●●Certesiidae Borror & Hill, 1995 (Certesia)
●●●●●●●●Euplotidae Ehrenberg, 1838 (Euplotes) (P)
●●●●●●●●Gastrocirrhidae Fauré-Fremiet, 1961 (Gastrocirrhus)
●●●●●●●●Uronychidae Jankowski, 1975 (Diophrys, Uronychia)
●●●●●●●Discocephalida Wicklow, 1982
Left and right marginal rows form intrakinetally; epiapokinetal stomatogenesis; left-most
frontal cirrus originates from anterior end of undulating membrane-anlage; many
frontoventral-transverse cirral anlagen; dorsal kinety anlagen formed in secondary mode;
caudal cirri originate from rightmost dorsal kineties anlagen by multi-segmentation mode;
development of frontoventral-transverse cirral anlagen of primary type; migrating cirri are not
formed, which are always derived from the right-most cirral anlage in all traditional
hypotrichs; anlage of undulating membranes splits transversely to form endoral and paroral
membranes.
●●●●●●●●Discocephalidae Jankowski, 1979 (Discocephalus, Prodiscocephalus,
Paradiscocephalus)
●●●●●●●●Pseudoamphisiellidae Song et al., 1997 (Leptoamphisiella, Pseudoamphisiella)
●●●●●●Perilemmaphora Berger, 2008
Perilemma present. Possibly, comprises also Diophrys and the discocephalids.
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●●●●●●●Hypotrichia Stein, 1859
Accepted Article
Adoral zone usually with numerous polykinetids (paramembranelles) along anterior and left
margins of dorsoventrally flattened body, rarely around broad apical end; right preoral ature
as paroral and/or endoral, paroral diplo- or polystichomonad, endoral mono-, rarely
diplostichomonad; somatic ature usually in dikinetidal rows on dorsal side and forming cirri
on ventral side, rarely with jumping bristles instead of kineties and cirri; somatic dikinetids
with cilia at anterior basal bodies and loss of kinetodesmal fibril; stomatogenesis
epiapokinetal or parakinetal; complete turn-over or replacement of ventral and dorsal
somatic ature; kinetosome-resorbing cysts.
●●●●●●●●Stichotrichida Fauré-Fremiet, 1961 (P)
Ventral cirri as one or more longitudinal and linear (not zig-zag as in Urostylida) files or as
frontoventral cirri, typically conspicuous, arranged in specific, localized frontal and ventral
groups (i.e., sporadotrichs); dorsal ature typically regularly distributed in longitudinal files;
stomatogenesis parakinetal or apokinetal, if apokinetal, may occur with five or six anlagen
streaks in two groups for differentiation of ventral somatic ature (i.e., sporadotrichs). Note
that this taxon is artificial. Many of the families listed here alphabetically are not
monophyletic and have limited support from molecular phylogenetics of small subunit rRNA.
●●●●●●●●●Amphisiellidae Jankowski, 1979 (Amphisiella, Bistichella)
●●●●●●●●●Atractosidae Bourland, 2015 (Atractos)
●●●●●●●●●Epiclintidae Wicklow and Borror, 1990 (Epiclintes)
●●●●●●●●●Gonostomatidae Small and Lynn, 1985 (Cotterillia, Gonostomum)
●●●●●●●●●Halteriidae Claparède and Lachmann, 1858 (Halteria, Meseres)
●●●●●●●●●Holostichidae Fauré-Fremiet, 1961 (Holosticha, Uncinata)
●●●●●●●●●Kahliellidae Tuffrau, 1979 (Deviata, Kahliella)
●●●●●●●●● Keronidae Dujardin, 1840 (Kerona)
●●●●●●●●●Oxytrichidae Ehrenberg, 1830 (P) (Cyrtohymena, Gastrostyla, Oxytricha,
Stylonychia)
●●●●●●●●●Parabirojimidae Dai and Xu, 2011 (Parabirojimia, Tunicothrix)
●●●●●●●●●Plagiotomidae Bütschli, 1887 (Plagiotoma)
●●●●●●●●●Psammomitridae Jankowski, 1979 (Psammomitra)
●●●●●●●●●Pseudoamphisiellidae Song et al., 1996 (Pseudoamphisiella)
●●●●●●●●●Psilotrichidae Bütschli, 1889 (Psilotricha, Urospinula)
●●●●●●●●●Schmidingerotrichidae Foissner, 2012 (Schmidingerothrix)
●●●●●●●●●Spirofilidae von Gelei, 1929 (Spirofilopsis, Strongylidium)
●●●●●●●●●Trachelostylidae Small and Lynn, 1985 (Trachelostyla)
This article is protected by copyright. All rights reserved.
●●●●●●●●●Uroleptidae Foissner and Stoeck, 2008 (Paruroleptus, Uroleptus)
Accepted Article
●●●●●●●●Urostylida Jankowski, 1979 (P)
Somatic ventral ature as frontoventral cirri in zig-zag files, running almost the full length of
ventral surface between right and left files of marginal cirri and ranging from a “single” file of
zig-zag or offset cirri to multiple and short files of cirri whose anterior and sometimes
posterior ends are offset (= developed zig-zag) (e.g., Eschaneustyla); transverse cirri may
be present; caudal cirri may be present; during division morphogenesis, zig-zag cirri
differentiating from anlagen of many short oblique kinetofragments.
●●●●●●●●●Bergeriellidae Liu et al., 2010 (Bergeriella, Neourostylopsis)
●●●●●●●●●Hemicycliostylidae Lyu et al., 2018 (Hemicycliostyla, Australothrix)
●●●●●●●●●Pseudokeronopsidae Borror & Wicklow, 1983 (Apoholosticha,
Pseudokeronopsis)
●●●●●●●●●Pseudourostylidae Jankowski, 1979 (Pseudourostyla)
●●●●●●●●●Urostylidae Bütschli, 1889 (Bakuella, Diaxonella, Urostyla)
●●●●●●●Oligotrichia Bütschli, 1887
Adoral zone around broad apical cell end, usually composed of large collar and small buccal
membranelles, C-shaped, circular, or with secondary ventral gap; endoral
monostichomonad; naked or with lorica; somatic ature in one to many rows arranged around
body; hypoapokinetal stomatogenesis; enantiotropic cell division.
●●●●●●●●Oligotrichida Bütschli, 1887
Adoral zone C-shaped, polykinetids become smaller towards cytostome; naked; rarely with
contractile tail that might be lost secondarily; usually two somatic kineties that might be
fragmented; somatic dikinetids with a cilium only at the anterior or left basal body; needleshaped extrusomes (trichites); usually with polysaccharidic cortical platelets; hypoapokinetal
stomatogenesis in a subsurface tube.
●●●●●●●●●Cyrtostrombidiidae Agatha, 2004 (Cyrtostrombidium)
●●●●●●●●●Pelagostrombidiidae Agatha, 2004 (Pelagostrombidium)
●●●●●●●●●Strombidiidae Fauré-Fremiet, 1970 (Strombidium) (P)
●●●●●●●●●Tontoniidae Agatha, 2004 (Laboea, Tontonia)
●●●●●●●●Choreotrichida Small & Lynn, 1985
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Accepted Article
Adoral zone circular, rarely with secondary ventral gap; collar polykinetids extend across
peristomial rim, proximalmost ones elongated, extending into buccal cavity; naked or with
lorica; structure of somatic kinetids highly diverse even within single specimens
(monokinetids, diated dikinetids, dikinetids with single um at anterior or posterior basal
body); somatic ature in one to many longitudinal or curved rows arranged around entire
body; hypoapokinetal stomatogenesis in a subsurface pouch; enantiotropic cell division less
pronounced (oral primordium parallel to lateral cell surface).
Incertae sedis Choreotrichida: Lynnella Liu et al., 2011 [Lynnellidae Liu et al., 2011;
Lynnellida Liu et al., 2015] (M)
Sistergroup relationship of this monotypic genus and order changes depending on the
algorithms used in molecular approaches. Morphological and ontogenetic data suggest an
affiliation with the aloricate choreotrichids: proximalmost collar membranelles elongated,
extending into buccal cavity; two longitudinal somatic kineties both of which with distinctly
derived kinetid structures: one is monokinetidal, the other composed of dikinetids with cilia
only at the posterior basal bodies; endoral membrane extends across peristomial field in
middle dividers; stomatogenesis in subsurface pouch; oral primordium parallel to ventral cell
surface; two macronuclear nodules. Adoral zone with (probably secondary) ventral gap.
Lynnella semiglobulosa.
●●●●●●●●●Strobilidiina Jankowski, 1980 (P)
Adoral zone circular, rarely with secondary ventral gap; naked.
●●●●●●●●●●Leegaardiellidae Lynn and Montagnes, 1988 (Leegaardiella)
●●●●●●●●●●Lohmanniellidae Montagnes and Lynn, 1991 (Lohmanniella)
●●●●●●●●●●Strobilidiidae Kahl in Doflein and Reichenow, 1929 (Strobilidium)
●●●●●●●●●●Strombidinopsidae Small and Lynn, 1985 (Strombidinopsis) (P)
●●●●●●●●●Tintinnina Kofoid & Campbell, 1929
Adoral zone circular; with hyaline, entirely or partially agglutinated lorica; somatic ature
arranged in specialized fields and rows; frequently with extrusive capsules; with contractile
peduncle. Molecular phylogenies distinctly contribute in far-reaching revision, but taxon
coverage and settlement of tree topology are currently still insufficient.
Incertae sedis Tintinnina: Helicostomella, Tintinnopsis (P), plus several further genera.
●●●●●●●●●●Ascampbelliellidae Corliss, 1960 (Ascampbelliella)
●●●●●●●●●●Cyttarocylididae Kofoid and Campbell, 1929 (Cyttarocylis)
(Probably, synonymous with Petalotrichidae)
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●●●●●●●●●●Dictyocystidae Haeckel, 1873 (Dictyocysta)
●●●●●●●●●●Epiplocylididae Kofoid and Campbell, 1939 (Epiplocylis)
Accepted Article
●●●●●●●●●●Eutintinnidae Bachy et al., 2012 (Dartintinnus, Eutintinnus)
●●●●●●●●●●Favellidae Kofoid and Campbell, 1929 (Favella)
●●●●●●●●●●Nolaclusiliidae Sniezek et al., 1991 (Nolaclusilis)
●●●●●●●●●●Petalotrichidae Kofoid and Campbell, 1929 (Petalotricha)
(Probably, synonymous with Cyttarocylididae)
●●●●●●●●●●Ptychocylididae Kofoid and Campbell, 1929 (Cymatocylis, Ptychocylis)
●●●●●●●●●●Rhabdonellidae Kofoid and Campbell, 1929 (Metacylis, Rhabdonella,
Schmidingerella
●●●●●●●●●●Stenosemellidae Campbell, 1954 (Stenosemella) (P)
●●●●●●●●●●Tintinnidae Claparède and Lachmann, 1858 (Amphorellopsis, Salpingacantha,
Salpingella, Tintinnus)
●●●●●●●●●●Tintinnidiidae Kofoid and Campbell, 1929 (Tintinnidium)
●●●●●●●●●●Undellidae Kofoid and Campbell, 1929 (Undella)
●●●●●●●●●●Xystonellidae Kofoid and Campbell, 1929 (Dadayiella, Parafavella, Xystonella)
●●●●●● Licnophoridae Bütschli, 1887
Body hour-glass shaped, both ends discoidal; posterior disc adhesive, with peripheral rings
of a; anterior disc with serial oral polykinetids around oral region; ectosymbionts, temporarily
attached to substrate or host by ated, mobile, posterior adhesive disc. Licnophora,
Prolicnophora.
●●●●●●Kiitrichidae, Nozawa, 1941
With weakly differentiated and non-grouped somatic ature, i.e., cirri on ventral side generally
uniform, no clearly defined marginal cirral rows, cirri mixed with dikinetids on dorsal side, i.e.,
no clearly differentiated dorsal kineties. Caryotricha, Kiitricha.
●●●●●Lamellicorticata Vd’ačný et al., 2010
Postary microtubular ribbons arranged in a single layer right of and between kineties; oral
apparatus composed of a dikinetidal paroral membrane and several multi-rowed adoral
membranelles; somatic dikinetids typically very narrowly spaced in anterior body portion;
stomatogenesis telokinetal, commencing in dorsal or dorsolateral somatic kineties, and with
migrating oral kinetofragments.
This article is protected by copyright. All rights reserved.
●●●●●●Armophorea Lynn, 2004 (R)
Accepted Article
Somatic dikinetids; energy-generating organelles as anaerobic mitochondria or
hydrogenosomes; contain cytoplasmic endosymbiotic methanogenic bacteria; extensive
chromosomal fragmentation; stomatogenesis typically pleurokinetal; in oxygen-depleted
habitats.
Incertae sedis Armophorea: Mylestomatidae Kahl in Doflein & Reichenow, 1929 (Mylestoma)
●●●●●●●Metopida (P) Jankowski, 1980. Free-living or endocommensal Armophorea with
five or fewer perizonal stripe kineties.
●●●●●●●●Metopidae Kahl, 1927 (P)
Anterior part of body uniquely twisted to the left; with series of five perizonal somatic
kineties. Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium,Tesnospira.
●●●●●●●●Apometopidae Foissner, 2016
Obpyriform to clavate Metopida with perizonal ciliary stripe composed of four kineties.
Cirranter, Urostomides.
●●●●●●●●Tropidoatractidae Rotterová et al., 2018
Preoral dome flattened, without torsion. Cortex,with interkinetal ridges. Sparse widelyspaced somatic ciliature. Short peristomium with deep, cup-like buccal cavity, adoral zone
reduced, more or less straight. Perizonal stripe with five rows arranged in false kineties.
Palmarella, Tropidoatractus
●●●●●●●Clevelandellida de Puytorac & Grain, 1976
Body typically flattened; somatic dikinetids with non-microtubular retrodesmal and
cathetodesmal fibrils; oral polykinetids with a fourth row of kinetosomes directly opposite
those of the third (heteromembranelles); paroral as diplostichomonad; macronucleus
anchored in a karyophore in many species; conjugation often synchronized with reproductive
life cycle of the host; endocommensals in digestive tracts of invertebrates and some
vertebrates.
●●●●●●●●Clevelandellidae Kidder, 1938 (Clevelandella)
●●●●●●●●Inferostomatidae Ky, 1971 (Inferostoma)
●●●●●●●●Neonyctotheridae Affa’a, 1987 (Neonyctotherus)
●●●●●●●●Nyctotheridae Amaro, 1972 (P) (Nyctotherus)
●●●●●●●●Sicuophoridae Amaro, 1972 (Sicuophora)
●●●●●●●Caenomorphidae Poche, 1913
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Accepted Article
Body globular or conical, rigid, twisted to the left; somatic cilia as small kineties or cirrus-like
tufts; several oral polykinetids in small oral cavity in posterior cell half; paroral possibly
absent; free-swimming. Complex perizonal ciliary stripe comprising more than five kineties.
Small subunit ribosomal DNA analysis suggests a sister group relationship with the
Litostomatea. Caenomorpha, Ludio, Sulfonecta.
●●●●●●●Odontostomatida Sawaya, 1940
Discoid, laterally compressed, wedge- or helmet-shaped, typically nearly as wide as long,
with armour-like cuirass and often short posterior spines; somatic cilia arising from cortical
pits; oral polykinetids inconspicuous, typically less than ten in number.
●●●●●●●●Discomorphellidae Corliss, 1960 (Discomorphella)
●●●●●●●●Epalxellidae Corliss, 1960 (Epalxella, Saprodinium)
Note that Epalxella has been genetically characterized with Plagiopylea but Saprodinium
with Armophorea.
●●●●●● Litostomatea Small & Lynn, 1981
Somatic monokinetids with two transverse ribbons, a slightly convergent postary ribbon, and
a laterally directed kinetodesmal fibril that does not overlap those of adjacent kineties; one
tangential transverse extending anteriorly into the somatic ridge to the left of the kinetid, one
radial transverse ribbon extending transversely into the adjacent somatic ridge; one to
several dorsal somatic kineties differentiated as brosse or brush kinetids with specialized
dikinetids bearing clavate a; lamina corticalis or ecto-endoplasmic fibrillar layer often present
and well-developed; oral ature as simple kinetids from which nematodesmata arise,
supporting the cytopharynx, but nematodesmata may also arise from “oralized” somatic
kinetids adjacent to the oral region; stomatogenesis telokinetal.
●●●●●●●Rhynchostomatia Jankowski 1980
Elongate to flask-shaped body with dorsal proboscis of varying relative length; oral region
circular or elliptical, possibly with permanent cytostome, distant from extreme anterior end of
body, i.e., at base of the proboscis, but with right branch of circumoral kinety accompanied by
at least one perioral kinety, extending along one border of the ventral surface of the
proboscis, and with left branch of circumoral kinety accompanied by many oblique preoral
kineties along the other border; toxicysts in the ventral band of the proboscis or distributed
around the cytostome.
●●●●●●●●Dileptida Jankowski, 1978
With a hybrid circumoral kinety; a staggered dorsal brush; and a stripe without cilia on the
left side of the proboscis.
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●●●●●●●●●Dileptidae Jankowski, 1980 (Apodileptus, Dileptus, Pseudomonilicaryon)
Accepted Article
●●●●●●●●●Dimacrocaryonidae Jankowski, 1978 (Dimacrocaryon, Monomacrocaryon,
Rimaleptus)
●●●●●●●●Tracheliidae Ehrenberg, 1838
Body broad ovoid; proboscis immobile or only slightly mobile, with dorsal side distinctly
shorter than ventral one; distinct groove (fossa) on right side containing and surrounded by
condensed somatic ciliature; dorsal brush three- to four-rowed and isoarchistichad;
circumoral kinety dikinetidal throughout; internal oral basket clavate. Trachelius.
●●●●●●●Haptoria Corliss, 1974 (P)
Oral region typically circular or elliptical, with circumoral dikinetids whose microtubules
support the cytostome-cytopharynx; where circumoral dikinetids are absent, oralized somatic
monokinetids bear nematodesmata forming the rhabdos; anterior condensation of dikinetidal
cilia forming a dorsal brush, partially reduced; somatic kinetids otherwise monokinetidal after
loss of anterior basal body; toxicysts; predatory life style. Questionable support for its
monophyly as several members group with Trichostomatia, and its genera Helicoprorodon
and/or Trachelotractus branch basally in the class Litostomatea.
Incertae sedis Haptoria: Chaenea.
●●●●●●●●Lacrymariidae de Fromentel, 1876
Anterior region of the body (=head), bulb-like, covered by short oblique kineties with densely
packed kinetids that abut the circumoral dikinetids. Lacrymaria.
●●●●●●●●Haptorida Corliss, 1974
Oral region typically circular or elliptical, surrounded by circumoral dikinetids whose
microtubules extend to support the cytostome-cytopharynx; where circumoral dikinetids are
absent, oralized somatic monokinetids bear nematodesmata forming the rhabdos.
●●●●●●●●●Enchelyodonidae Foissner et al., 2002 (Enchelyodon, Fuscheria)
●●●●●●●●●Homalozoonidae Jankowski, 1980 (Homalozoon)
●●●●●●●●●Pleuroplitidae Foissner, 1996 (Pleuroplites)
●●●●●●●●Didiniidae Poche, 1913
Somatic cilia as series of apparently short kinetofragments in one or more girdles around
body, but in non-ciliated regions, non-ciliated kinetosomes are arranged in meridional
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Accepted Article
kineties; brosse typically a field of clavate cilia or “sensory bristles” usually clearly detectable
in 3-5 kineties. Didinium, Monodinium.
●●●●●●●●Pleurostomatida Schewiakoff, 1896
Body leaf-like or laterally compressed; free-swimming, typically gliding on the substrate;
somatic ation on both body sides, typically more dense on the right side; brosse dorsal,
integrated in one or two dorsolateral kineties; oral region ventral and elongated, with oral
kinetids as left and right components extending along the ventral edge of the laterally
flattened body, bordering a slit-like cytostome, surrounded by toxicysts; micronucleus lying
between two macronuclear nodules; voracious cytotrophs.
●●●●●●●●●Amphileptidae Bütschli, 1889 (Amphileptus)
●●●●●●●●●Litonotidae Kent, 1882 (Litonotus)
●●●●●●●●●Kentrophyllidae Wu et al., 2015 (Kentrophyllum, Epiphyllum)
●●●●●●●●Spathidiida Foissner & Foissner, 1988
Somatic kineties curved anteriorly; three-rowed dorsal brush.
●●●●●●●●●Acropisthiidae Foissner & Foissner, 1988 (Acropisthium, Chaenea)
●●●●●●●●●Actinobolinidae Kahl, 1930 (Actinobolina)
●●●●●●●●●Apertospathulidae Foissner et al., 2005 (Apertospathula)
●●●●●●●●●Enchelyidae Ehrenberg, 1838 (Enchelys)
●●●●●●●●●Pseudoholophryidae Berger et al., 1984 (Pseudoholophrya)
●●●●●●●●●Spathidiidae Kahl in Doflein & Reichenow, 1929 (Spathidium)
●●●●●●●●●Trachelophyllidae Kent, 1882 (Trachelophyllum)
●●●●●●●Helicoprorodontidae Small & Lynn, 1985
Body, elongate, vermiform, contractile; somatic ation holotrichous; 2-5 brosse kineties;
toxicysts distributed along perioral ridge that makes from one to serveral turns around
anterior end; oral region apical; marine psammobiont. Helicoprorodon.
●●●●●●●Trichostomatia Bütschli, 1889
Oral region or oral cavity densely ated, sometimes organized as “polykinetids”; oralized
somatic monokinetids; narrowly spaced somatic dikinetids form a clavate field; toxicysts
absent; alveoli often filled with “skeletal” material; hydrogenosomes developed from
mitochondria; stomatogenesis telokinetal, cryptotelokinetal in entodiniomorphids; typically
anaerobic endosymbionts in vertebrates.
This article is protected by copyright. All rights reserved.
●●●●●●●●Vestibuliferida de Puytorac et al., 1974
Accepted Article
Cortex often with thick microfilamentous layer between ecto- and endoplasm; oral region a
depression or vestibulum, densely ated by extensions of somatic kineties whose cilia do not
appear organized as “polykinetids”; endocommensals in fish and herbivorous placental
mammals, except for marsupials.
●●●●●●●●●Balantidiidae Reichenow in Doflein and Reichenow, 1929 (Balantidium,
Neobalantidium) (P)
●●●●●●●●●Buetschliidae Poche, 1913 (Buetschlia)
●●●●●●●●●Paraisotrichidae da Cunha, 1917 (Paraisotrichia)
●●●●●●●●●Protocaviellidae Grain in Corliss, 1979 (Protocaviella)
●●●●●●●●●Protohalliidae da Cunha & Muniz, 1927 (Protohallia)
●●●●●●●●●Pycnotrichidae Poche, 1913 (Pycnothrix, perhaps Buxtonella)
●●●●●●●Isoendo (R)
Group identified by SSU rRNA phylogenies. With a node-based definition: the clade
stemming from the most recent common ancestor of the Isotrichidae (Iso),
Entodiniomorphida (endo), and Macropodiniida.
●●●●●●●●Isotrichidae Bütschli, 1889
Endoplasmic polysaccharide reserves; somatic mucocysts; oral cavity at or near posterior
pole, lined by extensions of somatic kineties, with parental vestibulum migrating anteriorly
during stomatogenesis to become the proter’s vestibulum; macronucleus may be anchored
by a karyophore; often endocommensals in ungulate ruminants. Dasytricha, Isotricha.
●●●●●●●●Entodiniomorphida Reichenow in Doflein & Reichenow, 1929
Pellicle firm and thickened, often drawn out into posterior spines; cortex with thick
microfilamentous layer between ecto- and endoplasm; somatic ature typically markedly
reduced, appearing only in bands, zones or tufts, often as polybrachykineties, and
functioning as syna; oral area as only a slight depression to a deep one, often with welldifferentiated “polykinetids”; often commensals in mammalian host.
●●●●●●●●●Blepharocorythina Wolska, 1971
Somatic ation markedly reduced, as tufts and bands; presumed remnant of concrement
vacuole complex present only as its overlying somatic kinetids.
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●●●●●●●●●●Blepharocorythidae Hsiung, 1929 (Blepharocorys)
●●●●●●●●●●Parentodiniidae Ito, Miyazaki & Imai, 2002 (Parentodinium)
Accepted Article
●●●●●●●●●●Pseudoentodiniidae Wolska, 1986 (Pseudoentodinium)
●●●●●●●●●Entodiniomorphina Reichenow in Doflein and Reichenow, 1929
Somatic ature markedly reduced, appearing in tufts, sometimes elongated as spiralled
bands, often arranged as polybrachykineties, and functioning as syna; pellicle firm and
thickened, often drawn out into spines; prominent skeletal plates in many species, composed
of polysaccharide reserves (e.g., amylopectin granules or plaques); oral cilia often
functioning as syna, of two parts, a pre-vestibular band in the peristomial region and a
vestibular part(s) sensu stricto.
●●●●●●●●●●Cycloposthiidae Poche, 1913 (Cycloposthium)
●●●●●●●●●●Gilchristidae Ito, Ishihara & Imai, 2014 (Gilchristia)
●●●●●●●●●●Ophryoscolecidae Stein, 1859 (Entodinium, Ophryoscolex, Polyplastron)
●●●●●●●●●●Polydiniellidae Corliss, 1960 (Polydiniella)
●●●●●●●●●●Rhinozetidae Van Hoven, Gilchrist & Hamilton-Attwell, 1988 (Rhinozeta)
●●●●●●●●●●Spirodiniidae Strelkow, 1939 (Spirodinium)
●●●●●●●●●●Telamodiniidae Latteur & Dufey, 1967 (Telamodinium)
●●●●●●●●●●Troglodytellidae Corliss, 1979 (Troglodytella)
●●●●●●●●Macropodiniida Lynn, 2008 (R)
Oral cavity as an anterior vestibulum lined by extensions of somatic kineties, supported by
nematodesmata arising from these kinetids; somatic mucocysts; stomatogenesis telokinetal
or cryptotelokinetal, possibly apokinetal; in terrestrial habitats as endocommensals in the
forestomach of macropodid and vombatid marsupials.
●●●●●●●●●●Amylovoracidae Cameron & O’Donoghue, 2002 (Amylovorax)
●●●●●●●●●●Macropodiniidae Dehority, 1996 (Macropodinium)
●●●●●●●●●●Polycostidae Cameron & O’Donoghue, 2003 (Polycosta)
●●●●CONTHREEP Lynn in Adl et al., 2012 [Ventrata Cavalier-Smith, 2004] (R)
Group identified by SSU rRNA phylogenies. With a node-based definition: the clade
stemming from the most recent common ancestor of the Colpodea (C), Oligohymenophorea
(O), Nassophorea (N), Phyllopharyngea (P), Prostomatea (P), and Plagiopylea (P), hence
CON-threeP. “Ventrata” suggests a ventral morphological synapomorphy for the group, but
this character does not exist.
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Incertae sedis CON-threeP: Askenasia Blochmann, 1895
Accepted Article
Groups near Plagiopylea in molecular phylogenies.
Incertae sedis CON-threeP: Cyclotrichiidae Jankowski, 1980
Groups near Plagiopylea in molecular phylogenies. Cyclotrichium.
Incertae sedis CON-threeP: Paraspathidium Noland, 1937
Groups within Plagiopylea in molecular phylogenies.
Incertae sedis CON-threeP: Pseudotrachelocercidae Song, 1990
Groups near Plagiopylea in molecular phylogenies. Pseudotrachelocerca.
Incertae sedis CON-threeP: Discotrichidae Jankowski, 1967 [Discotrichida Fan et al., 2014]
Conspicuous cortical papillae on both dorsal and ventral faces; mucocysts rod-shaped;
cytopharyngeal basket asymmetric. Discotricha, Lopezoterenia.
●●●●● Phyllopharyngea de Puytorac et al., 1974
The ciliated stage with somatic kineties mostly as monokinetids that each have a lateral
kinetodesmal fibril, a reduced or absent transverse microtubular ribbon that is usually
accompanied by a left-directed transverse fibre, and a somewhat convergent postary ribbon
extending posteriorly to accompany ribbons of more anterior monokinetids; oral region with
radially arranged microtubular ribbons, called phyllae.
●●●●●●Synhymeniida de Puytorac et al. in Deroux, 1978
Ribbon-like subkinetal nematodesmata arising from somatic monokinetids and extending
beneath kineties as nematodesmata; cyrtos conspicuous.
●●●●●●●Nassulopsidae Deroux in Corliss, 1979 (Nassulopsis)
●●●●●●●Orthodonellidae Jankowski, 1968 (Orthodonella, Zosterodasys)
●●●●●●●Scaphidiodontidae Deroux in Corliss, 1979 (Chilodontopsis, Scaphidiodon)
●●●●●●●Synhymeniidae Jankowski in Small & Lynn, 1985 (Synhymenia)
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●●●●●●Subkinetalia Gong et al., 2009
Accepted Article
Ribbon-like subkinetal nematodesmata arising from somatic monokinetids and extending,
either anteriorly in Cyrtophoria/Chonotrichia or posteriorly, beneath kineties as subkinetal
ribbons in Rhynchodia/Suctoria.
●●●●●●●Cyrtophoria Fauré-Fremiet in Corliss, 1956
Oral ature typically composed of one preoral kinety and two circumoral kineties; true
cytostome and cytopharynx surrounded by phyllae and rod-shaped nematodesmata;
macronucleus heteromerous.
●●●●●●●●Chlamydodontida Deroux, 1976 (P)
Body typically dorsoventrally flattened, broad; free-swimming, but may attach to substrate by
thigmotactic ventral somatic a; somatic kineties typically ventrally arranged in two roughly
equal fields, which may be separated midventrally (except in Family Kryoprorodontidae);
without non-ated adhesive region or flexible podite.
●●●●●●●●●Chilodonellidae Deroux, 1970 (Chilodonella)
●●●●●●●●●Chitonellidae Small & Lynn, 1985 (Chitonella)
●●●●●●●●●Chlamydodontidae Stein, 1859 (Chlamydodon)
●●●●●●●●●Gastronautidae Deroux, 1994 (Gastronauta)
●●●●●●●●●Kryoprorodontidae Alekperov and Mamajeva, 1992 (Gymnozoum)
●●●●●●●●●Lynchellidae Jankowski, 1968 (Chlamydonella, Lynchella)
●●●●●●●●Dysteriida Deroux, 1976
Body typically laterally compressed with dorsal surface rounded, in extreme; free-swimming,
but often temporarily attached; ventral cilia not thigmotactic, but ate attached to substrate by
non-ated adhesive region or by flexible podite (except Atelepithites); macronucleus
juxtaposed heteromerous.
●●●●●●●●●Dysteriidae Claparède & Lachmann, 1858 (Dysteria (P), Trochilia)
●●●●●●●●●Hartmannulidae Poche, 1913 (P) Hartmannula)
●●●●●●●●●Kyaroikeidae Sniezek & Coats, 1996 (Kyaroikeus)
●●●●●●●●●Plesiotrichopidae Deroux, 1976 (Plesiotrichopus)
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●●●●●●●●●Chonotrichia Wallengren, 1895
Accepted Article
Sedentary and sessile forms with somatic cilia only on walls of perioral funnel or coneshaped region, which may be flared or compressed; oral cilia absent or only as several
inverted kineties next to cytostome; cytopharyngeal apparatus with phyllae, but no
nematodesmata; macronucleus heteromerous; unequal cell division typical, producing “bud”
for dispersal; most species are ectosymbionts on crustacean appendages. Small subunit
rDNA phylogenies place this group as sister to Hartmannulidae.
●●●●●●●●●●Exogemmida Jankowski, 1972
Body typically long and cylindrical with a well-developed collar (except Family
Chilodochonidae); spines absent or poorly developed; usual attachment by undistinguished
peduncle (rather than a “true” stalk, except in Family Chilodochonidae); a few to several
tomites or buds produced by external budding; macronucleus heteromerous, with orthomere
directed apically towards funnel.
●●●●●●●●●●●Chilodochonidae Wallengren, 1895 (Chilodochona)
●●●●●●●●●●●Filichonidae Jankowski, 1973 (Filichona)
●●●●●●●●●●●Helichonidae Jankowski, 1972 (Heliochona)
●●●●●●●●●●●Lobochonidae Jankowski, 1967 (Lobochona)
●●●●●●●●●●●Phyllochonidae Jankowski, 1972 (Phyllochona)
●●●●●●●●●●●Spirochonidae Stein, 1854 (Spirochona)
●●●●●●●●●●Cryptogemmida Jankowski, 1975
Body often flattened, leaf-like, and angular; spines common and of several types; collar
reduced; stalk typically present; internal budding with up to eight tomites produced in a crypt
or marsupium; macronucleus heteromerous, with orthomere directed antapically away from
funnel.
●●●●●●●●●●●Actinichonidae Jankowski, 1973 (Actinichona)
●●●●●●●●●●●Echinichonidae Jankowski, 1973 (Echinichona)
●●●●●●●●●●●Inversochonidae Jankowski, 1973 (Inversochona)
●●●●●●●●●●●Isochonidae Jankowski, 1973 (Isochona)
●●●●●●●●●●●Isochonopsidae Batisse & Crumeyrolle, 1988 (Isochonopsis)
●●●●●●●●●●●Stylochonidae Mohr, 1948 (Stylochona)
●●●●●●●Rhynchodia Chatton & Lwoff, 1939
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Accepted Article
Oral apparatus a suctorial tube supported by radially arranged microtubular ribbons (=
phyllae) enclosing toxic (?) extrusomes (acmocysts or haptotrichocysts); cytotrophic or
endosymbiotic parasites of bivalve molluscs and other marine invertebrates.
●●●●●●●●Hypocomidae Bütschli, 1889
Body dorsoventrally flattened; somatic kineties essentially restricted to ventral surface with a
short anterio-lateral left kinety, a presumed homologue of the dorsal right kinetofragment of
cyrtophorines; posterior adhesive region bounded by somatic kineties in right-ventral pit or
fosette; oral ature absent or reduced to a few pericytostomial kinetosomes; macronucleus
homomerous. Hypocoma.
●●●●●●●●Rhynchodida Chatton & Lwoff, 1939
Free-swimming, but typically attached to the host by the oral region; somatic kineties
sometimes with non-ated kinetosomes, typically organized in a thigmotactic field, which may
extend to cover the entire body or which may be divided in two, leaving a large part of the
cell surface bare; no posterior adhesive region.
●●●●●●●●●Ancistrocomidae Chatton & Lwoff, 1939 (Ancistrocoma)
●●●●●●●●●Sphenophryidae Chatton & Lwoff, 1921 (Sphenophrya)
●●●●●●●Suctoria Claparède & Lachmann, 1858
Mature sessile trophonts, usually non-ated, with one to many tentacles that ingest prey;
extrusomes at tentacle tips as haptocysts; tentacles supported by an outer ring of
microtubules and an inner set of microtubular ribbons (= phyllae); unequal cell division
typical, with ated, migratory dispersal “larvae” or swarmers usually bearing neither tentacles
nor stalk.
●●●●●●●●Exogenida Collin, 1912
Often stalked and loricate; tentacles borne on actinophores in some species, and others with
prehensile as well as suctorial tentacles; exogenous budding, most often monogemmic, but
polygemmic in some species, or by binary fission with no appreciable invagination of
parental cortex; migratory larval form typically large or long, the former with complex ventral
ature, derived from the parental kinetosomal field, but some of the longer larvae practically
devoid of a, vermiform, and incapable of swimming; some endocommensals.
●●●●●●●●●Allantosomatidae Jankowski, 1967 (Allantosoma)
●●●●●●●●●Dentacinetidae Batisse, 1992 (Dentacineta)
●●●●●●●●●Dendrosomididae Jankowski, 1978 (Dendrosomides)
●●●●●●●●●Ephelotidae Kent, 1882 (Ephelota)
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●●●●●●●●●Lecanophryidae Jankowski, 1973 (Lecanophrya)
●●●●●●●●●Metacinetidae Bütschli, 1889 (Metacineta)
Accepted Article
●●●●●●●●●Manuelophryidae Dovgal, 2002 (Manuelophrya)
●●●●●●●●●Ophryodendridae Stein, 1867 (Ophryodendron)
●●●●●●●●●Paracinetidae Jankowski, 1978 (Paracineta)
●●●●●●●●●Phalacrocleptidae Kozloff, 1966 (Phalacrocleptes)
●●●●●●●●●Podophryidae Haeckel, 1866 (Podophrya)
●●●●●●●●●Praethecacinetidae Dovgal, 1996 (Praethecacineta)
●●●●●●●●●Rhabdophryidae Jankowski, 1970 (Rhabdophrya)
●●●●●●●●●Severonidae Jankowski, 1981 (Severonis)
●●●●●●●●●Spelaeophryidae Jankowski in Batisse, 1975 (Spelaeophrya)
●●●●●●●●●Tachyblastonidae Grell, 1950 (Tachyblaston)
●●●●●●●●●Thecacinetidae Matthes, 1956 (Thecacineta)
●●●●●●●●Endogenida Collin, 1912
Often loricate; tentacles frequently in fascicles; endogenous budding occurring in a pouch,
monogemmic or polygemmic, with swarmers produced completely internally and becoming
free-swimming in brood pouch before emergence through birth pore; swarmer ated;
ectosymbiotic forms common, some endocommensals.
●●●●●●●●●Acinetidae Stein, 1859 (Acineta)
●●●●●●●●●Acinetopsidae Jankowski, 1978 (Acinetopsis)
●●●●●●●●●Choanophryidae Dovgal, 2002 (Choanophrya)
●●●●●●●●●Corynophryidae Jankowski, 1981 (Corynophrya)
●●●●●●●●●Dactylostomatidae Jankowski, 1978 (Dactylostoma)
●●●●●●●●●Dendrosomatidae Fraipont, 1878 (Dendrosoma)
●●●●●●●●●Endosphaeridae Jankowski in Corliss, 1979 (Endosphaera)
●●●●●●●●●Erastophryidae Jankowski, 1978 (Erastophrya)
●●●●●●●●●Pseudogemmidae Jankowski, 1978 (Pseudogemma)
●●●●●●●●●Rhynchetidae Jankowski, 1978 (Rhyncheta)
●●●●●●●●●Solenophryidae Jankowski, 1981 (Solenophrya)
●●●●●●●●●Tokophryidae Jankowski in Small & Lynn, 1985 (Tokophrya)
●●●●●●●●●Trichophryidae Fraipont, 1878 (Trichophrya)
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●●●●●●●●Evaginogenida Jankowski in Corliss, 1979
Accepted Article
Trophonts sessile; with or without stalk, occasionally in lorica; tentacles either scattered
singly or in fascicles at the ends of sometimes massive arms or trunks; kinetosomes of larval
kineties first develop on “parental” surface of a brood pouch, but cytokinesis of a single
swarmer completed exogenously after full emergence of the “everted” bud (i.e., evaginative
budding); often symphorionts, with species of one endosymbiotic genus showing a strikingly
aberrant life cycle.
●●●●●●●●●Cometodendridae Jankowski, 1978 (Cometodendron)
●●●●●●●●●Cyathodiniidae da Cuhna, 1914 (Cyathodinium)
●●●●●●●●●Dendrocometidae Haeckel, 1866 (Dendrocometes)
●●●●●●●●●Discophryidae Collin, 1912 (Discophrya)
●●●●●●●●●Enchelyomorphidae Augustin & Foissner, 1992 (Enchelyomorpha)
●●●●●●●●●Heliophryidae Corliss, 1979 (Heliophrya)
●●●●●●●●●Periacinetidae Jankowski, 1978 (Periacineta)
●●●●●●●●●Prodiscophryidae Jankowski, 1978 (Prodiscophrya)
●●●●●●●●●Rhynchophryidae Jankowski, 1978 (Rhynchophrya)
●●●●●●●●●Stylocometidae Jankowski, 1978 (Stylocometes)
●●●●●●●●●Trypanococcidae Dovgal, 2002 (Trypanococcus)
●●●●● Colpodea Small & Lynn, 1981
Ciliated somatic dikinetids with one transverse ribbon and at least one postary microtubule
associated with the anterior kinetosome and one transverse ribbon, one postary ribbon, and
one kinetodesmal fibril associated with the posterior kinetosome; posteriorly directed
transverse ribbons overlap one another, forming the so-called transversodesmata. Oral
structures as a dikinetidal row in the right field and brick- or ribbon-shaped polykinetids in the
left field; micronucleus may be in perinuclear space of macronucleus; division in freely motile
condition or in reproductive cysts; stomatogenesis pleurotelokinetal or merotelokinetal,
parental ature maintained or reorganized; mucocysts; mostly terrestrial.
●●●●●●Bursariomorphida Fernández-Galiano, 1978
Oral structures in oral cavity, often very deep or trough-like; right oral field composed of one
or many dikinetidal rows; left oral field composed of few to many polykinetids forming a
conspicuous ribbon resembling an adoral zone of membranelles.
●●●●●●●Bryometopidae Jankowski, 1980 (Bryometopus (P), Thylakidium)
●●●●●●●Bursaridiidae Foissner, 1993 (Bursaridium, Paracondylostoma)
●●●●●●●Bursariidae Bory de St. Vincent, 1826 (Bursaria)
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●●●●●●Colpodida de Puytorac et al., 1974
Accepted Article
Oral structures in oral cavity; right oral field as single row of monokinetids, dikinetids, or a
complex organelle including roof kineties and/or monokinetidal ary fields; left oral field
composed of one to several brick-shaped polykinetids and/or a comparatively large
polykinetid comprising few to many monokinetidal rows; silverline pattern colpodid or
platyophryid; usually divide in reproductive cysts; stomatogenesis merotelokinetal or
pleuromerotelokinetal, parental ature reorganized; mostly terrestrial.
Incertae sedis Colpodida:
Bardeliellidae Foissner, 1984 (Bardeliella)
Hausmanniellidae Foissner, 1987 (Avestina, Hausmanniella)
Ilsiellidae Bourland et al., 2011 (Ilsiella)
Pseudochlamydonellidae Buitkamp et al., 1989 (Hackenbergia, Pseudochlamydonella)
Marynidae Poche, 1913 (Maryna)
●●●●●●●Bryophryina de Puytorac et al., 1979
Oral cavity almost flat; right oral field a single row of dikinetids or a complex organelle
including roof kineties; left field as described for order; silverline pattern platyophryid or
colpodid; division in reproductive cysts; terrestrial.
●●●●●●●●Bryophryidae de Puytorac et al., 1979 (Bryophrya)
●●●●●●●●Sandmanniellidae Foissner & Stoeck, 2009 (Sandmanniella)
●●●●●●●Colpodina Foissner et al., 2011
Oral cavity small to very large, in the latter case densely ated by roof kineties having supraepiplasmic microtubules; right oral field composed of a dikinetidal row and a crescentic
accumulation of slightly disordered monokinetids; left oral field as a crescentic polykinetid
composed of many monokinetidal rows; postorally, a more or less pronounced (diagonal)
groove extending obliquely onto left body side; extrusomes globular or oblong; silverline
pattern colpodid; division usually in reproductive cysts; stomatogenesis
pleuromerotelokinetal; terrestrial and limnetic.
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●●●●●●●●Colpodidae Bory de St. Vincent, 1826 (Colpoda) (P).
●●●●●●●●Grandoriidae Corliss, 1960 (Grandoria)
Accepted Article
●●●●●●●●Tillinidae Foissner et al., 2011 (Tillina)
●●●●●●● Grossglockneriidae Foissner, 1980 [Grossglockneriina Foissner, 1980]
Oral apparatus on cell surface; with unique feeding tube used for puncturing cell walls of
fungi and yeasts; right oral field as single monokinetidal row; left oral field composed of one
to several brick-shaped polykinetids; silverline pattern colpodid; division in reproductive
cysts; stomatogenesis merotelokinetal; terrestrial. Grossglockneria, Pseudoplatyophrya.
●●●●●●Cyrtolophosidida Foissner, 1978
Oral cavity shallow; right oral field as a single dikinetidal row, forms an elliptical figure with
left oral field comprising up to ten brick-shaped polykinetids; occasionally micronucleus in
perinuclear space of macronucleus; silverline pattern colpodid or kreyellid; division in freely
motile condition; stomatogenesis pleurotelokinetal, parental oral ature partially reorganized;
limnetic and terrestrial, some marine.
●●●●●●●Cyrtolophosididae Stokes, 1888 (Cyrtolophosis)
●●●●●●●Kreyellidae Foissner, 1979 (Kreyella)
●●●●●●Platyophryida de Puytorac et al., 1979
Oral structures on cell surface; right oral field as a single dikinetidal row, usually forms an
elliptical figure with the left oral field composed of few to many brick-shaped polykinetids;
occasionally micronucleus in perinuclear space of macronucleus; some with postoral
pseudomembrane consisting of short kineties with two dikinetids each along left slope of oral
aperture; silverline pattern platyophryid, rarely colpodid or kreyellid; division in reproductive
cysts or in freely motile condition; stomatogenesis pleurotelokinetal, parental oral ature not
reorganized; with or without the ability to form aerial sorocarps; mostly terrestrial or
semiterrestrial, few limnetic.
●●●●●●●Ottowphryidae Foissner et al., 2011 (Ottowphrya, Platyophryides)
●●●●●●●Platyophryidae de Puytorac et al., 1979 (P) (Platyophrya)
●●●●●●●Sagittariidae Grandori & Grandori, 1935 (Sagittaria)
●●●●●●●Sorogenidae Bradbury & Olive, 1980 (Sorogena)
●●●●●●●Woodruffiidae Gelei, 1954 (Etoschophrya, Rostrophrya, Woodruffia)
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●●●●● Nassophorea Small & Lynn, 1981 (P)
Accepted Article
Somatic cilia as monokinetids and dikinetids; monokinetid with an anterior, tangential
transverse ribbon, a divergent postary ribbon, and anteriorly directed kinetodesmal fibril;
somatic alveoli well-developed with paired alveolocysts sometimes present; oral
nematodesmata well-developed as cyrtos in several groups.
●●●●●●Colpodidiidae Foissner, 1995
Oral region in middle third of cell, with a paroral and three oral polykinetids that can be
reduced in size to only one or two kinetosomes; cytostome-cytopharynx supported by a
delicate cyrtos (?), which extends anteriorly, then dorsally and posteriorly. Colpodidium.
●●●●●●Nassulida Jankowski, 1967
Alveolocysts present; somatic ciliature with distinct preoral suture; somatic basal bodies with
a proximal and distal cartwheel; somatic extrusomes rod-like, when present; synhymenium
or hypostomial frange begins in postoral region, always to the right of the stomatogenic
kinety, and extending to lateral left onto dorsal surface, but sometimes reduced to three or
four polykinetids restricted to a shallow oral cavity; cyrtos typically large, with complete
palisade of nematodesmata.
●●●●●●●Furgasoniidae Corliss, 1979 (Furgasonia, Wolfkosia)
●●●●●●●Nassulidae de Fromentel, 1874 (Nassula, Obertrumia)
●●●●●●Microthoracida Jankowski, 1967
Body frequently broadly ellipsoidal with right side more rounded, occasionally crescentic,
and often laterally flattened; alveolocysts present; pellicle, firm and rigid, with thickened
epiplasm in some forms; typically with a few somatic kineties, separated by wide interkinetal
spaces, composed of monokinetids and/or dikinetids; somatic extrusomes as fibrous
trichocysts with anchor-like tip (fibrocysts); usually three left oral polykinetids; right paroral
dikinetid, variably developed, but its vestige always appears during stomatogenesis; cyrtos
small, with complete palisade of nematodesmata.
●●●●●●●Microthoracidae Wrzesniowski, 1870 (Drepanomonas, Microthorax)
●●●●●●●Leptopharyngidae Kahl, 1926 (Pseudomicrothorax, Leptopharynx)
●●●●● Prostomatea Schewiakoff, 1896 (P)
Oral dikinetids radial to tangential to perimeter of oral area with postary microtubular ribbons
extending laterally from each dikinetid, overlapping one another, and, in some species,
forming a circular microtubular band that supports the wall of a shallow precytostomial
cavity; associated oral ciliature as two or more assemblages of dikinetids, often called a
“brush”.
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●●●●●● Apsiktratidae Foissner et al., 1994 [Prostomatida Schewiakoff, 1896]
Accepted Article
Somatic ciliature “radially symmetrical”; paratenes typically conspicuous; oral region apical,
surrounded by circumoral dikinetids; brosse absent; toxicysts absent. Apsiktrata.
●●●●●●Prorodontida Corliss, 1974
Alveoli well-developed, including calcium carbonate concretions as skeletal plates in the
Family Colepidae; somatic ation may be reduced in posterior half of cell, which typically
bears one to many caudal a; somatic extrusomes as mucocysts; oral extrusomes as
toxicysts, may be in oral palps or extra-oral, near kinetids of “brosse”; oral region apical to
subapical, surrounded by circumoral dikinetids; brosse typically of three or more dikinetidal
rows bearing clavate a, varying from parallel to perpendicular to body axis, and developing
on parental ventral surface; cytostome sometimes in shallow atrium, which is lined by oral
ridges supported by two unequal rows of microtubules; most species cytotrophic or
scavengers on detritus.
●●●●●●●Balanionidae Small & Lynn, 1985 (Balanion)
●●●●●●●Cryptocaryonidae Wright & Colorni, 2002 (Cryptocaryon)
●●●●●●●Colepidae Ehrenberg, 1838 (Coleps, Plagiopogon)
●●●●●●●Holophryidae Perty, 1852 (Holophrya)
●●●●●●●Lagynidae Sola et al., 1990 (Lagynus)
●●●●●●●Metacystidae Kahl, 1926 (Metacystis, Vasicola)
●●●●●●●Placidae Small & Lynn, 1985 (Placus)
●●●●●●●Plagiocampidae Kahl, 1926 (Plagiocampa)
●●●●●●●Prorodontidae Kent, 1881 (Prorodon)
●●●●●●●Urotrichidae Small & Lynn, 1985 (Urotricha)
●●●●● Plagiopylea Small & Lynn, 1985 (R)
Alveoli well-developed, often filled with dense material; somatic monokinetid with divergent
postary ribbon, well-developed anteriorly-directed kinetodesmal fibril, and a transverse
ribbon arising from dense material near triplets 2 and 3, but if Epalxella is correctly placed
here, they typically have dikinetids; somatic extrusomes as mucocysts; cytostome partially
encircled by one or two files of dikinetids (?), but if Epalxella is correctly placed here, oral
ciliature can include polykinetids; stomatogenesis holotelokinetal, but may be apokinetal in
Epalxella (?); mitochondria may be replaced by hydrogenosomes, which in many species
are associated with endosymbiotic methanogens.
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●●●●●●Plagiopylida Small & Lynn, 1985
Accepted Article
Typically with sandwich-like arrangement of the hydrogenosome-methanogen assemblages.
●●●●●●●Epalxellidae Corliss, 1960
Morphology suggests an affiliation with the Odontostomatida, while SSU rRNA phylogenies
indicate a relationship of Epalxella with Plagiopylea. Saprodinium groups with
Discomorphella (Odontostomatida) in molecular genealogies. Epalxella.
●●●●●●●Plagiopylidae Schewiakoff, 1896 (Plagiopyla)
●●●●●●●Sonderiidae Small & Lynn, 1985 (Sonderia)
●●●●●●●Trimyemidae Kahl, 1933 (Trimyema)
●●●●● Oligohymenophorea de Puytorac et al., 1974
Oral apparatus with a distinct right paroral kinety and typically three left oral polykinetids,
residing in a ventral oral cavity or deeper infundibulum (maybe secondarily lost (?) in
Astomatia and some astomatous Hymenostomatia); somatic monokinetids with anteriorlydirected overlapping kinetodesmal fibrils, divergent postary ribbons, and radial transverse
ribbons (except in Peniculia).
●●●●●●Apostomatia Chatton & Lwoff, 1928
Cells with a polymorphic life cycle; usually as epibionts of marine Crustacea; in some forms,
novel cortical structures including a “rosette” organelle and the x, y, and z kineties.
●●●●●●●Apostomatida Chatton & Lwoff, 1928
Somatic ature with x, y, and z kineties that can be associated with an a kinety or a, b, and c
kineties; oral apparatus may have rosette; tomites formed by multiple fission, either by
palintomy in a cyst or by catenulation; trophonts, sanguicolous or exuviotrophic.
●●●●●●●●Colliniidae Cépède, 1910 (Collinia, Metacollinia)
●●●●●●●●Cyrtocaryidae Corliss, 1979 (Cyrtocaryum)
●●●●●●●●Foettingeriidae Chatton, 1911 (Foettingeria)
●●●●●●●●Pseudocolliniidae Chantangsi et al., 2013 (Fusiforma, Pseudocollinia)
●●●●●●●Astomatophorida Jankowski, 1966
Trophont vermiform; free-swimming, but attached to host tissue; kineties distinctly spiralled
and somatic ature markedly thigmotactic; no cytostome (in stages of life cycles known to
date), but with remnants of oral ciliature; fission of tomont-trophont by sequential formation
of tomites (catenulation) or by multiple transverse fission with tomites remaining connected.
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Accepted Article
●●●●●●●●Opalinopsidae Hartog, 1906 Opalinopsis.
●●●●●●●Pilisuctorida Jankowski, 1966
Body ovoid to elongate; free-swimming, but attached to host in the feeding state; with ventral
adhesive organelle; species of most genera permanently in so-called “neotenic” tomite
stage; somatic kineties of tomite arched, following rim of flattened ventral surface; mature
trophonts non-ciliated, immobile, characteristically attached to seta or cuticle of host;
migrating tomite, which is ciliated but lacks a cytostome; tomites produced by synchrony or
strobilation; feeding on tissue fluids of marine amphipods, isopods, decapods, and cirripeds.
●●●●●●●●Conidophryidae Kirby, 1941 Conidophrys.
●●●●●●Astomatia Schewiakoff, 1896
Without cytostome; symbionts typical in digestive tracts of annelids, especially oligochaetes;
cortical cytoskeleton in the anterior region may be conspicuously developed as attachment
structure(s). Small subunit rDNA phylogenies indicate that many families may not be
monophyletic.
●●●●●●●Anoplophryidae Cépède, 1910 (Anoplophrya)
●●●●●●●Buetschliellidae de Puytorac in Corliss, 1979 (Buetschliella)
●●●●●●●Clausilocolidae de Puytorac in Corliss, 1979 (Clausilocola)
●●●●●●●Contophryidae de Puytorac, 1972 (Contophyra)
●●●●●●●Haptophryidae Cépède, 1923 (Haptophrya)
●●●●●●●Hoplitophryidae Cheissin, 1930 (Hoplitophrya)
●●●●●●●Intoshellinidae Cépède, 1910 (Intoshellina)
●●●●●●●Maupasellidae Cépède, 1910 (Maupasella)
●●●●●●●Radiophryidae de Puytorac, 1972 (Radiophrya)
●●●●●●Hymenostomatia Delage & Hérouard, 1896
Stomatogenesis by proliferation of kinetosomes typically in mid-ventral region of the cell,
posterior to and somewhat apart from parental oral apparatus.
●●●●●●●Tetrahymenida Fauré-Fremiet in Corliss, 1956
Somatic kineties with anteriormost kinetid as a dikinetid; oral region, inconspicuous, except
in species that undergo microstome-to-macrostome transformation; oral structures with right
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Accepted Article
oral b segment of paroral (haplokinety, undulating membrane) and three left oral polykinetids
(membranelles) in oral cavity; stomatogenesis monoparakinetal, typically involving the
rightmost postoral somatic kinety; microphagous forms primarily bacterivorous, but some
histophagous and several polymorphic forms with cytotrophic macrostome stage; complex
life cycle in histophagous and parasitic species; in freshwater habitats, sometimes terrestrial,
and others as facultative or obligate parasites associated mainly with invertebrate hosts.
Incertae sedis Tetrahymenida: Trichospiridae Kahl, 1926 (Trichospira)
●●●●●●●●Curimostomatidae Jankowski, 1968 (Curimostoma)
●●●●●●●●Glaucomidae Corliss, 1971 (Glaucoma)
●●●●●●●●Spirozonidae Kahl, 1926 (Spirozona)
●●●●●●●●Tetrahymenidae Corliss, 1952 (Tetrahymena)
●●●●●●●●Turaniellidae Didier, 1971 (Colpidium, Dexiostoma, Turaniella)
●●●●●●●Ophryoglenida Canella, 1964
Somatic ciliature very dense, with preoral suture; oral region inconspicuous, with paroral and
three oral polykinetids, its wall “supported” by the organelle of Lieberkühn in at least one
stage in the life cycle; stomatogenesis teloparakinetal, with dedifferentiation and
replacement of parental oral structures, accompanied by marked regression of the paroral in
the differentiated oral apparatus; division free-swimming or by palintomy in a cyst;
histophagous forms generally feeding on moribund or wounded invertebrates, though
several species attack healthy fishes; in freshwater habitats; polymorphic life cycle, including
resting cysts.
●●●●●●●●Ichthyophthiriidae Kent, 1881 (Ichthyophthirius)
●●●●●●●●Ophryoglenidae Kent, 1881 (Ophryoglena)
●●●●●●Peniculia Fauré-Fremiet in Corliss, 1956 (P)
Somatic kinetids with tangential transverse ribbons and prominently overlapping
kinetodesmal fibrils; cortical alveoli lie between kinetosomal rows of oral polykinetids;
extrusomes as typical fibrous trichocysts.
●●●●●●●Peniculida Fauré-Fremiet in Corliss, 1956
Somatic kinetids predominantly dikinetids; somatic extrusomes as trichocysts.
●●●●●●●●Clathrostomatidae Kahl, 1926 (Clathrostoma)
●●●●●●●●Frontoniidae Kahl, 1926 (Disematostoma, Frontonia (P))
This article is protected by copyright. All rights reserved.
●●●●●●●●Lembadionidae Jankowski in Corliss, 1979 (Lembadion)
●●●●●●●●Maritujidae Jankowski in Small & Lynn, 1985 (Marituja)
Accepted Article
●●●●●●●●Neobursaridiidae Dragesco & Tuffrau, 1967 (Neobursaridium)
●●●●●●●●Parameciidae Dujardin, 1840 (Paramecium)
●●●●●●●●Paranassulidae Fauré-Fremiet, 1962 (Paranassula)
●●●●●●●●Stokesiidae Roque, 1961 (Stokesia)
●●●●●●●Urocentridae Claparède & Lachmann, 1858 [Urocentrida de Puytorac, Grain &
Mignot, 1987]
Body broadly cylindroidal, with larger, rounded anterior half; free-swimming, but may be
temporarily attached to the substratum by a mucous thread; somatic ation as a distinct
equatorial girdle; caudal cilia form a conspicuous tuft that is used for temporary attachment
to substrates by a mucous thread; somatic kinetids only as monokinetids with broad,
tangential transverse ribbon; somatic extrusomes as mucocysts; oral structures as a paroral
along the right margin of the oral opening and three oral polykinetids of three rows each
along the dorsal-left wall. Urocentrum.
●●●●●●Peritrichia Stein, 1859
Body divided into three major areas: (1) oral, with a prominent peristome bordered by a
dikinetid file (haplokinety) and an oral polykinetid that both originate in an oral cavity
(infundibulum) at the base of which is the cytostome; (2) aboral, including kinetosomes as
part of the scopula, which secretes the stalk of sessile species; and (3) telotroch,
permanently ated on mobile species.
●●●●●●●Sessilida Kahl, 1933
Body inverted bell- or goblet-shaped or conical-cylindrical; zooids dimorphic, with mature
zooids or trophonts, sedentary or sessile, commonly stalked or with inconspicuous adhesive
disc, attached to substrate by scopula, but a few species presumed to be secondarily
mobile; dispersal stage as migratory telotroch; division isotomic or anisotomic, followed in
many species by development into arboroid colonies; resting cysts; free-living or
ectosymbionts, rarely endosymbionts.
●●●●●●●●Astylozoidae Kahl, 1935 (Astylozoon, Hastatella)
●●●●●●●●Ellobiophryidae Chatton and Lwoff, 1929 (Ellobiophrya)
●●●●●●●●Epistylididae Kahl, 1933 (Epistylis)
●●●●●●●●Lagenophryidae Bütschli, 1889 (Lagenophrys)
●●●●●●●●Operculariidae Fauré-Fremiet in Corliss, 1979 (Opercularia)
●●●●●●●●Rovinjellidae Matthes, 1972 (Rovinjella)
This article is protected by copyright. All rights reserved.
●●●●●●●●Scyphidiidae Kahl, 1933 (Scyphidia( (P)
●●●●●●●●Termitophryidae Lom in Corliss, 1979 (Termitophrya)
Accepted Article
●●●●●●●●Usconophryidae Clamp, 1991 (Usconophrys)
●●●●●●●●Vaginicolidae de Fromentel, 1874 (Cothurnia, Pyxicola, Thuricola, Vaginicola)
●●●●●●●●Vorticellidae Ehrenberg, 1838 (Carchesium, Epicarchesium (P), Ophrydium,
Pelagovorticella, Pseudovorticella (P), Vorticella (P))
●●●●●●●●Zoothamniidae Sommer, 1951 (Haplocaulus, Zoothamnium)
●●●●●●●Mobilida Kahl, 1933
Body conical, cylindrical, or goblet-shaped, sometimes discoidal and orally-aborally
flattened; zooid mobile, with permanently ciliated trochal band, typically composed of three
rings of cilia; adhesive disk on aboral pole, slightly contractile; with a ring-like, complex
skeletal armature of denticles and fibers surrounding a vestigial scopula; oral region not
contractile; oral structures with infundibular portions of oral polykinetids 1 and 2 always
running together in a “ribbon” and oral polykinetid 3 short, perpendicular to the other two oral
polykinetids; bacterivorous, obtaining prey from water or from detritus adhering to the host,
and microphagous on cellular debris from host; ectosymbionts, often on the integument or
gills of invertebrates, rarely endosymbionts.
●●●●●●●●Polycyclidae Poljansky, 1951 (Polycycla)
●●●●●●●●Trichodinidae Claus, 1874 (Trichodina)
●●●●●●●●Trichodinopsidae Kent, 1881 (Trichodinopsis)
●●●●●●●●Urceolariidae Dujardin, 1840 (Leiotrocha, Urceolaria)
●●●●●●Scuticociliatia Small, 1967 (P)
Paroral dikinetid with a, b, and c segments; stomatogenesis by proliferation of kinetosomes
from the c segment or a “scutico”-vestige posterior to a and b segments, with varying
involvement of kinetosomes in the a and b segments; typically three oral polykinetids, often
as membranoids; somatic dikinetids usually with both basal bodies ciliated; mucocysts;
mitochondria cortically located, often-fused to chondriome; stomatogenesis
scuticobuccokinetal.
●●●●●●●Philasterida Small, 1967
Paroral dikinetid shorter than other oral structures, typically by reduction of paroral a and c
segments; scutica typically present.
●●●●●●●●Cohnilembidae Kahl, 1933 (Cohnilembus)
●●●●●●●●Cryptochilidae Berger in Corliss, 1979 (Cryptochilum.)
This article is protected by copyright. All rights reserved.
●●●●●●●●Entodiscidae Jankowski, 1973 (Entodiscus)
●●●●●●●●Entorhipidiidae Madsen, 1931 (Entorhipidium)
Accepted Article
●●●●●●●●Orchitophryidae Cépède, 1910 (P) (Orchitophrya)
●●●●●●●●Paralembidae Corliss and de Puytorac in Small & Lynn, 1985 (Anophrys,
Paralembus)
●●●●●●●●Parauronematidae Small & Lynn, 1985 (Parauronema (P)) (P)
●●●●●●●●Philasteridae Kahl, 1931 (Kahlilembus, Philaster)
●●●●●●●●Pseudocohnilembidae Evans & Thompson, 1964 (Pseudocohnilembus)
●●●●●●●●Schizocaryidae Jankowski, 1979 (Schizocaryum)
●●●●●●●●Thigmophryidae Chatton and Lwoff, 1926 (Thigmophrya)
●●●●●●●●Thyrophylacidae Berger in Corliss, 1961 (Thyrophylax)
●●●●●●●●Uronematidae Thompson, 1964 (Uronema)
●●●●●●●●Urozonidae Grolière, 1975 (Urozona)
●●●●●●●Pleuronematida Fauré-Fremiet in Corliss, 1956
Paroral often prominent forming a velum, with short a and elongate b segment and with c
segment as a permanent scutica or scuticovestige; mucocysts; stomatogenesis from proter’s
paroral and scutica.
●●●●●●●●Calyptotrichidae Small & Lynn, 1985 (Calyptotricha)
●●●●●●●●Conchophthiridae Kahl in Doflein and Reichenow, 1929 (Conchophthirus)
●●●●●●●●Ctedoctematidae Small & Lynn, 1985 (Ctedoctema)
●●●●●●●● Cyclidiidae Ehrenberg, 1838 (Cristigera, Cyclidium) (P)
●●●●●●●●Dragescoidae Jankowski, 1980 (Dragescoa)
●●●●●●●●Eurystomatellidae Miao et al., 2010 (Eurystomatella)
●●●●●●●●Histiobalantiidae de Puytorac & Corliss in Corliss, 1979 (Histiobalantium)
●●●●●●●●Peniculistomatidae Fenchel, 1965 (Peniculistoma)
●●●●●●●●Pleuronematidae Kent, 1881 (P) (Pleuronema)
●●●●●●●●Thigmocomidae Kazubski, 1958 (Thigmocoma)
●●●●●●●Thigmotrichida Chatton & Lwoff, 1922
Thigmotactic cilia as anterior differentiations of somatic kineties, attach to host tissues;
somatic kineties often spiralled around posterior cell pole, where cytostome is located;
paroral not velum-like; oral polykinetid 3 reduced or absent; stomatogenesis from proter’s
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Accepted Article
paroral and scutica. In molecular analyses, often nested within the Pleuronematida close to
the cyclidiids.
●●●●●●●●Ancistridae Issel, 1903 (Ancistrum)
●●●●●●●●Hemispeiridae König, 1894 (Hemispeira)
●●●●●●●●Hysterocinetidae Diesing, 1866 (Hysterocineta)
●●●●●●●●Paraptychostomidae Ngassam et al. 1994 (Paraptychostomum)
●●●●●●●Loxocephalida Jankowski, 1964 (P)
Non-monophyletic group that is most closely related to Astomatia and Apostomatia; further
studies are needed in order to clarify the systematics of the loxocephalids.
●●●●●●●●Cinetochilidae Perty, 1852 (Cinetochilum, Sathrophilus) (P)
●●●●●●●●Loxocephalidae Jankowski, 1964 (Cardiostomatella, Dexiotricha, Loxocephalus)
● Rhizaria Cavalier-Smith 2002
With fine pseudopodia varying as simple, branching, or anastomosing patterns, often
supported by microtubules in those groups examined by electron microscopy.
Incertae sedis Rhizaria: Gymnosphaerida Poche 1913, emend. Mikrjukov 2000
Axopodial microtubules in irregular hexagonal prism; kinetocyst and other types of
extrusomes along axopodia; tubular mitochondrial cristae; in some genera, cells attached to
substrate with cytoplasmic stalk; free-swimming as amoeboid or motile biciliated cells; one or
more nuclei, often located in the amoeboid base of stalk when present; complex life cycle
unresolved. Actinocoryne*, Cienkowskya*, Gymnosphaera*, Hedraiophrys* (possible junior
synonym of Cienkowskya), Wagnerella*. Note: This group is placed here based solely on
morphology, as there is no DNA sequence information.
●● Cercozoa Cavalier-Smith 1998, emend. Adl et al. 2005, emend. Cavalier-Smith 2018
Diverse clade lacking distinctive morphological or behavioural characters; biciliated and/or
amoeboid, usually with filopodia; most with tubular mitochondrial cristae; cysts common;
kinetosomes connecting to nucleus with cytoskeleton; usually with microbodies and
extrusomes.
Incertae sedis Cercozoa: Discocelia Cavalier-Smith 2013 [Discocelis Vørs 1988].
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Incertae sedis Cercozoa: Psammonobiotidae* Golemansky 1974, emend Meisterfeld, 2002
Accepted Article
This clade is considered as most likely belonging to Euglyphida. However, this position
remains to be confirmed as they do not secrete scales. Test resembling a Greek vase with
terminal collar either straight or angled, test circular in cross-section with aboral end
spherical, flattened or pointed; mostly in marine interstitial sand, but also in freshwater and
soils. Including Alepiella, Chardezia, Edaphonobiotus, Feuerbornia, Frenzelina, Lesquerella,
Micramphora, Micropsammella, Nadinella, Ogdeniella, Psammonobiotus,
Propsammonobiotus, and Rhumbleriella.
Incertae sedis Cercozoa: Volutellidae Sudzuki 1979
Test half-coiled, either totally organic or with some attached particles; marine.
Pseudovolutella, Volutella.
Incertae sedis Cercozoa: Kraken Dumack, Schuster, Bass et Bonkowski, 2016
Very slow moving filose amoeboid cell, roundish in shape; usually a single highly branched
filopodium originating between the cell body and the substrate through a ring-like structure
sometimes visible by light microscopy; filopodium branching and anastomoses forming a
network; cell division longitudinal; phagocytosis of bacteria, prey transported through the
filopodium to the cell body; with one, rarely two, nuclei with a round nucleolus, one
contractile vacuole, and usually one food vacuole.
Incertae sedis Cercozoa: Dictiomyxa, Katabia, Myxodictyium, Pontomyxa, Protomyxa,
Protogenes, Pseudospora, Rhizoplasma.
●●● Cercomonadida Poche 1913, emend. Vickerman 1983, emend. Mylnikov 1986, emend.
Karpov et al. 2006; emend Howe et al 2009; emend Cavalier-Smith 2012;
[=Cercomonadidae Kent 1880, emend. Mylnikov and Karpov 2004; Cercobodonidae
Hollande 1942].
Phagotrophic and heterotrophic biciliate Cercozoa from soil and freshwater; usually do not
swim, but glide on surfaces by means of the long posterior cilium to which the ventral
surface of their typically soft bodies adheres (except Cavernomonas). Posterior centriole
(C1) attached to side of younger anterior centriole (C2) at usually strongly obtuse angle
(orthogonal only in clade A1a2) by fibrillar connections, the distal one weakly striated; both
typically attached to anteriorly tapering nucleus. C2 points forwards, somewhat downwards
and/or to left; C1 directed backwards, pointing downwards towards the substratum or to the
left. Anterior cilium beats asymmetrically to the left; posterior typically does not undulate
during smooth forward gliding. All but Cavernomonas have spindle-shaped body when
gliding; cytoplasm adherent to posterior cilium drawn out into a posterior tail, often pointed;
high propensity for making extensive non-locomotory feeding pseudopodia of seven types
(depending on species): lamellipodia, filopodia (unbranching or branching), bulbous, fingerlike, reticulopodia or axopodia (Filomonas radiata only). Most have contractile vacuoles and
resting cysts; some have multinucleate and multiciliate syncytial or plasmodial stages in
older cultures. Ciliar transition zone very short; with proximal hub-lattice structure; unlike
glissomonads, cryothecomonads or Katabia, have a slender distal hub-spoke structure
instead of a conspicuous dense distal transverse plate. Anterior centriole has two
microtubular roots (vp2 without an associated dense plate, unlike glissomonads and
thaumatomonads, and da of two microtubules), sometimes a third (dp2; Eocercomonas
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Accepted Article
only); posterior centriole has nucleated at its basal half ventral root vp1 and sometimes
(Paracercomonas only) also dorsal dp1 of two or three microtubules. A root of one or two
microtubules (lr) nucleates near the junction of amorphous fibrillar material projecting from
both centriole bases. Ventral posterior (vp1) and ventral anterior (but posterior-pointing)
roots (vp2) typically mutually closely attached by dense material at least in their anterior
region, where one crosses over the other. Microtubule nucleating centre (MNC) that
nucleates a small cone of singlet microtubules associated with either or both centrioles:
medial and ventral centrosome-like fibrillar root (fr) attached directly or indirectly to posterior
centriole close to centriolar junction and base of dp1 if present, often connecting to nucleus;
another fibrillar root (fs) usually present on dorsal side of C2; either or both of fr and fs may
nucleate a small cone of microtubules. Cercomonas, Eoercomonas, Filomonas,
Neocercomonas, Cavernomonas.
●●● Paracercomonadida Cavalier-Smith 2018
Cercomonads with a medial posterior microtubular root of two or three microtubules (dp1)
attached to dorsal side of posterior centriole (unlike Cercomonadidae, whose only C1 root is
vp1). Fibrillar MNC (fr) linked to and partially surrounding base of dp1, attached to nuclearfacing side of both centrioles, but mainly C1. Sheet-like MNC (fs) on dorsal side of C2
nucleates diverging single micro- tubules including two parallel conspicuous ones pointing
backwards. Ventral roots vp1 and vp2 con- sistently to the right of plane passing
longitudinally through posterior cilium (if viewed from its tip to base) and orthogonally to cell
surface. Ciliar transition zone proximal hub-lattice with broad obvious hub; peripheral lattice
not partially obscured by dense diaphragm-like material. Conspicuous dense ciliar axosome
at base of central pair, sometimes with noticeable denser central hub structure; spokes
radiating from it more obvious than nonagonal fibre. Centrioles in one plane, posterior
centriole not offset. Left root, if present, points left; does not nucleate secondary
microtubules. Pseudopodia most often finger-like or long thick, often branched filopodia;
more rarely purely lamellipodial. Gliding cells typically smaller than Cercomonadida (3-18
m). Brevimastigomonas, Metabolomonas, Nucleocercomonas, Paracercomonas,
Phytocercomonas.
●●●Glissomonadida Howe & Cavalier-Smith 2009 [Heteromitidae Kent 1880, emend.
Mylnikov 1990, emend. Mylnikov & Karpov 2004; Bodomorphidae Hollande 1952]
Heterotrophic biciliates that are covered by a plasma membrane only but are not strongly
amoeboid; ancestrally biciliates that glide upon substrata on the longer posterior cilium, but
includes also one derived non- gliding genus (Proleptomonas); if exceptionally the anterior
cilium is longer the posterior one is adherent to the cell and not used for gliding
(Proleptomonas only); in gliding species the cell posterior is usually rounded and the cell
most often oval or ovoid, not highly elongated; although some species may extend a
protoplasmic tail temporarily, it is not drawn out along the posterior cilium as in most
cercomonads; no cytopharynx or deep ciliar groove or pocket is evident and most species
are singularly lacking in obvious morphological specializations; apart from Proleptomonas,
which is exceptionally elongated and has a modified cytoskeleton, the nucleus is anterior
and attached to the kinetid by well-developed fibrous roots; typically at least two posterior
and one anterior microtubular centriolar roots; contractile vacuole usually in cell posterior;
cilia of equal thickness, simple without paraxonemal rod, hairs, or scales, sometimes
acronematic; unlike in cercomonads, the ciliary transition region has a single dense
transverse plate at its distal end; anterior cilium beats in ciliary fashion towards the left (as in
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Accepted Article
cercomonads), and is sometimes reduced to a very short stub without an axoneme; only
aerobic species currently known; mitochondria with tubular cristae; microbody attached to
nuclear posterior except in Proleptomonas; almost exclusively inhabit soil or freshwater;
Golgi dictyosomes typically associated with the nucleus, as is not the case in all Cercozoa;
smooth walled cysts commonly present; sex unknown.
●●●● Sandonidae Howe et al. 2009
Jerky gliders; anterior pointing anterior cilium: Sandona, Flectomonas, Neoheteromita,
Mollimonas.
●●●● Dujardinidae Howe & Cavalier-Smith, 2011
Jerky gliders; antero-lateral pointing anterior cilium: Dujardina.
●●●● Bodomorphidae Hollande 1952 emend. Cavalier-Smith in Howe et al. 2009
Smoothly gliding biciliate cells with a shorter anterior cilium that points mainly sideways or
posteriorly in parallel with the posterior one; in one genus with a prominent anterior rostrum;
posterior centriolar base asymmetric, sharply angled with basally extended triplets on side
facing nucleus. Bodomorpha.
●●●● Proleptomonadidae Howe et al. 2009
Swimmers. Proleptomonas.
●●●● Allapsidae Howe & Cavalier-Smith 2009
Smooth gliders; anterior cilium points sideways and somewhat backwards; centrioles
symmetric. Allapsa, Teretomonas, Allantion.
●●● Viridiraptoridae Hess & Melkonian 2013
Biciliate, naked cells, mostly occurring as rigid, variously shaped ciliates, without rostrum or
bulge. In ciliate state markedly exceeding 10 m (contrasting most known glissomonad
families). Capable of transforming into surface-attached amoeboid state, retaining cilia and
showing bridge-like morphology with several distinct adhesion sites. Cell containing single
‘vesicular’ nucleus, close to ciliary apparatus, thus apical in ciliate state. Nucleolus spherical,
roughly central, occasionally exhibiting lacuna/ae. Golgi bodies in close proximity to nuclear
envelope. Cytoplasm colourless, often opaque due to diverse globules, granules and
crystals. Digestive stages containing several globules of medium refractivity. Crystal-like
structures restricted to starving cells, showing various shapes: 1) Small, isodiametric or
slightly elongate, glisten- ing particles, ∼ 0.5–1 m. 2) Slender, fusiform or needle-like rods,
often 2–3 m in length, rarely up to ∼ 6 m. Several mitochondria scattered throughout cell,
slightly elongate to botuliform. Isodiametric extrusomes, ∼ 0.5 m as seen with light
microscope, directly beneath plasma membrane, but not in pseudopodia. Several contractile
vacuoles at non-defined positions in cell periphery, ≤ 2 m in diameter (late diastole), nonsynchronous. Cilia naked and heterodynamic, arising very close to each other in a slightly
acute or right angle. Cells gliding on posterior cilium (mostly longer than anterior cilium), cell
body not attaching to gliding cilium or to substrate. Flapping motion of anterior cilium often
causing motions of cell body during gliding (rotation, jiggling, vibrating). Cells capable of
fluttering swimming locomotion to different extent, involving both cilia. Heterotrophic nutrition,
feeding by phagocytosis on dead or live eukaryotic cells, capable of local cell wall lysis to
feed exclusively on protoplast material (e.g. in certain green algae), not bacterivorous.
Propagation by binary fission, plasmodia not observed. Inhabiting freshwater-fed
ecosystems. Phylogenetically defined as a well-supported, clade including the genera
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Accepted Article
Orciraptor and Viridiraptor, but excluding the genera Agitata, Allantion, Allapsa,
Aurigamonas, Bodomorpha, Dujardina, Flectomonas, Mollimonas, Neoheteromita,
Proleptomonas, Sandona and Teretomonas. Viridiraptor, Orciraptor
●●● Pansomonadidae Vickerman in Vickerman et al. 2005
Heterotrophic cell with two heterodynamic cilia, both cilia free from body; motile
ciliate phase alternates with sedentary amoeboid phase; one amino acid insertion only
between ubiquitin monomers. Clade includes last common ancestor of Aurigamonas and
Agitata. Agitata, Aurigamonas.
●●● Sainouroidea 33 Schuler et al. 2018 (R)
Ancestrally amoeboid bi-ciliates, typically without scales or theca; cells often gliding on
posteror cilium; tubular cristae or flat cristae; microbody attached to nucleus.
●●●●Sainouridae Cavalier-Smith 2008
Biciliate or tetraciliate phagotrophic, with one or two long, motile and highly acronematic
posterior cilia possessing transition region hub-lattice and nonagonal fibre; posterior
centrioles attached basally to a dense spiral fibre, and laterally to a microtubular root; one or
two anterior stubby nipple-like cilia without these structures or roots, but with a nine-fold
submembrane skeleton; nucleus attached to cell surface and centrioles by striated
rhizoplasts; centriole shorter (1—1.5X width) than in most Cercozoa (2—2.5 X width); fine
tubular invaginations of inner membrane of nuclear envelope; peroxisome attached to the
nuclear envelope; mitochondrial cristae flat or with peripheral vesicles, not elongated tubules
as in most Cercozoa. Acantholus, Cholamonas, Homocognata, Sainouron.
●●●● Helkesimastigidae Cavalier-Smith 2008.
Biciliate semi-rigid cells with two parallel, longitudinally offset centrioles, one bearing a
trailing cilium for gliding, the other bearing a ciliary stump or rarely a short motile laterally
beating cilium; non-amoeboid phagotrophs with resting cysts; apical centrosomal plate with
dorsal cape of single microtubules; dense forked fibre attaches the centriole bearing the long
cilium to the centrosomal plate and nucleates the single ventral microtubule; both centrioles
attached to nucleus by striated rhizoplasts. Helkesimastix.
●●●● Guttulinopsidae Olive 1970 (R)
Guttulinopsis, Olivorum, Puppisaman, Rosculus.
●●●Thecofilosea 33Cavalier-Smith 2003, emend. Cavalier-Smith 2011
Ancestrally with robust organic extracellular theca, unlike most other Cercozoa, which are
usually naked or with scales; ventral filose pseudopodia emerge from ventral groove; two
cilia with diver gent kinetosomes, secondarily lost in Rhizaspidae and the euglyphid
amoebae, and restricted to zoospores in Phaeodarea; ancestrally benthic gliding on
posterior cilium only, but some secondarily planktonic swimmers amongst which Ebriacea
have lost pseudopodia; theca with perforations for cilia and for pseudopodia, and three
perforations in Phaeodarea (thus Tripylea Hertwig 1879), which have surrounded it by a
pseudopodial net containing a pigmented phaeodium, thus converting it into a ‘central
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Accepted Article
capsule’, but not homologous with that of Polycystinea of Radiolaria; silica scales absent,
unlike many Imbricatea (see below), but hollow silica endoskeleton in all ebriids and most
phaeodarians.
33
A node including a probably monophyletic clade composed of Sainouridae and
Thecofilosea is proposed, called Helkesida Cavalier-Smith 2018 (R)
●●●●Thecofilosea: Chlamydophryidae de Saedeleer 1934 (R)
Chlamydophrys, Lecythium, Trachyrhizium, Diaphoropodon, Clypeolina,
Leptochlamydophrys.
Incertae sedis Thecofilosea: Mataza.
●●●●Phaeodarea Haeckel 1879 [Tripylea Hertwig 1879]
Central capsule with thickened, double-layered, capsular wall containing two kinds of
pores or openings; large opening known as an “astropylum” or oral pore with a protruding
mass of cytoplasm, and smaller, typically lateral openings, as “parapylae”, with thinner
protruding strands of cytoplasm; dense mass of darkly pigmented granular cytoplasm, the
“phaeodium,” containing undigested debris, suspended in the extracapsulum; mineral
skeletons, when present, composed of scattered spicules or hollow silica bars, joined by
organic material; a wide variety of forms, including geodesic frameworks, spherical to
polyhedral shells, or more solid, porous clam-shaped, bivalve shells; tubular mitochondrial
cristae.
●●●●● Phaeoconchia Haeckel 1879.
Central capsule enclosed within bivalve lattice shell composed of dorsal and
ventral boat-shaped valves, which are completely separated and rarely connected by a
ligament on the aboral pole. Coelodendrum, Coelographis, Conchellium, Conchopsis.
●●●●● Phaeocystina Haeckel 1879
Central capsule suspended in the centre of the extra-capsular cytoplasmic network; skeleton
absent or incomplete, composed of numerous solitary, scattered pieces or spicules without
organic connections. Aulacantha, Aulographis, Cannoraphis.
●●●●● Phaeogromia Haeckel 1879.
Central capsule located eccentrically, aborally, in simple lattice shell typically
provided with large shell opening placed on the oral pole of the main axis; capsule opening
surrounded by “teeth” or by peculiar elongate extensions known as “feet”, sometimes with
elaborate branches. Castanella, Challengeron, Haeckeliana, Medusetta, Tuscarora.
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●●●●● Phaeosphaeria Haeckel 1879.
Accepted Article
Central capsule located in the centre of a simple or double spherical lattice shell, not bivalve,
with a simple shell opening, lacking “feet” or “teeth”. Aulosphaera, Cannosphaera,
Sagosphaera.
●●●●Cryomonadida Cavalier-Smith 1993 (R)
rDNA trees show Rhogostoma (Rhizaspididae) within the cryomonads, so they evolved after
the hypothesized ciliated common ancestor of Ebriacea and Cryomonadida by loss of cilia
and are unrelated to Pseudodifflugia. Includes Rhogostoma (previously misidentified as
Lecythium), Cryothecomonas, Protaspis (re-named Protaspa in Howe et al. 2011 as the
name Protaspis was pre-occupied).
●●●●● Rhogostomidae Dumack et al 2017.
Thecate amoebae with ventral slit-like and not flexible cleft that emits filopodia; theca thin,
flexible, in active cells adherent throughout to cell surface, consisting of single smooth dense
layer outside and scarcely thicker than the plasma membrane; thus with bilateral symmetry;
theca with exosomes (Capsellina) or without (Rhogostoma, Sacciforma); phagotrophic
(mainly bacteria, also yeasts, algae); division longitudinal, binary; sexual reproduction
unknown. Electron microscopy of Capsellina and Rhogostoma by Simitzis and Le Goff
(1981). Rhogostoma, Sacciforma, Capsellina.
●●●●● Protaspidae Cavalier-Smith 1993 (R)
Heterodynamic biciliated cells with cilia sub-apical separated by a protrusion; ciliary pit with
funnel; dorsoventrally flattened and oval-shaped with parallel lateral sides; ventral
longitudinal furrow in anterior half of cell; nucleus posterior with permanently condensed
chromosomes; thickened cell wall with seven layers with pores for extrusome discharge;
pseudopodia emerge from slits. Cryothecomonas, Protaspa (P)
●●●●Ventricleftida Cavalier-Smith 2011
Strongly flattened oval cell with rigid theca without scales; two unequal cilia emerging
subapically, often from apical notch – posterior cilium used for gliding on surfaces; ventral
cleft from which branched filose pseudopods emerge for feeding separate from and posterior
to ciliary groove unlike Thaumatomonadida and Auranticordis; with extrusomes.
Ventrifissura, Verrucomonas.
●●●● Tectofilosida Cavalier-Smith 2003
Uninucleate cells (some may form fused multicellular aggregates) surrounded by an organic
flexible tectum with one basal aperture for filopodia, sometimes including foreign mineral
particles (agglutinated); cilia or silica scales absent; tubular mitochondrial cristae,
cytotrophic. Pseudodifflugia, Rhizaspis, Fisculla.
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●●●●Ebriacea Lemmermann 1901 [Ebriidae Poche 1913; Ebriida Deflandre 1936]
Accepted Article
Cells with two subapically inserting cilia; open internal skeleton of silica; phagotrophic
without plastids. Ebria, Hermesinum, Botuliforma.
●●●Imbricatea Cavalier-Smith 2011 [Cavalier-Smith 2003]
Secreted surface silica scales or secondarily lost, except in basal lineages where ancestrally
absent; tubular mitochondrial cristae; ciliary transition region longer than in cercomonads
and sainouroids, and unlike them with dense distal plate but without the internal dense
aggregates and elaborate extra structures opposite the thecal contact zone in cryomonads;
groove and cilia secondarily lost by euglyphids; centrioles multiplied and reoriented to make
four posteriorly-directed gliding cilia in Auranticordis, which also lost pseudopodia; centrioles
independently made parallel in the thaumatomonad/ spongomonad subclade. 35
Incertae sedis Imbricatea: Discomonas Chantangsi and Leader, 2010
35
Ancestral condition probably a gliding heterotrophic cell with two cilia with divergent
kinetosomes, and relatively rigid pellicle that helped to define a distinct ventral groove from
which filose pseudopods extended, but without the dense extracellular theca of Thecofilosea
or internal silica skeleton of Ebriacea and Phaeodaria. Includes Cercozoa with often
imbricate silica scales and their closest nonscaly relatives.
●●●●Spongomonadida Hibberd, 1983 [Spongomonadidae Karpov 1990]
Biciliated cells with asymmetrical cell projection at anterior. Rhipidodendron,
Spongomonas.
●●●●Marimonadida Cavalier-Smith & Bass 2011
Without scales and without theca; marine heterotrophic biciliate swimming cells
(Pseudopirsonia: diatom parasites) or interstitial gliding cells with somewhat deformable,
semi-rigid pellicle underlain by muciferous bodies and four posterior cilia associated with
ventral cleft (Auranticordis), or ciliated amoebaes with two gliding posterior cilia and a
nonciliate feeding stage with broad lobose fan-like pseudopods (Rhabdamoeba). Differ from
Euglyphida by the absence of silica scales and presence of cilia, and from thaumatomonads,
the only other gliding imbricates, by absence of scales. Auranticordis, Pseudopirsonia,
Rhabdamoeba, Abollifer, Cyranomonas
●●●● Variglissida Cavalier-Smith, 2014 (R)
Clautriavia, Nudifila, Quadricilia.
●●●●Silicofilosea Adl et al. 2005, emend. Adl et al. 2012
Secreted surface silica scales or secondarily lost; tubular mitochondrial cristae.
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●●●●●Thaumatomonadida Shirkina, 1987
[Thaumatomastigidae Patterson and Zoelfell 1991]
Accepted Article
Heterotrophic, cells usually gliding that may swim also; body flattened and with two
heterodynamic cilia inserting subapically and/or ventrally; some unikont; with extrusomes;
filopodia produced subapically or from ventral groove; cysts; multinucleate and multiciliate
stages known.
●●●●●●Thaumatomonadidae Hollande, 1952
Biciliated cells with ventral pseudopodia, long ventral posterior pointing cilium used
for gliding on surfaces unlike Peregriniidae (see below), and a much shorter anterior cilium,
which is naked (Thaumatomonas, Allas) or with small scales (Reckertia, Thaumatomastix);
siliceous scales formed in vesicles attached to mitochondria cover the rigid cell surface
except for a ventral zone that emits pseudopodia for feeding; unlike Peregriniidae, do not
transform completely into an amoeba; all have oval or triangular two-tiered body scales, with
an upper plate bearing species-specific perforations supported at the oval ends or triangle
corners by discrete struts, unlike Gyromitus; upper plate lacks central cleft with inrolled
sides, unlike Peregrinia; Thaumatomastix only additionally has long spine scales with nearcircular or rounded triangular bases. Allas, Hyaloselene, Reckertia, Thaumatomonas,
Thaumatomastix, Ovaloplaca, Scutellomonas, Thaumatospina, Penardeugenia.
●●●●●●Esquamula Shiratori, Yabuki & Ishida, 2012
Unicellular heterotrophic, with a short anterior cilium and a long posterior cilium; cells gliding
with a posterior cilium; both cilia emerge from the same ciliar pit; cells with a rigid surface
and without thecae or scales; filose or lobose pseudopodia sometimes emerging; slender
extrusomes consist of shaft with a horizontal-stripe pattern and cap structure on the tip.
●●●●●●Peregriniidae Cavalier-Smith, 2011
With only oval two-tiered body scales and without scales on cilia or spine scales;
scales either symmetric ovals with heavily out-turned upper and lower rims (as in Gyromitus)
or asymmetric ovals with concave to flat lower surface and convex upper surface with rims
more strongly laterally inrolled than at the ends (as in Peregrinia); in contrast to
Thaumatomonas, ciliary pit apical not subapical and ventral, or cells so amoeboid as to lack
defined shape; cilia not clearly differentiated into anterior and posterior; unlike
Thaumatomonadidae no evidence for ciliary gliding; locomotion by swimming or slow
amoeboid creeping. Gyromitus, Peregrinia.
●●●●●Euglyphida Copeland 1956, emend. Cavalier-Smith 1997
Testate amoebae, with a shell built of organic material; most taxa with secreted silica scales
held together by organic cement; tubular mitochondrial cristae; filamentous pseudopodia;
large and conspicuous nucleus easy to see in active cells using light microscopy,
surrounded by vesicles.
Incertae sedis Euglyphida: Ampullataria*, Euglyphidion*, Heteroglypha*, Matsakision*,
Pareuglypha*, Pileolus*.
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Accepted Article
●●●●●● Euglyphina Kosakyan et al., 2016
Test covered with elliptical, discoid or denticulated siliceous plates. The least inclusive clade
containing Assulina, Euglypha, Sphenoderia and Trinema.
●●●●●●● Assulinidae Lara et al., 2007
Test with a terminal aperture composed of elliptic plates disposed in a regular, alternate
pattern; test strongly compressed; no specialized type of scales around the aperture; shape
flattened in cross-section; in litter and mosses. Assulina, Placocista, Valkanovia*.
●●●●●●● Sphenoderiidae Chatelain et al., 2013
Circular to elliptical silica scales that can be of different sizes and shapes, but without
indentations; aperture surrounded with small round or oval scales; slightly subterminal
aperture; shape flattened or circular in cross-section in litter and mosses, and freshwater
plants; . Sphenoderia, Trachelocorythion, Deharvengia*.
●●●●●●● Trinematidae Hoogenraad & De Groot 1940, emend Adl et al. 2012
Test with bilateral symmetry; scales oval or round, sometimes of both types; specialized
tooth-shaped scales around the aperture, which is located on the side of the shell; aperture
invaginated in some taxa; shape flattened in cross-section; in litter and mosses; Corythion,
Playfairina*, Puytoracia*, Trinema.
●●●●●●● Euglyphidae Wallich 1864, emend Lara et al. 2007
Test with a terminal aperture; thin elliptical scales; presence of specialized scales around the
aperture with typical indentation; shape flattened or circular in cross-section; in litter and
mosses, freshwater sediments and plants. Euglypha, Scutiglypha.
●●●●●●● Tracheleuglypha Deflandre, 1928
Test reinforced with relatively large, discoid plates; cross-section circular; without specialized
scales around the aperture. (There is a single sequence from this genus, which typically
causes long branches in SSU rRNA gene phylogenies (Lara et al., 2007) and the node is
unresolved).
●●●●●● Cyphoderiidae de Saedeleer 1934
Scales circular, oval or kidney-shaped, juxtaposed or imbricated; test aperture angled, some
with collar; shape circular in cross-section; in freshwater sediments and plants, supralittoral
sands. Campascus*, Corythionella, Cyphoderia, Messemvriella*, Pseudocorythion,
Schaudinnula*.
●●●●●● Paulinellidae de Saedeller 1934, emend. Adl et al. 2012
Test with self-secreted siliceous reinforcements, or proteinaceous; when present, scales are
elongated, with length perpendicular to aperture. At least two genera (Micropyxidiella and
Ovulinata) with totally organic test without silica scales; in litter and mosses, freshwater
plants, marine sediments and plankton. Micropyxidiella, Ovulinata, Paulinella.
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●●●Metromonadea Cavalier-Smith 2007, emend. Cavalier-Smith 2011
Accepted Article
Nonpseudopodial marine gliding biciliated cells; cytotrophic predator; nonthecate but with
a dense single or double layered surface coat that may extend up cilium; extrusomes highly
elongated. Metromonas, Metopion, Micrometopion, Kiitoksia.
●●●Granofilosea Cavalier-Smith & Bass 2009
With very fine branching or unbranched granuloreticulopodia bearing obvious extrusomes as
the granules at frequent rather regular intervals, or with radiating, sometimes branched,
axopodia with similar granules; pseudopodia supported by internal microtubules and typically
appressed to the sub- stratum during feeding, in a semi-immobile state; in most species,
pseudopodia do not anastomose; some with biciliated swimming or gliding stage.
Incertae sedis Granofilosea*: Apogromia, Kibisidytes, Leucodictyon, Limnofila, Mesofila,
Microcometes, Microgromia, Nanofila, Reticulamoeba, and probably Belaria, Ditrema,
Heliomorpha (=Dimorpha), and Paralieberkuehnia.
●●●● Massisteridae Cavalier-Smith 1993 (R)
Massisteria, Minimassisteria.
●●●●Clathrulinidae Claus 1874 [Desmothoracida Hertwig and Lesser 1874]
Extracellular capsule or lorica attached to substrate, or cell free-floating; sometimes mucous
sheath aroud cell; pseudopodia branching capable of anastomosis, and with microtubules,
but not organized in any recognizable pattern; kinetocyst extrusomes on pseudopodia;
tubular mitochondrial cristae; biciliated and amoeboid stages; can be colonial; cysts.
Actinosphaeridium, Cienkowskya*, Clathrulina, Hedriocystis, Penardiophrys.
Incertae sedis Clathrulinidae: Servetia.
●●●Chlorarachnea Hibberd & Norris, 1984
Amoeboid with plastids of secondary origin; plastid containing chlorophylls a and b,
associated with a nucleomorph and surrounded by four membranes in total; usually
reticulate pseudopodia with extrusomes; cell bodies often anastomosing; with a biciliated
dispersal stage. Also includes minute marine picoplanktonic bacterivorous cell with single
long acronematic smooth cilium (Minorisa Del Campo, 2013). Amorphochlora, Bigelowiella,
Chlorarachnion, Cryptochlora; Gymnochlora, Lotharella, Minorisa, Partenskyella, Viridiuvalis.
●●Endomyxa Cavalier-Smith 2002, emend. Bass & Berney in Adl et al. 2019 (R)
This clade has varied somewhat in definition and composition but retains a core group of
Rhizaria robustly distinct from Cercozoa and Retaria. Retaria as defined here is either a
sister clade to Endomyxa, or branches within it. Numerous environmental lineages exist
without morphological data. It is defined here as the least inclusive clade containing the last
common ancestor of Vampyrellida, Phytomyxea, Filoreta, Gromia, Ascetosporea, and all its
descendants.
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●●●Vampyrellida West 1901, emend. Hess et al. 2012
Accepted Article
Exclusively heterotrophic, naked, phagotrophic amoeboid organisms; life cycle includes
amoeboid, free-moving trophozoites alternating with an obligatory digestive cyst, in which
cell division usually take place; several taxa can fuse to form plasmodia and reach
considerable sizes; sexual processes unknown; cytoplasm often differentiated into a finely
granular, sometimes highly vacuolated part and structure-less hyaloplasm, the latter often
surrounding the main cell body, but at least constituting the pseudopodia; free-living in
freshwater, soil, or marine environments. Arachnula, Gobiella, Hyalodiscus, Lateromyxa,
Leptophrys, Platyreta, Thalassomyxa, Theratromyxa, Vampyrella, Vernalophrys, Penardia.
●●●Phytomyxea Engler & Prantl, 1897
Amoeboid or plasmodial feeding cells producing biciliate or tetraciliate cells; some with
specialized solid extrusome—“satchel”—for penetrating host cells; with distinctive cruciform
mitotic profile due to elongate persistent nucleolus lying orthogonal to metaphase plate;
parasites or parasitoids of plants or stramenopiles.
●●●● Plasmodiophorida Cook, 1928. Plasmodiophora, Polymyxa, Woronina, Ligniera,
Sorosphaerula, Spongospora.
●●●● Phagomyxida Cavalier-Smith 1993 (R)
Phagomyxa, Maullinia.
●●●Filoreta Bass & Cavalier-Smith, 2009
Aciliate, naked, free-living, mainly bacterivorous reticulose amoebae that form extensive
multinucleate open-mesh nets. Filoreta.
●●●Gromia Dujardin, 1835
Test of organic material, brown and opaque, with single aperture; filopodia branched, with
non-granular cytoplasm; filopodia anastomose but not into a reticulum; multinucleate; tubular
mitochondrial cristae; ciliated dispersal cells or gametes. Gromia
●●●Ascetosporea Sprague 1979, emend. Cavalier-Smith 2009
Complex spore structure - one or more cells, with one or more sporoplasms, without polar
capsules or filaments; parasites of invertebrates.
●●●●Haplosporida Caullery & Mesnil, 1899
Distinctive lidded spores; during spore development, spore wall produced inside of outer
membrane of invaginated area; without polar capsules or polar filaments; spore anterior
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Accepted Article
opening covered by hinged operculum; intranuclear spindle, a rudiment of which persists in
interphase nuclei (“kernstab”); tubular mitochondrial cristae; plasmodial endoparasites of
marine and sometimes freshwater animals. Bonamia, Haplosporidium, Minchinia,
Urosporidium.
●●●● Microcytida Hartikainen et al. 2013
Microcell parasites within the genera Mikrocytos Farley et al., 1988 and Paramikrocytos
Hartikainen et al. 2013 infecting aquatic invertebrates. Plasmodial (Paramikrocytos) and
unicellular (Mikrocytos and Paramikrocytos) stages. Phylogenetically highly distinct, and
defined as all lineages branching in a clade including Mikrocytos mackini and
Paramikrocytos canceri. Spores unknown, in contrast to most haplosporids. Mikrocytos,
Paramikrocytos
●●●● Paramyxida Chatton, 1911
Spore bicellular, consisting of a parietal cell and one sporoplasm; without orifice. Marteilia,
Paramyxa, Paramarteilia, Marteilioides, Eomarteilia
●●●● Claustrosporidium Larsson, 1987
Uninucleate sporoplasm with haplosporosomes; spore wall with no orifice and formed on
sporoplasm surface, not intracellular; spores without operculum and lingula.
●●●● Paradiniidae Schiller 1935
Unlike other ascestosporans, have a biciliated dispersal phase with two unequal cilia; marine
parasites of Crustacea with multinucleate plasmodial trophic phase. Paradinium, “spot prawn
parasite”
●● Retaria Cavalier-Smith 2002 (R)
Mainly marine heterotrophs, with reticulopodia or axopodia, and usually having various types
of skeleton.
●●● Foraminifera d’Orbigny 1826
Filopodia with granular cytoplasm, forming branching and anastomosing network
(reticulopodia); bidirectional rapid (10 mm/s) transport of intracellular granules and plasma
membrane domains; tubular mitochondrial cristae; fuzzy-coated organelle of unknown
function in reticulopodia; polymorphic assemblies of tubulin as (i) conventional microtubules
singly or in loosely organized bundles, (ii) single helical filaments, and (iii) helical filaments
packed into paracrystalline arrays; majority of forms possess a test, which can be organic
walled, agglutinated, or calcareous; unusual characteristic beta-tubulin; wall structure in
naked and single-chambered forms quite variable for “naked” athalamids, such as
Reticulomyxa, thicker veins vested with an amorphous, mucoid material; for thecate (soft-
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Accepted Article
walled) species, such as members of the genus Allogromia, proteinaceous with little or no
foreign material; for agglutinated species, foreign materials bound with an amorphous or
fibrous organic matrix; for multi-chambered (polythalamous) forms, walls containing
agglutinated material or mineralized with calcite, aragonite, or silica; life cycle often
comprising an alternation of asexually reproducing agamont and sexually reproducing
gamont.
Incertae sedis Foraminfera: Lagenida Delage and Hérouard 1896
Incertae sedis Foraminfera: Heterogromia, Komokiacea*.
●●●● Monothalamea Pawlowski et al. 2013
Single chamber (monothalamous) test with an organic or agglutinated wall; the group
comprises all genera traditionally included into the Allogromiida, Astrorhizida, and the
Xenophyophorea; although considered marine there are 4-5 clades of fresh water species ;
the diversity of this mainly unfossilized group is poorly known and has been largely
overlooked in micropaleontologically-oriented foraminiferal research. Allogromia,
Astrammina, Crithionina, Notodendrodes, Psammophaga, Bathysiphon Reticulomyxa.
●●●● Tubothalamea Pawlowski et al. 2012
Bi- or multi-chambered test with tubular chambers at least in the juvenile stage; wall
agglutinated or calcareous; in ancestral forms the test is composed of a spherical proloculus
followed by a planispirally enrolled tubular chamber in Ammodiscus, Spirillina, and
Cornuspira; more derived forms have multi-chambered tests; the highly diverse group of
extinct large Fusulinida probably also belong to this clade.
●●●●● Miliolida Delage & Hérouard 1896
Test bi- or multi-chambered, wall agglutinated or calcareous of high-magnesium calcite with
randomly oriented crystals refracting light in all directions and resulting in a porcelaneous
appearance of the test; generally imperforate walls; chambers tubular or elongate, often
planispirally coiled; some with complex internal structures adapted to host algal
endosymbionts. Alveolina, Cornuspira, Miliammina, Pyrgo, Quinqueloculina, Sorites.
●●●●● Spirillinida Hohenegger & Piller 1975
Test composed of proloculus followed by an enrolled tubular chamber, undivided or with few
chambers per whorl; wall of low-magnesium calcite, optically a single crystal. Patellina,
Spirillina.
●●●●● Ammodiscidae Reuss 1862
Test composed of globular proloculus followed by a coiled undivided tubular chamber with
terminal aperture; wall agglutinated. Ammodiscus, Glomospira.
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●●●● Globothalamea Pawlowski et al. 2012
Accepted Article
Test multi-chambered, typically trochospirally enrolled but may be triserial, biserial or
uniserial; chambers globular or crescent-shaped in early stage; wall agglutinated or
calcareous.
●●●●● Rotaliida Delage & Hérouard 1896
Wall of low-magnesium calcite, optically radial, bilamellar, perforate; some with internal canal
system. Subdivisions proposed below.
●●●●●● Planorbulinidae Schwager 1877 (Planorbulinella, Hyalinea)
●●●●●● Discorboidea Ehrenberg 1838
●●●●●●● Discorbidae Ehrenberg 1838 (Discorbis)
●●●●●●● Rosalinidae Reiss, 1963) (Rupertina, Discanomalina, “Rosalina”, Gavelinopsis,
Planorbulina)
●●●●●● Rotalioidea Ehrenberg 1839 emend. Pawlowski 2013
●●●●●●● Elphidiidae Galloway 1933 (Elphidium)
●●●●●●● Ammoniidae Saidova, 1981 (Ammonia)
●●●●●●● Elphidiellidae Holzmann & Pawlowski 2017 (Elphidiella)
●●●●●●● Haynesinidae Mikhalevich 2013 (Haynesina, Aubignyna)
●●●●●●●Incertae sedis Cribroelphidium, “Elphidium”, Protelphidium
●●●●●● Glabratelloidea (Loeblich & Tappan, 1964)
●●●●●●● Rotaliellidae Loeblich & Tappan, 1964 (Rotaliella, Rossyatella)
●●●●●●● Buliminoididae Seiglie, 1970 (Buliminoides)
●●●●●●● Glabratellidae Loeblich & Tappan, 1964 (Glabratella, Glabratellina,
Angulodiscorbis, Planoglabratella)
●●●●●● Calcarinoidea (Schwager, 1876)
●●●●●●● Calcarinidae Schwager, 1876 (Neorotalia, Baculogypsina, Baculogypsinoides,
Schlumbergerella, Pararotalia)
●●●●●● Nummulitoidea de Blainville, 1827
●●●●●●● Nummulitidae de Blainville, 1827 (Nummulites, Operculinella, Cycloclypeus,
Heterostegina, Operculina, Planoperculina, Planostegina)
●●●●●● Serioidea (Holzmann & Pawlowski 2017)
●●●●●●● Uvigerinidae Haeckel, 1894 (Uvigerina, Rectuvigerina, Trifarina)
●●●●●●● Bolivinitidae Glaessner, 1937 (Bolivina, Brizalina, Saidovina)
This article is protected by copyright. All rights reserved.
●●●●●●● Cassidulinidae d’Orbigny, 1839 (Globocassidulina, Cassidulinoides,
Evolvocassidulina, Islandiella, Ehrenbergina)
Accepted Article
●●●●●●● Sphaeroidinidae Cushman, 1927 (Sphaeroidina)
●●●●●●● Globobuliminidae Cushman, 1927 (Globobulimina)
Incertae sedis Rotaliida:
●●●●●●● Nonionidae Schultze, 1854 (Nonion, Nonionella, Nonionellina, Nonionoides)
●●●●●●● Virgulinellidae Loeblich & Tappan, 1984 (Virgulinella)
●●●●●●● Buliminidae Jones, 1875 (Bulimina)
●●●●●●● Epistominellidae Holzmann & Pawlowski 2017 (Epistominella)
●●●●●●● Stainforthiidae Reiss, 1963 (Stainforthia, Gallitellia)
●●●●●●● Cibicididae Cushman, 1927 (Cibicides, Cibicidoides, Heterolepa)
●●●●●●● Chilostomellidae Brady, 1881 (Chilostomella)
●●●●●●● Pullenidae Schwager, 1877 (Pullenia)
●●●●●●● Nuttalidae Saidova, 1981 (Nuttalides)
●●●●●●● Discorbinellidae Sigal, 1952 (Discorbinella, Hanzawaia)
●●●●●●● Astrononionidae Cushman & Edwards, 1937 (Astrononion)
●●●●●●● Oridorsalidae Loeblich & Tappan, 1984 (Oridorsalis)
●●●●●●● Melonidae Holzmann & Pawlowski 2017 (Melonis)
●●●●●●● Cymbaloporidae Cushman 1927 (Cymbaloporella)
●●●●●●● Rubratelliidae Holzmann & Pawlowski 2017 (Rubratella)
●●●●●●●Murrayinelliidae Holzmann & Pawlowski 2017 (Murrayinella)
●●●●● Globigerinida Delage & Hérouard 1896 (P)
Wall of low-magnesium calcite, bilamellar, perforate; surface may be covered with fine,
elongate spines; planktonic mode of life. Globigerina, Globigerinoides, Globorotalia,
Orbulina.
●●●●● Robertinida Loeblich & Tappan 1984
Wall of hyaline, perforate, optical radial aragonite; chambers with internal partition.
Hoeglundina, Robertina, Robertinoides.
●●●●● Textulariida Delage & Hérouard 1896 (P)
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Accepted Article
Wall agglutinated, with foreign particles attached to organic lining or cemented by lowmagnesium calcite. Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
●●●●● Carterina Brady 1884 [Carterinida Loeblich & Tappan 1981]
Wall composed of rod-like spicules of low-magnesium calcite held in organic lining;
chambers numerous, trochospirally coiled. Carterina.
●●● Radiolaria Müller 1858, sensu Adl et al., 2005
Cells with distinctive organic, non-living, porous capsular wall surrounding the intracapsulum, which contains the nucleus or nuclei and cytoplasmic organelles; tubularcristae;
axopodia supported by internal microtubules, extending distally through thecapsular wall
pores and connecting to a frothy external layer, the extracapsulum; ex-tracapsulum
containing digestive vacuoles and in some cases algal and/or cyanobacterial symbionts;
skeletons, when present, of amorphous silica (opal) or strontiumsulphate (in Acantharia) and
varying in shape from simple scattered spicules to highly ornate geometric-shaped shells,
within and/or surrounding the central capsule; thesiliceous skeleton is secreted within a
specialized cytoplasmic envelope (cytokalymma) that dynamically determines the shape of
the skeletal matter.
●●●● Acantharea Haeckel 1881, emend. Mikrjukov 2000
Cell surrounded by fibrillar capsule outside of cell membrane; axopodia, spicules, and
amoeboid anastomosing dynamic network of irregular pseudopodia extending from the
capsule; this outer network (ectoplasm) surrounded by fibrillar periplasmic cortex; inner cell
region inside capsule (endoplasm) holding the organelles; axopodia, supported by
microtubular arrays, with kinetocyst extrusomes and with a centroplast-type centrosome at
base of each spicule; 20 radial spicules of strontium sulphate merged at cell centre; spicule
tips attached to contractile myonemes at periplasm; tubular mitochondrial cristae; often with
algal symbionts in endoplasm, and captured prey in ectoplasm network; asexual
reproduction unknown; sexual reproduction involving consecutive mitotic and meiotic
divisions that ultimately release biciliated isogametic cells; only marine isolates known.
●●●●● Chaunocanthida Schewiakoff 1926
Pigmented endoplasm, clears towards periphery; many small nuclei in endoplasm; clear
ectoplasm with periplasmic cortex; sexual reproduction in gamontocyst; small plaques as
lithosomes synthesized in Golgi and forming the gamontocyst wall; litholophus stage prior to
reproduction; hexagonal microtubular arrays in axopodia; contractile matrix at base of
spicules. Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
●●●●● Holocanthida Schewiakoff 1926
Pigmented endoplasm, clears towards periphery; many small nuclei in endoplasm; sexual
reproduction in gamontocyst; with lithosomes forming the gamontocyst wall; dodecagonal
microtubular arrays in axopodia. Acanthochiasma, Acanthocolla, Acanthoplegma.
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●●●●● Symphyacanthida Schewiakoff 1926
Accepted Article
Pigmented endoplasm, clears towards periphery; ectoplasm clear; single large central
nucleus; outer endoplasm with anastomosing pseudopodia; capsule and periplasmic cortex
visible with light microscopy; sexual reproduction in gamontocyst with lithosomes forming the
gamontocyst wall. Amphilithium, Astrolonche, Pseudolithium.
●●●●● Arthracanthida Schewiakoff 1926
Thick capsule clearly demarcates pigmented endoplasm from ectoplasm; axopodia with
hexagonal microtubular arrays; many nuclei in endoplasm; algal symbionts in all known
species, except at reproduction; sexual reproduction without gamontocyst. Acanthometra,
Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis,
Stauracantha.
●●●● Taxopodida Fol 1883
Axopodial pseudopods without kinetocysts (extrusomes), used for motility as oars; axopodial
microtubules originate from depressions in nuclear envelope; microtubules in axoneme
arranged in irregular hexagons; siliceous tangential spicules, with external radial spicules.
Sticholonche, several environmental clades.
●●●● Polycystinea Ehrenberg 1838, emend. Haeckel 1887
Central capsule spherical to ovate with round pores in the capsular wall either distributed
uniformly on the surface of a spherical capsular wall or localized at one pole of an ovate
capsular wall; skeleton either absent or when present, composed of spicules or forming
elaborate geometric-shaped, porous or latticed shells.
●●●●● Spumellaria Ehrenberg 1875, Haeckel 1887, emend. Riedel 1967
Central capsule typically spherical with uniformly distributed round pores in the capsular wall;
skeleton either absent or when present, composed of spicules or forming latticed shells
(spicules single, or multiple and concentrically arranged). Subdivisions not fully resolved.
Actinomma, Didymocyrtis, Euchitonia, Hexacontium, Hexalonche, Hexastylus, Octodendron,
Plegmosphaera, Saturnalis, Spongaster, Spongosphaera.
●●●●● Nassellaria Ehrenberg 1875, emend. Haeckel 1887
Central capsule ovate with pores localized at one pole; skeleton, when present, composed of
a simple tripod, a sagittal ring without tripod or porous helmet-shaped “cephalis” enclosing
the central capsule. Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
●●●●● Collodaria Haeckel 1887
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Accepted Article
Skeleton either absent or when present, composed of scattered spicules within the
extracapsulum; solitary or colonial forms. Acrosphaera, Collosphaera, Collozoum,
Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
●● Aquavolonida Bass & Berney, 2018
Defined as the least inclusive clade containing the last common ancestor of the rhizarian
lineages sharing a unique combination of 18S rRNA sequence signatures consisting of two
complementary substitutions from U-A to G-C and from G-C to C(U)-G(A) in helix 11, one
comple- mentary substitution from A-T to C(T)-G(A) in helix 48, and a specific motif of two
adjacent substitutions (AU instead of YG) in a nonbinding part of the 3° stem of helix 25 and
all their descendants.
●●● Aquavolon Tikhonenkov, Mylnikov, & Bass, 2018
With two smooth subapical heterodynamic cilia; kinetosomes approximately at right angle to
each other and connected by at least one fibril; posterior kinetosome is very long (> 1 µm);
shape slightly flexible, not flattened, with remarkable lateral depression in the middle lateral
point of the cell body; single contractile vacuole and nucleus located anteriorly; several
mitochondria with tubular cristae; rapidly swimming and rarely gliding protist; cytotrophic.
●●Tremula Howe et al. 2011 [=Tremulida Howe et al. 2011] M
Heterotrophic and phagotrophic biciliates with long anterior and posterior cilia; glide on
surfaces by means of both cilia, one pointing forwards and one backwards; without light
microscopically visible theca, scales or cytostome. Molecular phylogenies show it is a sister
clade outside of Aquavonida. Tremula longifila.
● Haptista Cavalier-Smith 2003
Thin microtubule-based appendages (haptonema or axopodia) used for feeding; complex
mineralized (siliceous or calcareous) scales.
●● Haptophyta Hibberd 1976, ex. Edvardsen & Eikrem 2000
Autotrophic, mixotrophic or heterotrophic single cells; some in colonies, or a few filamentous;
motile cells mostly possessing a haptonema, a filiform appendage situated between pair of
cilia; characteristic cell covering of unmineralized and/or mineralized scales; motile cells with
two a generally without appendages, inserted apically or sub-apically; usually 1 or 2
chloroplasts with thylakoids in groups of three and with no girdle lamella; chloroplasts with
immersed or bulging pyrenoid; nucleus usually posterior or central; outer membrane of
nuclear envelope continuous with outer chloroplast membrane; major pigments chlorophylls
a, c1, and c2 with c3 in prymnesiophyceans, fucoxanthin (e.g. 19’ hexanoyloxyfucoxanthin,
19’butanoyloxyfucoxnthin), beta-carotene, diadinoxanthin, and diatoxanthin; chrysolaminarin
often the main storage product; eyespots recorded in a few genera (Pavlova, Diacronema);
haplo-diploid life cycles including heteromorphic alternating stages; motile, ciliated stage
may alternate with nonmotile palmelloid (colonial), single celled or filamentous stages, or
with motile, ciliated stages; sexual reproduction may be common in prymnesiophyceans;
some species ichthyotoxic.
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●●● Pavlovales Green 1976
Accepted Article
Biciliated with unequal cilia inserted subapically or laterally; body scales absent; shorter
cilium may have a swelling with densely staining projections on the side adjacent to the cell,
the longer cilium may have thin hairs or scales; haptonema short, tapered and noncoiling;
single chloroplast, sometimes with an eyespot beneath the short cilium. Diacronema,
Exanthemachrysis, Pavlova, Rebecca.
●●● Prymnesiophyceae Hibberd 1976
Unicellular or colonial, mostly ciliated cells with mineralized and/or unmineralized scales
covering the cells; some species exhibit two stages in the life cycle, with a diploid non-motile
or motile stage alternating with a ciliated haploid stage; haptonema may be long and coiling
to short and noncoiling; cilia of equal or sub-equal lengths inserted apically or subapically.
●●●● Prymnesiales Papenfuss 1955, emend. Edvardsen & Eikrem 2000
Motile or nonmotile cells, usually with two cilia and a coiling or flexible haptonema; covering
of organic, sometimes spiny scales, sometimes absent; some alternate life cycle stages
reported. Chrysochromulina, Chrysocampanula, Dicrateria, Haptolina, Prymnesium,
Pseudohaptolina.
●●●● Phaeocystales Medlin 2000
Motile cells with two cilia and short noncoiling haptonema; one to four chloroplasts per cell;
the cell covered with scales of two sizes; life cycle may consist of nonmotile and motile
stages; nonmotile cells colonial and embedded in gelatinous material. Phaeocystis.
●●●● Isochrysidales Pascher 1910, emend. Edvardsen & Eikrem 2000
Motile or nonmotile cells; haptonema rudimentary or absent; motile cells covered with small
organic scales; nonmotile cells usually covered with coccoliths. Emiliania, Gephyrocapsa,
Isochrysis, Ruttnera, Tisochrysis.
●●●● Coccolithales Schwarz 1932, emend. Edvardsen & Eikrem 2000
Cells with calcified organic scales during some stage of the life cycle; single or alternating
stages in the life cycle; haptonema short or highly reduced; some species lack chloroplasts.
Balaniger, Calciosolenia, Coccolithus, Hymenomonas, Chrysotila, Wigwamma.
●● Centroplasthelida Febvre-Chevalier & Febvre 1984 35 [Centrohelea Kühn 1926 sensu
Cavalier-Smith in Yabuki et al. 2012; Centroheliozoa Dürrschmidt & Patterson 1987]
Without cilium; naked or covered with mucous, usually with organic or mineralized elements
(scales) embedded in it; axopodia supported by microtubules forming hexagon-related
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Accepted Article
pattern; ball-and-cone structure containing kinetocyst extrusomes along axopodia;
centrosome as trilaminar disc with fibrous electron-dense cortex, flat mitochondrial cristae.
35
Centrohelida Kühn was introduced to include both centrohelids and gymnosphaerids;
Febvre-Chavalier and Febvre (1984) were the first who recognized and named this taxon.
Incertae sedis Centroplasthelida: Spiculophryidae 36 Shishkin & Zlatogursky 2018 (M)
Centrohelids typically lacking silica scales but with numerous thin, pointed organic spicules
tapering towards acute apices; expansions (but sometimes noticeably short) in
panacanthocystid increase regions (PINs) 2, 6, 7, 10, 12 of SSU rRNA gene present.
Spiculophrys.
Incertae sedis Centroplasthelida: Parasphaerastrum.
36
One more genus name – Heteroraphidiophrys, mentioned in Mikrjukov (2002) was never
formally introduced and needs to be avoided; the organisms designated by it need to be reisolated, carefully studied and provided with formal description.
●●● Pterocystida Cavalier-Smith and von der Heyden 2007 emend. Shishkin and
Zlatogursky 2018 (R)
The least inclusive clade, containing Pterocystis devonica, Raphidiophrys heterophryoidea
and Choanocystis curvata but not Acanthocystis nichollsi.
●●●● Raphidista Shishkin & Zlatogursky 2018
Typically with unconsolidated layer of flattened siliceous plate scales, which consist of upper
and lower plates, connected by internal septae or with two types of scales: plate scales of
inner layer are flattened, simple in structure, usually ornamented with axial rib, outer spine
scales with cylindrical shaft attached on the heart-shaped base plate, which provides
bilateral symmetry.
●●●●● Choanocystidae Cavalier-Smith & von der Heyden 2007 (M)
Two contrasting types of siliceous scales, oval or bilobed tangential plate scales (margin not
hollow and inrolled) forming the inner layer and outer bipartite spine scales consisting of a
vertical stalk, sometimes curved or branched but lacking lateral wings, emanating from near
a strong indentation on one side of a flat horizontal base. Choanocystis.
●●●●● Raphidiophryidae Febvre -Chevalier & Febvre 1984 emend. Shishkin & Zlatogursky
2018 (M)
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Accepted Article
Typically with unconsolidated layer of flattened siliceous plate scales, which consist of upper
and lower plates, connected by internal septae; scales usually surrounded by a hollow
margin; organic spicules may occur. Raphidiophrys.
●●●● Pterista Shishkin & Zlatogursky 2018
Two contrasting types of siliceous scales: tangential inner plate scales usually oval (margin
not hollow and inrolled but sometimes thickened) sometimes slightly (rarely markedly)
narrower at one end, sometimes slightly indented on one side (rarely slightly on both) but
never distinctly bilobed; outer bipartite spine scales typically consisting of leaf-like blade with
an axial rib, usually in various degree extended apically as a projecting needle-like point
(blunt or pointed, but unbranched) and with lateral wings; spine scale base may be rounded
or truncated and may be in the same plane as the blade or somewhat bent away from it
(Pterocystis) or markedly extended as a distinct shelf or basal disc (sometimes called basal
wing) orthogonal to the main blade (Raineriophrys); species with a pronounced basal wing
may have lateral wings that are greatly reduced or absent; siliceous scales may be
secondarily missing with or without replacing it with organic spicules.
●●●●● Oxnerellidae Cavalier-Smith & Chao 2012 (M)
Naked, without scales, spicules or mucus coat; axopodia either radiating from the
centrosome in all directions or appressed to substratum; extrusomes conspicuous.
Oxnerella.
●●●●● Pterocystidae Cavalier-Smith & von der Heyden 2007
With two contrasting layers of siliceous scales: inner plate scales and outer bipartite leaf-like
spine scales; if siliceous scales secondarily missing (Chlamydaster) cell has a distinct
mucous coat. Pterocystis, Raineriophrys, Chlamydaster; Pseudoraphidiophrys;
Pseudoraphidocystis 37.
37
Genera Pseudoraphidiophrys, Pseudoraphidocystis, Pterocystis, Raineriophrys altogether
obviously unify a group of closely related organisms which need a careful taxonomic revision
involving morphological and molecular data. The genus name Echinocystis sometimes used
instead of Raineriophrys is multiply preoccupied and should be avoided.
●●●●● Heterophryidae Poche 1913 emend. Cavalier-Smith & von der Heyden 2007
Lacking siliceous scales but with numerous thin pointed organic spicules tapering towards
acute apices; SSU rRNA gene short, lacking expansions in panacanthocystid increase
regions 38 (PINs) 1, 2, 6, 7, 9-12, 14 found in Marophryidae. Heterophrys, Sphaerastrum 39.
38
For more detailed description of the location and nomenclature of SSU rRNA gene
expansions in centrohelids see Shishkin et al., 2018.
39
Separation of this genus from Heterophrys requires further justification.
This article is protected by copyright. All rights reserved.
●●● Panacanthocystida Shishkin & Zlatogursky 2018
Accepted Article
Usually with siliceous scales or with organic spicules: scale-bearing species with both inner
plate scales and outer scales of different morphology or only plate scales with a hollow
inrolled margin; outer scales may be of different types based on the plate scale morphology
or radially symmetrical spine scales, present in one of two forms: funnel-shaped, or needlelike with a radially symmetrical base. Gene of SSU rRNA usually has at least five expansions
in panacanthocystid increase regions (PINs). The most inclusive clade containing
Acanthocystis nichollsi, Marophrys marina and Yogsothoth knorrus but not a Pterocystis
devonica.
●●●● Yogsothothidae Shishkin & Zlatogursky 2018 (M)
Typically with two types of siliceous scales: scales of inner layer are flattened, simple in
structure, usually ornamented with axial rib, outer scales may be of different types but more
similar to plate, than to spine scales. Gene of SSU rRNA usually having expansions only in
panacanthocystid increase regions (PINs) 2, 6, 7, 10, 12. Yogsothoth.
●Cryptista 40 Adl et al., 2018 [Cavalier-Smith 1989, 2018] (R)
This is a node-based definition for the clade stemming from the most recent common
ancestor of Cryptomonas, Goniomonas, Kathablepharis, and Palpitomonas. The name does
not apply if any of the following fall within the specified clade: Glaucocystis nostochinearum,
Chlamydomonas reinhardtii, Telonema subtilis, Emiliana huxleyi.
40
Cryptista has been used since 1989 with a variety of definitions, and varying in
composition and rank. Unless the authority and date is specified, it is uncertain which
meaning, or rank, of Cryptista is meant. However, the term has uses in phylogenetic trees
and it has been somewhat adopted in the literature, although without precision over its
meaning. For nomenclatural stability Cryptista is defined here according to its latest use in
phylogenetic trees.
●●Palpitomonas Yabuki & Ishida 2010 (M)
Marine isolate, free-living heterotrophic, heterokont biciliate, with unilateral bipartite
mastigonemes on anterior cilium; cilia emerge on left side with anterior cilium vigorous and
trailing posterior cilium; when swimming, in slow gyromotion; one cilium can adhere to
substratum; double-layered MLS-like structure on one ciliary root; vacuolated cytoplasm;
phagotrophic on bacteria; without ejectisomes; flat mitochondrial cristae. Palpitomonas bilix.
●● Cryptophyceae Pascher 1913, emend. Schoenichen 1925, emend. Adl et al. 2012
[Cryptophyta Silva 1962; Cryptophyta Cavalier-Smith 1986]
Autotrophic, mixotrophic or heterotrophic with ejectisomes (trichocysts); mitochondrial cristae
flat tubules; two cilia emerging subapically or dorsally from right side of an anterior
depression (vestibulum); longitudinal grooves (furrows) and/or tubular channels (gullets) or a
combination of both, extending posteriorly from the vestibublum on the ventral side;
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Accepted Article
gullet/furrow complexes lined with large ejectisomes; with or without plastid nucleomorph
complex; chloroplasts when present contain chlorophylls a and c2 and phycobiliproteins,
located in thylakoid lumen; chloroplast covering comprised of inner and superficial periplast
components (IPC, SPC, respectively); includes heterotrophic species formerly known as
Chilomonas and some genera diplomorphic such as Cryptomonas and Proteomonas.
Incertae sedis Cryptophyceae: Bjornbergiella.
●●● Cryptomonadales Pascher 1913
Chloroplasts or leucoplasts present. Chroomonas, Cryptomonas, Falcomonas, Geminigera,
Guillardia, Hanusia, Hemiselmis, Plagioselmis, Proteomonas, Rhinomonas, Rhodomonas,
Storeatula, Teleaulax.
●●● Cyathomonadacea Pringsheim 1944
Chloroplasts absent. Goniomonas (previously Cyathomonas), Hemiarma.
●●● Kathablepharidacea Skuja 1939 [Kathablepharidae Vørs 1992]
Free-swimming cells with two heterodynamic cilia inserting subapically/medially; cell
membrane thickened by lamellar sheath; ingest eukaryotic prey through an apical cytostome
supported by bands of longitudinal microtubules; extrusomes are large coiled-ribbons
arrayed near kinetosomes; tubular mitochondrial cristae; plastids not observed. Hatena,
Kathablepharis, Leucocryptos, Platychilomonas, Roombia.
Incertae sedis EUKARYA
Excavates [Excavata Cavalier-Smith 2002, emend. Simpson 2003] (P)
Typically with suspension-feeding groove of the “excavate” type, secondarily lost in many
taxa; feeding groove used for capture and ingestion of small particles from feeding current
generated by a posteriorly directed cilium (F1); right margin and floor of groove are
supported by parts of the R2 microtubular root, usually also supported by microtubular fibres
(B fibre, composite fibre), and the left margin by the R1 microtubular root and C fibre.
Grouping of Metamonada and Discoba and Malawimonads is somewhat controversial,
although recent multigene phylogenies have markedly increased support for monophyly of
Metamonada, and of Discoba, separately. Apomorphy: Suspension-feeding groove,
homologous to that in Jakoba libera. Recent phylogenies indicate Metamonada and Dicoba
probably do not share the same node.
●Metamonada Grassé 1952 emend. Cavalier-Smith 1987
Anaerobic/microaerophilic, either with modified mitochondria that lack cristae, are
nonrespiratory, and lack a genome (e.g., hydrogenosomes or mitosomes), or without
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Accepted Article
mitochondria; mostly ciliated cells, ancestrally with four kinetosomes per kinetid, though a
great variation exists; some free-living, many endobiotic, some parasitic. Apomorphies:
mitochondrial organelles anaerobic, and nonrespiratory (secondarily lost in oxymonads); four
kinetosomes per kinetid (secondarily modified in a number of lineages).
Incertae sedis Metamonada: Barthelona
●●Fornicata Simpson, 2003
With a single kinetid and nucleus, or a pair of kinetids and nuclei; 2-4 kinetosomes and 1-4
cilia per kinetid; usually with a feeding groove or cytopharyngeal tube associated with each
kinetid. Nonrespiratory mitochondria without cristae. Apomorphy: “B fibre” originates against
R2 microtubular root (secondarily lost in Diplomonadida and Caviomonadidae).
●●● “Carpediemonas-like organisms” (Kolisko et al. 2010) (P)
Free-living, marine, anaerobic/microaerophilic ciliated cells with a broad ventral suspensionfeeding groove; biciliated, but with 2-4 kinetosomes; posterior cilium with 1-3 vanes and
beating within the groove; with relatively large cristae-lacking mitochondria; paraphyletic
assemblage within Fornicata in molecular phylogenies. Aduncisulcus, Carpediemonas,
Dysnectes, Ergobibamus, Hicanonectes, Kipferlia.
●●●Diplomonadida Wenyon, 1926
Usually with ‘diplomonad’ cell organization, namely a pair of kinetids and two nuclei; some
taxa (‘enteromonads’) have a single kinetid and nucleus, probably secondarily; each kinetid
usually with four ciliated kinetosomes but sometimes only 2 or 3 ciliated; at least one cilium
per kinetid directed posteriorly, associated with a cytopharyngeal tube or groove, or
stretching as free axoneme axially within the cell; various nonmicrotubular fibres supporting
the nucleus and cytopharyngeal apparatus; free-living or endobiotic, often parasitic.
Apomorphy: diplomonad cell organization.
●●●●Hexamitinae Kent, 1880
With cytopharyngeal tube or groove; with an alternate genetic code – TAR codon for
glutamine; several have a single kinetid and nucleus; endobiotic or secondarily free-living.
Enteromonas, Gyromonas, Hexamita, Spironucleus, Trepomonas, Trigonomonas, Trimitus.
●●●●Giardiinae Kulda & Nohýnková, 1978
Without distinct feeding apparatus; one posteriorly directed cilium from each kinetid (F1)
runs through the length of the cell axially and is intracytoplasmic; with standard genetic code;
all endobiotic and with ‘diplomonad’ cell organization. Brugerolleia, Giardia, Octomitus.
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●●●Retortamonadida Grassé, 1952 (P)
Accepted Article
Single ciliary apparatus with four kinetosomes and either two (Retortamonas) or four
(Chilomastix) emergent cilia; posterior cilium has 2–3 vanes and is associated with a ventral
feeding groove with posterior cytostome; cell surface often underlain by a corset of
microtubules; all endobiotic, except for one free-living species. Apomorphy: “lapel” structure
as an electron-dense sheet supporting the anterior origin of the peripheral microtubules.
Chilomastix, Retortamonas. Note that molecular phylogenetic studies currently do not
support monophyly, perhaps due to misidentification/polyphyly of Retortamonas spp.
●●●Caviomonadidae Cavalier-Smith, 2013
Single ciliary apparatus with two or four kinetosomes and a single cilium without vanes;
ventral groove rudimentary of lost; microtubular cytoskelet simple, consisting from nuclear
fibre and dorsal fan; endobiotic or free-living. Caviomonas, Iotanema.
●●Parabasalia Honigberg, 1973
Cells with a parabasal apparatus – two or more striated parabasal fibres connecting the
Golgi apparatus to the ciliary apparatus; kinetid ancestrally with four cilia/kinetosomes, but
frequently with additional cilia (one to thousands); one kinetosome bears sigmoid fibres that
connect to a pelta–axostyle complex; reduction or loss of the ciliary apparatus in some taxa,
multiplication of complete or parts of the ciliary apparatus in other taxa; closed mitosis with
an external spindle, including a conspicuous microtubular bundle; mitochondria transformed
to acristate hydrogenosomes; mostly endobiotic, some parasitic, some free-living,
presumably secondarily. Apomorphy: parabasal apparatus.
Incertae sedis Parabasalia: Tricercomitus.
●●●Trichomonadida Kirby, 1947
Four–six (4 ancestrally) cilia with one ciliary axoneme supporting a lamelliform undulating
membrane; B-type costa, sometimes absent; comb-like structure and infrakinetosomal body
absent; axostyle usually of “Trichomonas type”; mostly endobiotic, some parasitic,
exceptionally free-living. Cochlosoma, Dientamoeba, Lacusteria, Pentatrichomonas,
Pentatrichomonoides, Pseudotrichomonas, Pseudotrypanosoma, Tetratrichomonas,
Trichomonas, Trichomonoides, Trichomitopsis.
●●●Honigbergiellida Čepička et al., 2010 (P?)
Two–more than 20 (4 ancestrally) cilia with one ciliary axoneme sometimes supporting a
lamelliform undulating membrane; costa, comb-like structure, and infrakinetosomal body
absent; axostyle usually of “Trichomonas type”, sometimes of “Tritrichomonas type”; usually
free-living, some endobiotic. Ditrichomonas, Cthulhu, Cthylla, Hexamastix, Honigbergiella,
Monotrichomonas.
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●●●Hypotrichomonadida Čepička et al., 2010
Accepted Article
Four cilia with one ciliary axoneme supporting a lamelliform undulating membrane; A-type
costa, sometimes absent; comb-like structure present, but no infrakinetosomal body;
biramous parabasal body; axostyle usually of “Trichomonas type”; endobiotic.
Hypotrichomonas, Trichomitus.
●●●Tritrichomonadida Čepička et al., 2010 (P?)
Uninucleate or binucleate; 0–5 (4 ancestrally) cilia; ancestrally with comb-like structure,
suprakinetosomal and infrakinetosomal body; if present, undulating membrane typically of
rail type, sometimes lamelliform; A-type costa, often absent; axostyle of “Tritrichomonas
type” or “Trichomonas type”; endobiotic, some parasitic. Dientamoeba, Histomonas,
Monocercomonas, Parahistomonas, Simplicimonas, Tritrichomonas.
●●●Cristamonadida Brugerolle & Patterson, 2001
Uninucleate to multinucleate; akaryomastigonts in addition to karyomastigonts in some
multinucleate genera; four-to-thousands of cilia per mastigont; kinetosomes, except for
‘privileged kinetosomes’, often discarded during cell division in highly ciliated taxa; some with
cresta and paraxonemal rod associated with the recurrent cilium; axostyle ancestrally of
“Tritrichomonas type’’, secondarily thin or reduced in some; multiple axostyles in
multinuclear forms; parabasal body single or multiple, ellipsoid or rod-shaped, often spiralled
or ramified; endobiotic. Caduceia, Calonympha, Coronympha, Deltotrichonympha,
Devescovina, Foaina, Gigantomonas, Joenia, Joenina, Joenoides, Joenopsis, Kofoidia,
Koruga, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Mixotricha,
Pachyjoenia, Projoenia, Pseudodevescovina, Rhizonympha, Snyderella, Stephanonympha.
●●●Spirotrichonymphida Grassé, 1952
Multiple kinetosomes in counterclockwise spiral rows; cilia retained during cell division with
the ciliary rows dividing between daughter cells; axostyle single of “Tritrichomonas type”, or
multiple in thin bands, or reduced; endobiotic. Holomastigotes, Holomastigotoides,
Microjoenia, Micromastigotes, Rostronympha, Spiromastigotes, Spironympha,
Spirotrichonympha, Spirotrichonymphella, Uteronympha.
●●●Lophomonadida Light, 1927
Multiple kinetosomes in a single kinetid arranged in an ear-shaped row partially encircling
the nucleus; single thin axostyle; endobiotic. Lophomonas.
●●● Trichonymphida Poche, 1913
Bilaterally or tetraradially symmetrical, with anterior rostrum divided into two hemirostra;
each hemirostrum bears one or two ciliary areas with hundreds to thousands of cilia; cilia
usually retained during cell division; one hemirostrum goes to each daughter cell; numerous
parabasal fibres originate from two or four parabasal plates that form a rostral tube in some;
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Accepted Article
numerous thin axostyles do not protrude outside the cell; endobiotic. Barbulanympha,
Eucomonympha, Hoplonympha, Leptospironympha, Macrospironympha,
Pseudotrichonympha, Rhynchonympha, Spirotrichosoma, Staurojoenina, Teranympha,
Trichonympha, Urinympha.
●●Preaxostyla Simpson 2003
Heterotrophic unicells with 4 cilia and kinetosomes per kinetid; nonrespiratory mitochondria
without cristae or absent. Apomorphy: “I fibre” associated with R2 root has ‘preaxostylar’
substructure – latticework paracrystalline layer of ‘double-cross’ thickness with a single, fine
outer layer.
●●●Oxymonadida Grassé 1952
Single kinetid (occasionally multiple kinetids) consisting of two pairs of ciliated kinetosomes
distantly separated by a preaxostyle (microtubular root R2 and paracrystalline I fibre), from
which arises a microtubular axostyle; axostyle consists of parallel rows of microtubules and
is contractile in some taxa; microtubular pelta present in some genera; mitochondrion either
absent or non-recognised, gut endosymbionts, mostly in lower termites and Cryptocercus,
many taxa attach to gut wall using an anterior holdfast; closed mitosis with internal spindle.
Apomorphy: Absence of ventral groove. Kinetosomes grouped in two pairs. Axostyle formed
by parallel rows of microtubules, (not homologous to that of Parabasalia). Absence of
recognisable mitochondrion. Barroella, Blattamonas, Brachymonas, Dinenympha,
Microrhopalodina, Monocercomonoides, Notila, Opisthomitus, Oxymonas, Paranotila,
Polymastix, Pyrsonympha, Sauromonas, Saccinobaculus, Streblomastix, Tubulimonoides.
●●●Trimastigidae Saville Kent, 1880-1882
Free-living excavate ciliates bearing four cilia stretched roughly in the anterior, right, left, and
posterior directions; a broad ventral feeding groove in which beats the posteriorly-directed
cilium; posterior cilium with two broad vanes without thickened vane margins, no
conspicuous lateral cytopharynx; nonrespiratory mitochondria without cristae. Marine and
freshwater. Trimastix.
●●●Paratrimastigidae Zhang et al. 2015
Similar to Trimastigidae but with thickened vane margins on posterior cilium; lateral
cytopharynx may be present; freshwater species only. Paratrimastix.
●Discoba Simpson in Hampl et al., 2009 (R)
A grouping robustly recovered in multi-gene phylogenetic analyses, containing
Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida; ancestrally biciliate. Nodebased definition: the clade stemming from the most recent common ancestor of Jakoba
libera, Andalucia godoyi, Euglena gracilis, Naegleria gruberi, and Tsukubamonas globosa.
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●●Jakobida Cavalier-Smith, 1993
Accepted Article
With two cilia at the head of a broad ventral feeding groove, in which beats the posterior
cilium; posterior cilium with a single dorsal vane that is distinctive among excavates but
possibly plesiomorphic; free-living.
●●●Andalucina Cavalier-Smith, 2013
Free-swimming cells, attaching temporarily to surfaces; aerobic with tubular mitochondrial
cristae or anaerobic with acristate mitochondria. With a G:C base pair within the base of the
stem of ‘‘helix 27’’ of the 18S rRNA molecule (positions 1050 and 1085 in the Andalucia
incarcerata 18S rRNA gene sequence AY117419)..
●●●●Andaluciidae Cavalier-Smith, 2013
Aerobic, mitochondria cristate. Andalucia.
●●●●Stygiellidae Pánek et al. 2016
Anaerobic, mitochondria acristate. Stygiella, Velundella.
●●●Histionina Cavalier-Smith 2013
Free-swimming or sessile cells, some genera with lorica; aerobes with flat mitochondrial
cristae. Without the Andalucina-specific G:C base pair within the base of the stem of ‘‘helix
27’’ of the 18S rRNA molecule. Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonas
nomen nudum.
●●Tsukubamonadida Yabuki et al., 2011 (M)
Rounded biciliate cell, with four kinetosomes per kinetid; aerobic; consumes prey through
ventral groove; dyctiosomes and ciliary vanes absent. Tsukubamonas.
●●Heterolobosea Page & Blanton 1985
Typically with ciliated and amoeboid phases, though many species lack the ciliated phase,
while some others lack the amoeboid phase; rarely amoeboid when ciliated; amoebae often
with eruptive pseudopodia; ciliated cells usually with two or four cilia (rarely uni- or
multiciliate), sometimes nonfeeding; if capable of feeding usually use a groove-like
cytostome; closed mitosis with internal spindle; mitochondrial cristae flattened, often
discoidal, mitochondria sometimes acristate; discrete dictyosomes not observed; ciliary
vanes usually absent. Apomorphy: complex life cycle containing amoeba, ciliate, and cyst.
●●●Pharyngomonada Cavalier-Smith 2008
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Accepted Article
Amoebae usually flabellate or ovoid, eruptive movement rare; with four cilia in side-by-side
obtuse pairs; feeding using a large groove and cytopharynx; with amoeboid phase; lack helix
17-1 region in SSU rRNA that is typical of Tetramitia. Pharyngomonas.
●●●Tetramitia Cavalier-Smith, 1993
Amoebae usually with cylindrical, eruptive pseudopodia; swimming form usually with four
cilia or two per kinetid. Apomorphy: distinct helix 17-1 in the SSU rRNA molecule.
●●●●Selenaionidae Hanousková et al. 2018
Amoeboid or ciliated; when present with two cilia per kinetid, with orthogonally arranged
kinetosomes; finger-like projection on the proximal part of the recurrent cilium; nucleus with
parietal nucleoli. Dactylomonas, Selenaion.
●●●●Neovahlkampfiidae Hanousková et al. 2018
Amoebae; nucleus with central nucleolus. Neovahlkampfia.
●●●●Eutetramitia Hanousková et al. 2018
Amoebae or ciliated; when present usually with four cilia or two per kinetid, with parallel
kinetosomes, although Stephanopogon has numerous monokinetids, Creneis has up to 14
cilia emerging from 2-3 places; nucleus with central or parietal nucleoli.
●●●●●Vahlkampfiidae Jollos 1917 (P)
Ciliated-amoebae or amoeboid without cilium; quadriciliate or biciliate; nucleolus persists
through mitosis; single nucleus Fumarolamoeba, Heteroamoeba, Naegleria,
Neovahlkampfia, Paravahlkampfia, Tetramitus, Vahlkampfia, Willaertia.
●●●●●Gruberellidae Page & Blanton 1985
Locomotion amoeboid or swimming with cilia; nucleolus fragments during mitosis;
uninucleate or multinucleate; ciliated form observed in unidentified species of
Stachyamoeba. Gruberella, Stachyamoeba.
●●●●●Acrasidae Poche, 1913
Amoebae of some species aggregate to form fruiting bodies; nucleus may or may not
fragment. Apomorphy: Formation of fruiting bodies. Acrasis, Allovahlkampfia, Pocheina.
●●●●●Percolomonadidae Cavalier-Smith, 2008
Swimming cells with four cilia; without amoeboid from; aerobic. Percolomonas.
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●●●●●Psalteriomonadidae Cavalier-Smith, 1993
Accepted Article
Amoeboid or ciliated-amoebae; when ciliated, with 4 cilia; anaerobic. Harpagon,
Psalteriomonas, Monopylocystis, Pseudoharpagon, Sawyeria.
●●●●●Stephanopogonidae Corliss, 1961
Always with multiple cilia; aerobic. Stephanopogon.
●●●●●Creneidae Pánek, et al. 2014 (M)
Amoeboid with a single cilium or multiciliate; anaerobic with acristate mitochondria. Creneis.
●●●●●Tulamoebidae Kirby et al. 2015
Biciliate, locomotion as ciliated amoeba or swimming ciliate; with elongate ingestion
apparatus opening slightly posterior to the ciliary insertion; halophilic or very halotolerant.
Pleurostomum, Tulamoeba.
●● Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997
Cells with two cilia, occasionally one, rarely more, inserted into an apical/subapical ciliary
pocket; with rare exceptions, emergent cilia with heteromorphic paraxonemal rods; usually
with tubular feeding apparatus associated with ciliary apparatus; basic ciliary apparatus
pattern consisting of two functional kinetosomes and three asymmetrically arranged
microtubular roots; single mitochondrion mostly with discoidal cristae. Apomorphy:
heteromorphic paraxonemal rods, tubular/whorled in anterior cilium F2 and a parallel lattice
in posterior cilium F1.
●●● Euglenida Butschli 1884, emend. Simpson 1997
With a pellicle of proteinaceous strips, fused in some taxa; when unfused and with > ~20
strips capable of active distortion (metaboly); where known, paramylon is the carbohydrate
store. Apomorphy: Pellicle of protein strips.
●●●● Heteronematina Leedale 1967 (P) 34
With ingestion apparatus capable of phagotrophy; lacking plastids; most glide on surfaces on
one or both cilia; a paraphyletic assemblage from which Euglenophyceae and Aphagea are
descended. Anisonema, Atraktomonas, Biundula, Calycimonas, Decastava, Dolium,
Dinema, Dylakosoma, Entosiphon, Heteronema, Jenningsia, Keelungia, Lentomonas,
Neometanema, Notosolenus, Pentamonas, Peranema, Peranemopsis, Petalomonas,
Ploeotia, Scytomonas, Serpenomonas, Sphenomonas, Teloprocta, Tropidoscyphus,
Urceolus.
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34
Accepted Article
Presently, there is no phylogenetic taxonomy for phagotrophic euglenids as a whole.
Traditional systems based on, for example, the presence or absence of conspicuous feeding
apparatuses, are artificial. Some possibly monophyletic taxa have been proposed that would
cover restricted subsets of the phagotrophic euglenids: for example, the Ploeotiida, including
Ploeotia, Entosiphon, Lentomonas, and presumably Keelungia; and the Petalomonadida,
including Petalomonas, Notosolenus, and Calycimonas, and presumably also taxa such as
Sphenomonas. The limited taxon sampling for molecular sequence data is a significant
impediment, especially as many traditional genera are probably polyphyletic.
●●●● Aphagea Cavalier-Smith, 1993, emend. Busse & Preisfeld, 2002
Osmotrophic euglenids lacking photosensory apparatus and plastids; one or two emergent
cilia; no ingestion apparatus. Astasia s.s., Distigma, Gyropaigne, Menoidium, Parmidium,
Rhabdomonas.
●●●● Euglenophyceae Schoenichen 1925, emend. Marin & Melkonian 2003 [Euglenea
Butschli 1884, emend. Busse and Preisfeld 2002]
Phototrophic, with one to several plastids of secondary origin with three bounding
membranes and chlorophylls a and b; some species secondarily nonphotosynthetic; most
with extraplastidic eyespot and photosensory apparatus associated with cilia; most motile.
●●●●● Rapaza Yamaguchi et al. 2012
Cells solitary, cytotrophic on microalgae with two heterodynamic cilia of unequal length;
pellicle with helically arranged strips capable of metaboly locomotion; discoidal chloroplast(s)
with pyrenoids surrounded by three membranes; marine species. Rapaza.
●●●●● Eutreptiales Leedale 1967, emend. Marin & Melkonian 2003
2–4 emergent heterodynamic cilia of equal or unequal length; cells not rigid, usually capable
of metaboly; mostly marine or brackish species, rarely freshwater. Eutreptia, Eutreptiella.
●●●●● Euglenales Leedale 1967, emend. Marin & Melkonian 2003
Single emergent cilium and second cilium within the reservoir, or both cilia non-emergent;
phototrophic or heterotrophic; mostly freshwater species.
●●●●●● Phacaceae Kim et al. 2010
Solitary, with one emergent cilium; palmelloid stages, cysts and envelopes unknown;
numerous small discoid chloroplasts without pyrenoids, large paramylon grains.
Discoplastis, Lepocinclis, Phacus.
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●●●●●● Euglenaceae Dujardin 1841, emend. Kim et al. 2010.
Accepted Article
Cells solitary or colonial, with one emergent cilium; one to several large chloroplasts of
various shapes with or without pyrenoid. Ascoglena, Colacium, Cryptoglena, Euglena,
Euglenaformis, Euglenamorpha, Euglenaria, Euglenopsis, Hegneria, Klebsina,
Monomorphina, Strombomonas, Trachelomonas.
●●● Diplonemea Cavalier-Smith 1993, emend. Simpson 1997
Heterotrophic cells exhibiting pronounced metaboly; both cilia are short and usually
supported with paraciliary rod; apical papilla, feeding apparatus with ‘pseudovanes’; few
giant, flattened mitochondrial cristae.
●●●● Diplonemidae Cavalier-Smith, 1993, emend. Adl et al. 2019
Perform extensive trans-splicing and editing of mitochondrial RNA; trophic stage present;
some species contain endosymbiotic bacteria; metaboly always present. Diplonema,
Rhynchopus, Lacrimia, Sulcionema, Flectonema.
●●●● Hemistasiidae Cavalier-Smith, 2016 emend. Adl et al. 2019
Anterior rostrum; large posterior vacuole; contain numerous extrusomes; Hemistasia.
●●●● Eupelagonemidae Okamoto & Keeling, 2018.
Previously refered to as the deep-sea pelagic diplonemids (DSPD1 clade). Possible lack of
metaboly, represent ~97% of all marine diplonemids, globally distributed. Eupelagonema.
●●● Symbiontida Yubuki et al. 2009
Microaerobic or anaerobic cells that possess rod-shaped epibiotic bacteria; lack euglenid
type pellicle strips. Currently treated as a major taxon within Euglenozoa, but are probably
derived phagotrophic euglenids. Apomorphy: Rod-shaped epibiotic bacteria above
superficial layer of mitochondrion-derived organelles with reduced or absent cristae,
homologous to the organization in Calkinisia aureus. Bihospites, Calkinsia, Postgaardi.
●●● Kinetoplastea Honigberg 1963
Cells with a kinetoplast, which is a large mass(es) of mitochondrial (=kinetoplast; k) DNA;
Apomorphy: kinetoplast; mitochondrial RNA editing; trans-splicing of splice leader RNA;
polycistronic transcription.
Incertae sedis Kinetoplastea: Bordnamonas, Cephalothamnium, Rhynchoidomonas.
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●●●● Prokinetoplastina Vickerman in Moreira et al. 2004 (R)
Accepted Article
Two genera: Ichthyobodo are polykinetoplastic and biciliated cells with the cilia originating in
a pocket that continues as a furrow; ectoparasitic, freshwater, and marine. Perkinsela-like
organisms (PLOs), oval cells with a single large kinetoplast, nonciliated, live as
endosymbionts (‘parasomes’) of certain amoebae (e.g. Paramoeba spp.), but are not
enclosed in parasitophorous membrane. Ichthyobodo, Perkinsela.
●●●● Metakinetoplastina Vickerman in Moreira et al. 2004 (R)
Group identified by SSU rRNA phylogenies. Node-based definition: clade stemming from the
most recent common ancestor of Neobodonida, Parabodonida, Eubodonida, and
Trypanosomatida.
●●●●● Neobodonida Vickerman in Moreira et al. 2004 (R)
Eu- or polykinetoplastic kDNA not in a single network, but in multiple loci throughout the
mitochondrion; biciliated, without conspicuous hairs; posterior cilium attached or free;
phagotrophic or osmotrophic; preciliary rostrum containing apical cytosome. Node:
Actuariola, Azumiobodo, Cruzella, Cryptaulax, Dimastigella, Klosteria, Neobodo,
Phanerobia, Rhynchobodo, Rhynchomonas.
●●●●● Parabodonida Vickerman in Moreira et al. 2004 (R)
Pankinetoplastic kDNA not in a single network, but evenly distributed in the mitochondrion;
biciliated, without mastigonemes; posterior cilium attached or free; phagotrophic or
osmotrophic; cytostome, when present, antero-lateral; free-living or commensal/parasitic.
Node: Cryptobia, Jarrellia, Parabodo, Procryptobia, Trypanoplasma.
●●●●● Eubodonida Vickerman in Moreira et al. 2004 (R)
Eukinetoplast with kDNA not in a single network, but in parakinetosomal position; biciliated
with anterior cilium with nontubular mastigonemes; phagotrophic; anterolateral cytostome
surrounded by lappets; free-living Bodo.
●●●●● Trypanosomatida Kent 1880, emend. Vickerman in Moreira et al. 2004
Eukinetoplastic with kDNA network associated with ciliary basal body; unciliated, lacking
mastigonemes and emerging from anterior pocket, or emerging laterally and attached to
body; phagotrophic or osmotrophic; cytostome, when present, simple and close to ciliary
pocket; exclusively parasitic. Node: monoxenous (= single host) genera Angomonas,
Blechomonas, Leptomonas, Paratrypanosoma, Sergeia, Strigomonas, Wallaceina and
dixenous (= two hosts) genera Phytomonas, Trypanosoma.
●●●●●● Leishmaniinae Maslov & Lukeš, 2012 (R)
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Accepted Article
Group identified by SSU rRNA and GAPDH phylogenies, with relatively slow evolution of the
gene sequences. Includes monoxenous genera Borovskyia, Crithidia, Leptomonas,
Lotmaria, Novymonas, Porcisia, Zelonia, and dixenous genera Endotrypanum, Leishmania.
● Malawimonadidae O’Kelly & Nerad 1999
Small free-living biciliated cells, superficially similar to Carpediemonas but not closely related
and with a typical respiratory mitochondrion with discoidal cristae and genome; two
kinetosomes, a single (Malawimonas) or two (Gefionella) ventral ciliary vane; typically from
freshwater or soil. Gefionella, Malawimonas.
● “CRuMs” (Brown et al., 2018) [not Varisulca Cavalier-Smith 2012] (R)
This probably sister clade in Amorphea, informally referred to as CRuMs, includes at least
Collodictyonidae, Rigifilida, and Mantamonas. All members exhibit some form of cellular
plasticity, some with pseudopodia.
Incertae sedis CRuMs: Glissandra.
●● Collodictyonidae Brugerolle et al. 2002, emend. Adl et al. 2019 [Diphylleidae CavalierSmith 1993, Diphylleida Cavalier-Smith 1993, Diphyllatea Cavalier-Smith 2003,
Sulcomonadidae Cavalier-Smith 2013]
Free-swimming 10–15 µm long cells with two or four equal apical cilia orthogonal to each
other; ciliary transition zone long, with a two-part axosome; phagocytosis of other eukaryotic
cells occurring through use of pseudopodia in a conspicuous longitudinal ventral groove that
extends to posterior end, giving a double-lobed appearance. Collodictyon, Diphylleia (=
Aulacomonas), Sulcomonas.
●● Rigifilida Cavalier-Smith in Yabuki et al. 2012
Cells rounded, 5–10 µm in diameter, aproximately circular in dorsoventral aspect although
somewhat plastic; pellicle underlies cell membrane on dorsal and lateral surfaces; central
circular depression on venter of cell, with collar-like margin of reflected pellicle; branching
fine pseudopodia arising from ventral depression, used to capture bacteria; flat mitochondrial
cristae. Micronuclearia, Rigifila.
●● Mantamonas Cavalier-Smith and Glücksman in Glücksman et al. 2011 (M)
Gliding marine biciliated ~5-µm cell; body flattened, characteristically seen wider than long
with left side of cell having angled shape or with short (~1 µm) rounded projection and right
side plastic, but cell can also be longer than wide, with rounded anterior with posterior end
tapering to point at posterior cilium, or any intermediate shape; long posteriorly-directed
cilium directed straight behind gliding cell; anterior cilium very short and thin, projecting stiffly
forward and left. Mantamonas plastica.
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● Ancyromonadida Cavalier-Smith 1998 [=Planomonadida Cavalier-Smith 2008]
Accepted Article
Small (~5 µm) benthic gliding cells, dorsoventrally compressed, with leftward-oriented
rostrum at anterior; two unequal cilia, each emerging in separate shallow pocket; short apical
anterior cilium may be very thin or terminate at cell membrane; long posterior cilium inserts
ventrally/left-laterally; rostrum contains extrusomes in rows; cell membrane supported by a
thin single-layered theca; discoidal/flat mitochondrial cristae; bacterivorous. This clade is the
likely sister clade to the Amorphea and CRuMs. Ancyromonas, Fabomonas, Nutomonas,
Planomonas.
● Hemimastigophora Foissner et al. 1988
Ellipsoid to vermiform cells, cilia typically 15–40 µm long, arranged in two lateral rows that
may or may not run the whole length of the cell, with up to about a dozen cilia per row;
submembranous thecal plates separate the cilia; thecal plates rotationally symmetrical,
supported by microtubules; anterior differentiated into a capitulum, which is the site of
phagocytosis; tubular and saccular mitochondrial cristae; with bottle-shaped extrusomes.
Incertae sedis Hemimastigophora: Paramastix.
●● Spironemidae Doflein 1916
Hemimastix, Spironema, Stereonema.
● Meteora Hausmann et al. 2002 (M)
Gliding 3–4 µm round cell with long, thin, stiff anterior and posterior protrusions; two (rarely
more) short paired lateral ‘arms’ that wave anteriorly and posteriorly as if rowing, generally at
same frequency but varying between moving in same or opposite directions; ‘arms’ usually
straight, ~cell diameter long, but may be branched; ‘arms’ often have linearly arranged
nodules, nodules occasionally also found in anterior/posterior protrusions. Meteora
sporadica.
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Accepted Article
Table 3. Genera incertae sedis in eukaryotes, with uncertain affiliation within protists.
Acinetactis
Actinastrum
Actinocoma
Actinolophus
Adinomonas
Aletium
Amphimonas
Amylophagus
Anaeramoeba
Aphelidiopsis
Asterocaelum
Asthmatos
Aurospora
Barbetia
Belaria
Belonocystis
Bertarellia
Bertramia
Bodopsis
Boekelovia
Branchipocola
Camptoptyche
Chalarodora
Cibdelia
Cichkovia
Cinetidomyxa
Cingula
Cladomonas
Clathrella
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Codonoeca
Accepted Article
Coelosporidium 41
Copromonas
Cyanomastix
Cyclomonas
Cytamoeba
Dallingeria
Dictyomyxa
Dimastigamoeba
Dinemula
Dinoasteromonas
Diplocalium
Diplomita
Diplophysalis
Diploselmis
Dobellina
Ducelleria
Ectobiella
Elaeorhanis
Embryocola
Endamoeba
Endemosarca
Endobiella
Endomonas
Endospora
Enteromyxa
Eperythrocytozoon
Errera
Fromentella
Gymnococcus
Gymnophrydium
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Haematotractidium
Accepted Article
Hartmannina
Heliobodo
Heliomonas
Hermisenella
Heterogromia
Hillea
Hyalodaktylethra
Immuno-plasma 42
Isoselmis
Janickina
Kamera
Kiitoksia
Lagenidiopsis
Liegeosia
Luffisphaera 43
Lymphocytozoon
Lymphosporidium
Macappella
Magosphaera
Malpighiella
Martineziella
Megamoebomyxa
Meringosphaera
Microcometes
Monochrysis
Monodus
Mononema
Myrmicisporidium
Naupliicola
Nephrodinium
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Neurosporidium
Accepted Article
Orbulinella
Ovicola
Palisporomonas
Pansporella
Paradinemula
Paraluffisphaera
Paramonas
Paraplasma
Parastasia
Parastasiella
Peliainia
Peltomonas
Petasaria
Phagodinium
Phanerobia
Phloxamoeba
Phyllomitus
Phyllomonas
Physcosporidium
Piridium
Pleuophrys
Pleuromastix
Protenterospora
Protomonas
Pseudoactiniscus
Pseudosporopsis
Rhizomonas
Rhynchodinium
Rigidomastix
Schewiakoffia
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Sergentella
Accepted Article
Serpentoplasma
Sphaerasuctans
Spongastericus
Spongocyclia
Stephanomonas
Strobilomonas
Tetradimorpha
Tetragonidium
Thaulirens
Topsentella
Toshiba
Trichonema
Urbanella
41
Probably a junior synonym of Nephridiophaga, a Zygomycete
42
Immuno-plasma Neumann 1909 (see Kar, 1990)
43
Belonocystis (Amoebozoa incertae sedis) and Luffisphaera maybe the same genus.
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ccepted Articl
Table 4. Recomended primers for environmental samples.
Supergroup or
highest rank
Amorphea
Amoebozoa
Apusomo
1
nadida
Tubulinea,
Discosea,
Variosea
Tubulinea,
Discosea,
Variosea
Nearly all
clades
Arcellinida
Opisthokonta
Porifera
Clades
3
Choanofla
2
gellata
Demospo
ngiae,
Homoscle
romorpha:
Primer pair
codes
18S, EK-42F &
APU-1R
18S, RibA &
RibB
18S, RibA &
S20R
Cox-I,
LCO1490 &
HCO2198
(modified
Folmer primers)
st
1 step, Euk
82F & Euk 1498
nd
R, 2 step,
cloning
18S, 42F &
1510R
Cox-I (Folmer
primers),
LCO1490 &
HCO2198
28S, C1 & D2,
universal
primers
28S D1–D2,
Por28S-15F &
Por28S-878R
28S D3–D5,
Por28S-830F &
Por28S-1520R
Sequence length
(bp)
Forward primer (5’->3’)
Reverse primer (5’->3’)
1,500-2,200
CTCAARGAYTAAGCCATGCA
CTTCCTTTGGTTAAAACAC
Entire SSU
molecule,
variable
ACCTGGTTGATCCTDCCAGT
TGATCCATCTGCAGGTTCACCTAC
~ 1,800
ACCTGGTTGATCCTDCCAGT
GACGGGCGGTGTGTACAA
~ 660
GGTCAACAAATCATAAAGATATTGG
TAAACTTCAGGGTGACCAAAAAATCA
Variable
GAAACTGCGAATGGCTC
CYGCAGGTTCACCTA C
1,750
CTCAARGAYTAAGCCATGCA
CCTTCYGCAGGTTCACCTAC
GGTCAACAAATCATAAAGATATTGG
TAAACTTCAGGGTGACCAAAAAATCA
658
800–900
790–830
650-660
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ACCCGCTGAATTTAAGCAT
TCCGTGTTTCAAGACGGG
GCGAGATCACCYGCTGAAT
CACTCCTTGGTCCGTGTTTC
CATCCGACCCGTCTTGAA
GCTAGTTGATTCGGCAGGTG
ccepted Articl
Calcarea:
Hexactinel
lida:
Fungi
Fungi
Chytridio
4,
mycota
5, 6, 7
8, 9
Haptista
Haptophyt
10, 11
a
28S D3-D5,
NL4F & NL4R
28S C-region,
C2 & D2, or
C2’modified &
D2
28S D3-D5,
NL4F & NL4R
16S partial
primers,
16S1fw & 16SH
modified
18S, NS1 &
NS4
PolySSU1 &
PolySSU1R
28S, LROR &
LR5
ITS1-5.8SITS2, ITS5 &
ITS4
EF-1a,* 983F &
EF1aZ-1R
EF-1a-like, **
983F & EFLRS2R
ITS (See
citation 9, Table
S1)
18S, AU2-F &
AU4-R, & inner
AUPH1
1F & 1528R (or
EukA & EukB)
650–660
GACCCGAAAGATGGTG AACTA
ACCTTGGAGACCTGA TGCG
430–470
GAAAAGAACTTTGRARAGAGAGT
or
GAAA AGCACTTTGAAAAGAGA
TCCGTGTTTCAAGACGGG
900–1,000
GACCCGAAAGATGGTG AACTA
ACCTTGGAGACCTGATGCG
TCGACTGTTTACCAAAAACATAGC
YRTAATTCAACATCGAGGTC
500
~950-1,100
variable
TGATCCTTCYGCAGGTTCACC
~800-950
AACTAAGAACGGCCATGCAC
~614-987
CCCGTGTTGAGTCAAATTAAGC
~ 1150
GAACGGCCATGCACCACCACC
- ~550-590
GTTCTTGTGTTAATCTCAC
variable
TTTCGATGGTA
GGATAGDGG
RTCTCACTAAGCCATTC, and inner
AGAGCTMTCAATCTGTCAATCCT
ACTTCTGGRTGICCRAARAAYCA
1,800
AACCTGGTTGATCCTGCCAGT
TGATCCTTCTGCAGGTTCACCTAC
1,795
ACCTGGTTGATCCTGCCAG
TGATCCTTCYGCAGGTTCAC
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ccepted Articl
Cryptista
13, 14
Stramenopiles
Centropla
12
sthelida
Sar
15
Euglyphid
16
EukF & EukR
TAReuk454FW
D1 &
TAReukREV3
Hapto4 &
Euk34r
LSU1 (Lhapto8
&
Lhapto20R_bis)
Prym03-3 &
Hapto1R
528FLong &
PRYM01+7
Pavlova-V4F &
1528R
1F & PavlovaV4F2R
Pry421F &
Pry1572R
Hap220F &
Pav1702R
830
GGGTTCGATTCCGGAGAG
CCGTGTTGAGTCAAATT
variable
CCAGCA(G⁄C)C(C⁄T)GCGGTAATTCC
ACTTTCGTTCTTGATYRA
1,000
ATGGCGAATGAAGCGGGC
GCATCGCCAGTTCTGCTTACC
350-400
GGTATCGGAGAAGGTGAGAATCCT
TCAGACTCCTTGGTCCGTGTTTCT
416
GTAAATTGCCCGAATCCTG
CGAAACCAACAAAATAGCAC
399
GCGGTAATTCCAGCTCCAA
GATCAGTGAAAACATCCCTGG
904
GTGAAATTCTTAGACCCACGGA
TGATCCTTCTGCAGGTTCACCTAC
593
see 1F above
GTGAAATTCTTAGACCCACGGA
1,070
AGCAGGCGCGTAAATTGCCCG
TCAACGYRCGCTGATGACA
1,400
ACCGGTCTCCGGTTGCGTGC
TAGATGATAAGGTTTGGGTG
Helio1979R
variable
Nu-SSU-00245’ F & NuSSU1757-3’ R
Nu-SSU-00245’ F & 28S5522-3’ R
18S, SAR-V3SSU F & R
st
1 step
EuglySSUF &
EuglyLSUR
nd
2 step
CACACTTACWAGGAYTTCCTCGTTSAAGACG
variable
CTGGTTGATCCTGCCAGTAGT
CAGGTTCACCTACGGAAACCT
variable
CTGGTTGATCCTGCCAGTAGT
GGCCGGCTTCTTAGAGGGAC
150
TCGTCGGCAGCGTCAGATGTGTATA
AGAGACA
ATGTGTATAAGAGACAGRACTACGAGCTTTTTAAC
TGC
variable
GCGTACAGCTCATTATATCAGCA
GTTTGGCACCTTAACTCGCG
variable
GCGTACAGCTCATTATATCAGCA
GCACCACCACCCATAGAATCWAGAAAGATC
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ccepted Articl
Alveolata
Assulinidae
17
Amphitremi
da
Diatomea
18, 19
Ciliophora
20
Apicomplex
21, 22
a
Dinoflagella
23, 24
ta****
0EuglySSUF
& EuglySSUR
st
1 step, COI:
Eucox1F &
Euglycox1R
nd
2 step,
Assucox 1F &
Assucox 1R
st
1 step, Euk
82F & Euk
nd
1498 R, 2
step, cloning
rbcL, 646F&
998R
variable
GAYATGGCKTTNCCAAGATTAAA
AGCACCCATTGAHAAAACRTAATG
variable
AAYATGAGRGCYAGRGG
5¢-CGTAATGAAARTGWCCYACC
variable
GAAACTGCGAATGGCTC
CYGCAGGTTCACCTAC
379
ATGCGTTGGAGAGARCGTTTC
GATCACCTTCTAATTTACCWACAACTG
Diat_rbcL_70
8F (mixture of
3 primers) &
two reverse
primers R3_1
& R3_2
312 (amplicon
263)
1:
AGGTGAAGTAAAAGGTTCWTACTTA
AA, and 2:
AGGTGAAGTTAAAGGTTCWTAYTTAA
A and 3:
AGGTGAAACTAAAGGTTCWTACTTAA
A
1: CCTTCTAATTTACCWACWACTG, and 2:
CCTTCTAATTTACCWACAACAG
18S V4,
variable
18S PF1 & R4
18S V4
TAReuk454F
WD1 &
TAReukREV3
1,800
GCGCTACCTGGTTGATCCTGCC
GATCCTTCTGCAGGTTCACCTAC
variable
ACTTTCGTTCTTGAT(C⁄T)(A⁄G)
ACTTTCGTTCTTGAT(C⁄T)(A⁄G)
18S V4,
346Fmix &
785R-mix
variable
18S V4, Next.
For & Rev
variable
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CADCGACGGGTAACGGGGAATTA;
CAGYGACGGGTAACGGGGAATTA;
CAGYGACGGGTAACGGGGAATTA;
CAGYGACGGGTAACGGGGAATTA
TCGTCGGCAGCGTCAGATGTGTATA
AGAGACAG[CCAGCASCYGCGGTAA
TTCC]
IIITATTCCATGCTGIAGTATTCA;
IIITATTCCATGCTAAASTATTCA
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
[ACTTTCGTTCTTGATYRATGA]
ccepted Articl
Rhizaria
Excavates
Syndiniales
Cercozoa
Cyphoderiid
25
ae
Foraminifer
26
a
27
Fornicata
Parabasalia
Jakobida
Heterolobo
sea
Preaxostyla
:
Oxymonadi
da
Preaxostyla
:
Paratrimasti
gida,
Trimastigid
a
Euglenida
Heterotroph
18S V4, 528F
& UnonMet
18S V4, 3NDF
& 1256R
18S V4***,
25F & 1256R
Cox-I,
Eucox1F &
Euglycox1R
18S, 14F1 &
s17
EukA & EukB*
16SI & 16S
RR (or EukA
& B)
ITS-F & ITS-R
EukA - EukB
ITS1-5.8S &
ITS2, JITS-F
& JITS-R, (or
EukA &
EukB)
Mon-F & MonR
variable
~500
GGCAAGTCTGGTGCCAG
GCACCACCACCCAYAGAATCAAGAAAGAWCTTC
1,200
CATATGCTTGTCTCAAAGATTAAGCC
A
GCACCACCACCCAYAGAATCAAGAAAGAWCTTC
variable
GAYATGGCKTTNCCAAGATTAAA
AGCACCCATTGAHAAAACRTAATG
300-400
AAGGGCACCACAAGAACGC
variable
variable
TACTTGGTTGATCCTGCC
TCACCTACCGTTACCTTG
variable
variable
variable
TTCAGTTCAGCGGGTCTTCC
GTAGGTGAACCTGCCGTTGG
GTCTTCGTAGGTGAACCTGC
CCGCTTACTGATATGCTTAA
variable
GAAGTCATATGCTGTCTCAA,
TCACCTACGGAAACCTT
EukA & EukB
1,800-3,100
CTGGTTGATCCTGCCAG
TGATCCTTCTGCAGGTTCACCTAC
See citation
Varies with the
primer pairs
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CGGTCACGTTCGTTGC
ccepted Articl
28
s
Euglenophy See citation
Varies with the
28
ceae
primer pair
Protist,
General
EukA-F &
27
general*
variable
CTGGTTGATCCTGCCAG
TGATCCTTCTGCAGGTTCACCTAC
Medlin
EukB-R
primers
Protist
General
See citation
variable
21
general
Stoeck
primers
* Selective amplification of species, some clades missed; **Spizellomycetales; *** Chytridiomycota except Spizellomycetales; ****See citations for DINOREF
in PR2 v.4.9.0.
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Accepted Article
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