- Access to this full-text is provided by Pensoft Publishers.
Download available
Content available from Phytokeys
This content is subject to copyright. Terms and conditions apply.
Phylogenomic analysis of 997 nuclear genes reveals
the need for extensive generic re-delimitation in
Caesalpinioideae (Leguminosae)
Jens J. Ringelberg1, Erik J.M. Koenen1,2, João R. Iganci3,4, Luciano P. de Queiroz5,
Daniel J. Murphy6, Myriam Gaudeul7, Anne Bruneau8, Melissa Luckow9,
Gwilym P. Lewis10, Colin E. Hughes1
1Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zu-
rich, Switzerland 2Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des
Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, Belgium 3Instituto
de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus
s/n, Capão do Leão 96010-900, Rio Grande do Sul, Brazil 4Programa de Pós-Graduação em Botânica, Uni-
versidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul,
91501-970, Brazil 5Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida
Transnordestina s/n – Novo Horizonte, 44036-900, Feira de Santana, Brazil 6Royal Botanic Gardens Vic-
toria, Birdwood Ave., Melbourne, VIC 3004, Australia 7Institut de Systématique, Evolution, Biodiversité
(ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France 8Institut
de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sher-
brooke St E, Montreal, QC H1X 2B2, Canada 9School of Integrative Plant Science, Plant Biology Section,
Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA 10Accelerated Taxonomy
Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
Corresponding author: Jens J. Ringelberg (jens.ringelberg@gmail.com)
Academic editor: Patrick Herendeen|Received 26 April 2022|Accepted 27 June 2022|Published 22 August 2022
Citation: Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M,
Lewis GP, Hughes CE (2022) Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-
delimitation in Caesalpinioideae (Leguminosae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume
Systematics 14. Classication of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 3–58. https://doi.
org/10.3897/phytokeys.205.85866
Abstract
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of leg-
umes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and
lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning
genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable ux,
especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylog-
Copyright Jens J. Ringelberg et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC
BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PhytoKeys 205: 3–58 (2022)
doi: 10.3897/phytokeys.205.85866
https://phytokeys.pensoft.net
RESEARCH ARTICLE
Launched to accelerate biodiversity research
A peer-reviewed open-access journal
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
4
enomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147
of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic
or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca.
25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive
generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of
important traits and, particularly, the repeated evolution of distinctive fruit types that were historically
emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses
and sampling in previous phylogenies and the consequent failure to identify clades that span the Old
World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are
critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in
the phylogenomic era and especially how assessing patterns of gene tree conict can provide additional in-
sights into generic delimitation. is new phylogenomic framework provides the foundations for a series
of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for
establishing a new higher-level phylogenetic tribal and clade-based classication of Caesalpinioideae that
is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversication and biogeography
of this important group of legumes which are presented elsewhere.
Keywords
Fabaceae, generic delimitation, mimosoid clade, monophyly, morphological homoplasy, phylogenomics
Introduction
In 2017, the Legume Phylogeny Working Group established a new subfamily classica-
tion of the Leguminosae (LPWG 2017), which dealt with the longstanding problem
of the paraphyly of old sense subfamily Caesalpinioideae DC. by formally dividing the
family into six subfamilies: Cercidoideae LPWG, Detarioideae Burmeist., Duparque-
tioideae LPWG, Dialioideae LPWG, Caesalpinioideae and Papilionoideae DC. Sub-
family Caesalpinioideae was especially impacted by this new classication because sev-
eral large clades previously included within it were aorded subfamily rank, while at the
same time the former subfamily Mimosoideae DC., which is nested within Caesalpin-
ioideae, was subsumed within the re-circumscribed Caesalpinioideae and is now simply
referred to as the mimosoid clade (LPWG 2017). e idea that Leguminosae comprises
six main lineages has since been amply conrmed by phylogenomic analyses of large
nuclear gene and plastome DNA sequence datasets (Koenen et al. 2020a; Zhang et al.
2020; Zhao et al. 2021) providing robust support for the six subfamilies. Establishment
of this new classication has shifted the focus of current legume systematics research to
development of phylogenetically-based tribal (e.g. de la Estrella et al. 2018 for Detari-
oideae) and clade-based (e.g. Sinou et al. 2020 for Cercidoideae) higher-level classica-
tions and, especially, towards establishment of robust generic systems for each subfamily.
Here, we present a phylogenomic backbone for the re-circumscribed subfamily Caesal-
pinioideae as the basis for a new higher-level and generic classication of that subfamily.
Caesalpinioideae sensu LPWG (2017) is the second largest subfamily of legumes
with ca. 4,600 species currently placed in 152 genera (LPWG 2017 plus additions, see
Phylogenomics of Caesalpinioideae: generic re-delimitation 5
below). Within this subfamily, ca. 3,400 species and 90 genera are placed in the mimosoid
clade corresponding to the former subfamily Mimosoideae, which is nested within new
sense Caesalpinioideae (LPWG 2017). Caesalpinioideae has a pantropical distribution
and many of its lineages form ecologically abundant or dominant elements across each
of the major lowland tropical biomes – seasonally dry tropical forests (“the succulent
biome” sensu Schrire et al. 2005 and Ringelberg et al. 2020), savannas and tropical rain
forests – thus spanning the full lowland tropical rainfall spectrum from arid to hyper-wet,
with just a small fraction of species extending into the warm temperate zone, a subset of
which are frost tolerant. Caesalpinioideae species are infrequent above 2500 m elevation
in the tropics and are notably absent from mid- and high-elevation tropical montane
forests, with only a few exceptions (e.g. some Inga Mill. spp., Paraserianthes lophantha
(Vent.) I.C. Nielsen subsp. montana (Jungh.) I.C. Nielsen). e ecological versatility of
the subfamily across the lowland tropical moisture availability spectrum is matched by its
great diversity of life-history strategies, from massive canopy-emergent rainforest trees to
small desert shrubs, and functionally-herbaceous savanna geoxyles to woody lianas and
aquatic plants (Lewis et al. 2005; LPWG 2013, 2017; Koenen et al. 2020b; Ringelberg
et al. 2022). Many species are economically important because of their highly-nutritious
fruits, valuable wood, nitrogen-rich leaves and other products (Lewis et al. 2005) and
are especially prominent as multipurpose trees in tropical silvo-pastoral and other agro-
forestry systems. Several other species constitute some of the world’s most serious inva-
sive weeds (e.g. Leucaena leucocephala (Lam.) de Wit, several Mimosa L. spp. and Acacia
Mill. spp., Prosopis juliora (Sw.) DC.). Generic diversity is highest in the Neotropics
and Africa and there are important centres of species diversity in Mexico and Central
America, lowland South America, Africa, Madagascar, parts of S.E. Asia and Australia.
Caesalpinioideae includes some of the largest genera in the legume family, such as Acacia
with>1,000 species concentrated in dry parts of Australia and Mimosa with > 500 spe-
cies mostly in the Neotropics, as well as Chamaecrista Moench and Senna Mill., each with
300+ species distributed pantropically, Inga Mill. with ca. 300 species restricted to the
Neotropics, almost entirely in rainforests and Vachellia Wight & Arn. (ca. 160 species)
and Senegalia Raf. (ca. 220 species), two pantropical genera concentrated in drier envi-
ronments, within which the iconic umbrella-crown trees of African savannas are found.
Numbers of genera across Caesalpinioideae have increased progressively through
the last 270 years, but are dicult to track, because of the altered delimitation of the
subfamily. However, the history of generic delimitation in mimosoids illustrates the
overall trajectory of numbers of genera. Linnaeus (1753) placed all known mimosoids
in a single genus Mimosa, which was later subdivided by Willdenow (1805) into ve
genera: Inga, Mimosa, Schrankia Willd., Desmanthus Willd. and Acacia. In 1825, de
Candolle added ve more genera, but the real foundations for all subsequent work
were established by Bentham (1842, 1875) notably in his ‘Revision of suborder Mi-
moseae’ in 1875, which recognised six tribes and 46 genera, based on examination of
1,200 species known at that time.
e legacy of Bentham’s generic system has been long-lasting. At the heart of
Bentham’s system were a set of large, geographically widespread genera, including
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
6
Acacia, Calliandra Benth., Pithecellobium Mart. and Prosopis L., all of which, with
the advent of molecular phylogenetics, have been shown to be non-monophyletic.
e disintegration of Acacia into (currently) seven segregate genera (Acacia, Acaciella
Britton & Rose, Mariosousa Seigler & Ebinger, Parasenegalia Seigler & Ebinger, Pseu-
dosenegalia Seigler & Ebinger, Senegalia and Vachellia), based on 20 years of molecular
phylogenetic studies (Clarke et al. 2000; Miller and Bayer 2000, 2001, 2003; Robin-
son and Harris 2000; Luckow et al. 2003; Miller et al. 2003, 2013, 2017; Murphy et
al. 2003; Seigler et al. 2006a, b; Brown et al. 2008; Bouchenak-Khelladi et al. 2010;
Gómez-Acevedo et al. 2010; Miller and Seigler 2012; Kyalangalilwa et al. 2013; Mish-
ler et al. 2014; Boatwright et al. 2015; Terra et al. 2017; Koenen et al. 2020b) (Figs 1
and 6–8) has been the most prominent example in legumes of the dissolution of one
of Bentham’s broadly circumscribed pantropical genera. Pithecellobium and Calliandra
have suered similar fates (Barneby and Grimes 1996, 1997; Barneby 1998; de Souza
et al. 2013, 2016). In contrast, although Bentham (1875) had restricted his concept
of the genus Albizia Durazz. to just Old World species, Nielsen (1981) expanded the
genus pantropically, creating the last big ‘dustbin genus’ of mimosoids (Koenen et al.
2020b). By far the most persistent generic delimitation problems surround those of
former tribe Ingeae, where starkly contrasting generic systems and numerous generic
transfers have caused much on-going confusion (reviewed by Brown 2008).
By 1981, the number of mimosoid genera had risen to 62 in Advances in Legume
Systematics Part 1 (Elias 1981), 78 in Legumes of the World (Lewis et al. 2005) and in
the most recent census (LPWG 2017) to 84, with 148 genera recognised in Caesalpin-
ioideae as a whole.
Across the non-mimosoid Caesalpinioideae generic delimitation has also seen
many changes. e most complex problems have been, without doubt, in the Cae-
salpinia Group and, especially, the genus Caesalpinia L. s.l. (Polhill and Vidal 1981;
Lewis 1998; Gagnon et al. 2016), but these have now largely been resolved with the
phylogenetically-based generic system of Gagnon et al. (2016), which recognised 26
genera, leaving just one residual generic problem in that group (see Clark et al. 2022).
Since LPWG (2017), two genera of Caesalpinioideae have been synonymised (i.e.
Cathormion Hassk. within Albizia (Koenen et al. 2020b) and Lemuropisum H. Perrier
within Delonix Raf. (Babineau and Bruneau 2017)) and six new genera have been
segregated or resurrected (i.e. Lachesiodendron P.G. Ribeiro, L.P. Queiroz & Luckow
(Ribeiro et al. 2018), Parasenegalia and Pseudosenegalia (Seigler et al. 2017), Jupun-
ba Britton & Rose and Punjuba Britton & Rose (Soares et al. 2021) and Robrichia
(Barneby & J.W. Grimes) A.R.M. Luz & E.R. Souza (de Souza et al. 2022a)), bringing
the current tally of Caesalpinioideae genera to 152, of which 90 are mimosoids.
Despite this rapid on-going progress to align genera with clades in recent years, ge-
neric delimitation across Caesalpinioideae and, especially, the mimosoid clade, remains
in a state of considerable ux and there is evidence to suggest that several more genera
are non-monophyletic: Prosopis (Catalano et al. 2008), Dichrostachys (DC.) Wight &
Arn. (Hughes et al. 2003; Luckow et al. 2005), Balizia Barneby & J.W. Grimes (Iganci
et al. 2016; Koenen et al. 2020b), Zygia P. Browne (Ferm et al. 2019), Entada Adans.
Phylogenomics of Caesalpinioideae: generic re-delimitation 7
(Luckow et al. 2003), Caesalpinia (Gagnon et al. 2016), Albizia, Senegalia and Leuc-
ochloron Barneby & J.W. Grimes (Koenen et al. 2020b; Fig. 1). One factor that has un-
doubtedly contributed signicantly to this widespread generic non-monophyly is the
potentially pervasive homoplasy of multiple morphological characters previously used
for generic delimitation, as well as reliance on only a few characters for delimiting taxa.
is has led to tribes dened solely on stamen number and fusion into a staminal tube
(Bentham 1875) and ‘fruit genera’, such as Calliandra, which was dened by Bentham
(1875), based on its characteristic elastically dehiscent fruit. All mimosoid tribes and
the genus Calliandra have since been shown to be non-monophyletic and their den-
ing characters shown to have evolved multiple times across the subfamily (e.g. LPWG
2013; Barneby 1998). Such over-reliance on a small number of potentially homopla-
sious morphological characters, such as fruit type, connation and number of stamens
and oral heteromorphy have likely repeatedly misled classication and resulted in
widespread generic non-monophyly.
Another issue has been delimitation of the mimosoid clade with on-going uncer-
tainties surrounding the inclusion or not of certain genera (Luckow et al. 2000, 2003;
Manzanilla and Bruneau 2012). Although lacking valvate petals in bud (the putative
synapomorphy of mimosoids), morphologically some members of the informal Di-
morphandra group of Polhill and Vidal (1981) and Polhill (1994) show many similari-
ties to mimosoids, with small, often numerous, regular owers arranged in spikes or
spiciform racemes, the hypanthium contracted, the anthers sagittate and introrse, the
stamens becoming the most conspicuous and attractive part of the ower and pollen in
tetrads in a few genera (Diptychandra Tul. and Dinizia Ducke) with possible anities
to the polyads that characterise many mimosoid lineages (Banks et al. 2010). ese
mimosoid-like features have prompted inclusion of some genera such as Dinizia in the
mimosoid clade in the past (e.g. Burkart 1943; Luckow et al. 2000). Although none of
these mimosoid-like genera has owers with petals valvate in bud, previous molecular
phylogenetic analyses have unexpectedly placed two Dimorphandra group genera in
the mimosoid clade: Chidlowia Hoyle and Sympetalandra Stapf. e monospecic west
African genus Chidlowia was placed with high support within the mimosoid clade in
analyses based on few genetic markers (Manzanilla and Bruneau 2012; LPWG 2017),
a result which was conrmed by the phylogenomic analyses of Koenen et al. (2020b;
Fig. 1). e small Asian genus Sympetalandra was also recovered in the mimosoid clade
in the matK tree of LPWG (2017), but was not sampled by Koenen et al. (2020b). Al-
though support for the mimosoid clade is robust and the branch subtending that clade
is long (Koenen et al. 2020b; Fig. 1), such that the monophyly of mimosoids is not in
doubt, not all Caesalpinioideae genera have been included in phylogenomic analyses.
By sampling widely and densely across Caesalpinioideae as a whole, we aim to further
resolve which genera are placed in the mimosoid clade.
Several other issues have hindered a more complete understanding of the phylog-
eny and tribal / generic classication of subfamily Caesalpinioideae. First, the legacy
of the traditional subfamily classication meant that taxon sampling in previous phy-
logenetic studies focused primarily on either old sense Caesalpinioideae (i.e. the grade
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
8
Dimorphandra macrostachya
Peltophorum africanum
Diptychandra aurantiaca
Tachigali odoratissima
Pachyelasma tessmannii
Erythrophleum ivorense
Chidlowia sanguinea
Pentaclethra macrophylla
Pseudoprosopis gilletii
Calpocalyx dinklagei
Xylia hoffmannii
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada rheedei
Elephantorrhiza elephantina
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Prosopis laevigata
Neptunia oleracea
Lemurodendron capuronii
Alantsilodendron pilosum
Dichrostachys cinerea
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Schleinitzia novoguineensis
Desmanthus leptophyllus
Kanaloa kahoolawensis
Lachesiodendron viridiflorum
Stryphnodendron pulcherrimum
Pseudopiptadenia contorta
Pityrocarpa moniliformis
Parapiptadenia zehntneri
Piptadenia robusta
Mimosa tenuiflora
Mimosa grandidieri
Adenopodia scelerata
Adenopodia patens
Mariosousa sericea
Senegalia ataxacantha
Senegalia sakalava
Cojoba arborea
Lysiloma candidum
Hesperalbizia occidentalis
Pithecellobium dulce
Havardia pallens
Sphinga acatlensis
Ebenopsis confinis
Falcataria moluccana
Serianthes nelsonii
Acacia longifolia
Paraserianthes lophantha
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron lucidum
Archidendron quocense
Cedrelinga cateniformis
Leucochloron bolivianum
Enterolobium contortisiliquum
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia brevifolia
Albizia anthelmintica
Albizia ferruginea
Albizia versicolor
Albizia polyphylla
Albizia atakataka
Albizia viridis
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia aurisparsa
Albizia obbiadensis
Albizia masikororum
Albizia sahafariensis
Albizia umbellata
Albizia saponaria
Albizia retusa
Jupunba trapezifolia
Balizia pedicellaris
Balizia sp.
Albizia obliquifoliolata
Hydrochorea corymbosa
Hydrochorea corymbosa
Albizia edwallii
Albizia burkartiana
Albizia inundata
Blanchetiodendron blanchetii
Leucochloron limae
Abarema cochliacarpos
Albizia dinklagei
Albizia altissima
Zygia claviflora
Zygia racemosa
Zygia sp.
Zygia inaequalis
Macrosamanea amplissima
Inga huberi
Inga tenuistipula
Inga edulis
Inga stipularis
Inga laurina
Inga alba
Pseudosamanea guachapele
Samanea saman
Chloroleucon tenuiflorum
Zapoteca caracasana
Faidherbia albida
Viguieranthus glaber
Acaciella villosa
Calliandra hygrophila
Vachellia tortilis
Vachellia viguieri
Parkia panurensis
Anadenanthera colubrina
0.1
Dimorphandra macrostachya
Peltophorum africanum
Diptychandra aurantiaca
Tachigali odoratissima
Pachyelasma tessmannii
Erythrophleum ivorense
Chidlowia sanguinea
Pentaclethra macrophylla
Pseudoprosopis gilletii
Calpocalyx dinklagei
Xylia hoffmannii
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada rheedei
Elephantorrhiza elephantina
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Prosopis laevigata
Neptunia oleracea
Lemurodendron capuronii
Alantsilodendron pilosum
Dichrostachys cinerea
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Schleinitzia novoguineensis
Desmanthus leptophyllus
Kanaloa kahoolawensis
Lachesiodendron viridiflorum
Stryphnodendron pulcherrimum
Pseudopiptadenia contorta
Pityrocarpa moniliformis
Parapiptadenia zehntneri
Piptadenia robusta
Mimosa tenuiflora
Mimosa grandidieri
Adenopodia scelerata
Adenopodia patens
Mariosousa sericea
Senegalia ataxacantha
Senegalia sakalava
Cojoba arborea
Lysiloma candidum
Hesperalbizia occidentalis
Pithecellobium dulce
Havardia pallens
Sphinga acatlensis
Ebenopsis confinis
Falcataria moluccana
Serianthes nelsonii
Acacia longifolia
Paraserianthes lophantha
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron lucidum
Archidendron quocense
Cedrelinga cateniformis
Leucochloron bolivianum
Enterolobium contortisiliquum
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia brevifolia
Albizia anthelmintica
Albizia ferruginea
Albizia versicolor
Albizia polyphylla
Albizia atakataka
Albizia viridis
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia aurisparsa
Albizia obbiadensis
Albizia masikororum
Albizia sahafariensis
Albizia umbellata
Albizia saponaria
Albizia retusa
Jupunba trapezifolia
Balizia pedicellaris
Albizia obliquifoliolata
Hydrochorea corymbosa
Hydrochorea corymbosa
Albizia edwallii
Albizia burkartiana
Albizia inundata
Blanchetiodendron blanchetii
Leucochloron limae
Abarema cochliacarpos
Albizia dinklagei
Albizia altissima
Zygia claviflora
Zygia racemosa
Zygia inaequalis
Macrosamanea amplissima
Inga huberi
Inga tenuistipula
Inga edulis
Inga stipularis
Inga laurina
Inga alba
Pseudosamanea guachapele
Samanea saman
Chloroleucon tenuiflorum
Zapoteca caracasana
Faidherbia albida
Viguieranthus glaber
Acaciella villosa
Calliandra hygrophila
Vachellia tortilis
Vachellia viguieri
Parkia panurensis
Anadenanthera colubrina
Zygia sp.
Balizia sp.
Mimosoid
clade
core
mimosoids
ingoid
clade
Xylia clade
Entada clade
Dichrostachys clade
Parkia clade
Stryphnodendron clade
Mimosa clade
Calliandra clade
Zapoteca clade
Cojoba clade
Pithecellobium clade
Archidendron clade
Samanea clade
Jupunba clade
Inga clade
Albizia clade
Figure 1. Phylogeny of Caesalpinioideae with clade names as inferred by Koenen et al. (2020b), the
starting point for this study.
Phylogenomics of Caesalpinioideae: generic re-delimitation 9
subtending mimosoids (the ‘Caesalpinieae grade’ of Manzanilla and Bruneau 2012)
of new sense Caesalpinioideae (Bruneau et al. 2008; Manzanilla and Bruneau 2012)),
or on the mimosoid clade (e.g. Luckow et al. 2003, 2005; Koenen et al. 2020b). Few
studies, apart from the family-wide analysis of plastid matK sequences (LPWG 2017),
have sampled densely and widely across Caesalpinioideae as a whole. Second, several
parts of the Caesalpinioideae phylogeny have been recalcitrant to phylogenetic resolu-
tion using traditional DNA sequence loci, most notably along the backbone of the
grade subtending the mimosoid clade (Bruneau et al. 2008; Manzanilla and Bruneau
2012; LPWG 2017) and across the large ingoid clade sensu Koenen et al. (2020b).
ird, lack of dense pantropical sampling of taxa in previous phylogenies means that
the monophyly of several key genera with wide pantropical distributions, such as the
‘dustbin genus’ Albizia, has not been adequately tested and that possible sister-group
relationships between New and Old World groups that are relevant to delimitation of
genera may have been missed.
More robust foundations to overcome these diculties were established by Koenen
et al. (2020b) in a phylogenomic study of the mimosoid clade. By developing a clade-
specic bait set (Mimobaits) for targeted enrichment of 964 nuclear genes, Koenen et
al. (2020b) opened the way for generating DNA sequence datasets orders of magni-
tude larger than those used previously, thereby providing much enhanced phylogenetic
resolution. Using these new data, Koenen et al. (2020b) established a new phylog-
enomic framework and recognised three large informally named higher-level clades
each successively nested within Caesalpinioideae (Fig. 1). e mimosoid clade, core
mimosoid clade and ingoid clade were all strongly supported by high proportions of
gene trees and subtended by long branches. In addition, a set of 15 smaller informally
named subclades across mimosoids were proposed by Koenen et al. (2020b) (Fig. 1)
to replace the previously dened tribes and informal groups and alliances, almost all
of which have been shown by numerous studies to be non-monophyletic (Luckow et
al. 2003; LPWG 2013, 2017; Koenen et al. 2020b). Furthermore, although the Mi-
mobaits bait set was designed based on RNA-seq data from species of four mimosoid
genera and used initially for the mimosoid clade, the results of Koenen et al. (2020b)
suggested that they work well across the non-mimosoid Caesalpinioideae, opening the
way to potentially sequence these genes across the subfamily as a whole. e Koenen
et al. (2020b) study also further revealed or conrmed the non-monophyly of several
genera, but it lacked sucient taxon sampling to fully test generic monophyly and
sampling was largely restricted to the mimosoid clade. Here, we capitalise on these
foundations using a slightly modied version of the Mimobaits gene set covering 997
nuclear genes to extend taxon sampling to 420 species from 147 of the 152 genera and
establish a robust phylogenomic hypothesis for subfamily Caesalpinioideae as a whole.
is new phylogeny provides the basis for testing the monophyly of genera (the
main focus of this paper and of this Special Issue Advances in Legume Systematics (ALS)
14, Part 1), establishing a new higher-level classication of the subfamily (the focus
of ALS 14, Part 2) and for downstream analyses of biogeography, trait evolution and
diversication (de Faria et al. 2022; Ringelberg et al. 2022). Caesalpinioideae pro-
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
10
vides an excellent clade for investigating evolutionary diversication and phylogenetic
turnover across the lowland tropics (Lavin et al. 2004; Gagnon et al. 2019; Ringel-
berg et al. 2020, 2022), as well as the evolution of several prominent plant functional
traits including compound leaves, armature, extraoral nectaries and ant associations
(Marazzi et al. 2019), agglomeration of pollen into polyads, plant growth forms (Gag-
non et al. 2019), oral morphology and pollination syndromes, fruit morphology and
seed dispersal syndromes and the ability to form nitrogen-xing root nodule symbiosis
(Sprent et al. 2017; de Faria et al. 2022). However, all of these opportunities require a
robust and well-sampled subfamily-wide phylogeny of Caesalpinioideae. In turn, some
of these traits have been used for generic delimitation in the past and, in this paper,
we also evaluate a handful of such traits in a preliminary way by mapping them on to
the phylogeny.
Methods
Phylogeny: taxon and gene sampling, and tree building
To test generic monophyly as thoroughly as possible, we sampled taxa to encompass
known or suspected cases of generic non-monophyly, as well as sets of representative
species spanning the root nodes of larger genera in Caesalpinioideae (Suppl. mate-
rial 1). e nal phylogenomic dataset comprised 420 Caesalpinioideae taxa cover-
ing 147 of the 152 genera. e ve missing genera are: Stenodrepanum Harms, the
monospecic sister genus of Homannseggia Cav. in the Caesalpinia Group (Gagnon
et al. 2016); Hultholia Gagnon & G.P. Lewis, another monospecic genus in the Cae-
salpinia Group (Gagnon et al. 2016); Microlobius C. Presl, which is also monospecic
and nested within the mimosoid genus Stryphnodendron Mart. (Simon et al. 2016;
Ribeiro et al. 2018; Lima et al. 2022); Vouacapoua Aubl., a genus of three species,
whose phylogenetic placement is uncertain, but most likely falls into the Cassia clade
(Bruneau et al. 2008; LPWG 2017); and Pterogyne Tul., another monospecic genus
whose placement has been uncertain (Manzanilla and Bruneau 2012; Zhang et al.
2020), but which is probably sister to all Caesalpinioideae, excluding the Arcoa and
Umtiza clades (Zhao et al. 2021). In total, 89 of 90 mimosoid genera and 58 of the 62
non-mimosoid Caesalpinioideae genera were sampled.
We sequenced a set of 997 nuclear genes specically selected for phylogenomic
analyses of the mimosoid clade (Koenen et al. 2020b) via targeted enrichment and hy-
brid capture. is Hybseq approach has quickly become the method of choice to gen-
erate phylogenomic data because of its versatility and relatively low cost (e.g. Nicholls
et al. 2015; Barrett et al. 2016; Hart et al. 2016; Dodsworth et al. 2019; Johnson et
al. 2019; Koenen et al. 2020b). Library preparation, hybrid capture, enrichment and
sequencing were performed by Arbor Biosciences (previously MYcroarray; Ann Arbor,
USA). Full details about how the new Caesalpinioideae phylogeny was inferred are
presented by Ringelberg et al. (2022), but briey, HybPiper (Johnson et al. 2016)
Phylogenomics of Caesalpinioideae: generic re-delimitation 11
was used to assemble the loci and the pipeline of Yang and Smith (2014) was used
for data cleaning and orthology assessment. Various phylogenetic methods, includ-
ing the multi-species coalescent approach using individual gene trees with ASTRAL
(Zhang et al. 2018), Maximum Likelihood based on concatenated alignments with
RAxML (Stamatakis 2014) and Bayesian gene jack-kning with PhyloBayes (Lartillot
et al. 2013), were used to infer ten nuclear species trees, which also dier in whether
nucleotide or amino acid sequences were used and in the way orthology was assessed
(Ringelberg et al. 2022). In addition, a chloroplast phylogeny was inferred using o-
target plastid sequences, bringing the total number of phylogenies to eleven. Topologi-
cal congruence between these eleven dierent phylogenies was assessed. Support for
relationships was expressed in numbers of supporting and conicting gene trees using
PhyParts (Smith et al. 2015) and QuartetScores (Zhou et al. 2020) (Figs 2–12), rather
than conventional bootstrap or posterior support values that are known to be inated
in large phylogenomic datasets (Rokas and Carroll 2006; Pease et al. 2018).
Character evolution
To explore evolution of morphological traits that have been important for generic de-
limitation, we scored variation in armature, aspects of oral heteromorphy and mode
of fruit dehiscence and mapped their distribution across the Caesalpinioideae phy-
logeny. Our goal was to highlight how an over-reliance on broadly-dened character
complexes or functional traits may have misled classication in the past, rather than to
perform detailed reconstructions of character evolution through time or to thoroughly
assess the homology of various character states.
e three character complexes and their states were dened as follows:
• armature (six states): unarmed; nodal or internodal prickles on stem; stipular
spines; nodal axillary thorns, including the axillary inorescence axes which are modi-
ed into spines in Chloroleucon (Benth.) Britton & Rose; spinescent shoots.
• oral heteromorphy (three states): homomorphic, i.e. with no conspicuous
modication or variation amongst owers within an inorescence (here we include
inorescences that do not show any conspicuous phenotypic variation beyond the
very common occurrence of variable proportions of male and bisexual owers within
inorescences of many mimosoid genera); heteromorphic 1 = basal owers of the in-
orescence with showy staminodia; heteromorphic 2 = the central ower (or owers)
enlarged/sessile cf. the peripheral (sometimes pedicellate) owers.
• pod dehiscence (six states): indehiscent; inertly dehiscent along one or both su-
tures; explosively dehiscent, the woody valves twisting and splitting along both sutures
along whole length of pod simultaneously; elastically dehiscent from the apex, the valves
recurving, but not laterally twisting; craspedium, fruits breaking up into free-falling
one-seeded articles leaving a persistent replum or whole valve breaking away intact from
replum (valvately dehiscent); lomentiform fruit, the valves readily cracking between the
seeds into one-seeded articles, taken here to include crypto-lomentiform fruits.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
12
Data were assembled from taxonomic monographs, revisions and oras. Character
evolution was simulated across the phylogeny using the ‘make.simmap’ function in the
phytools (Revell 2012) R (R Core Team 2022) package, with 300 independent simula-
tions and a symmetrical rates’ (SYM) model. In each analysis, the character complex
of interest (i.e. armature, oral heteromorphy and pod dehiscence) was treated as a
single character with multiple states. A rooted phylogeny, without outgroups, was used
for the analyses. e root character state was assigned an uninformed prior (i.e. each
character state had the same initial probability of occurrence).
Data availability
A tree le of the ASTRAL phylogeny based on the single-copy genes (depicted in
Figs 2–12) is included as online Suppl. material 4. In this tree le, all taxon names
have been updated to reect taxonomic changes made in all the entries in Advances in
Legume Systematics 14 Part 1.
Results
Phylogenomics
For full results of the sequencing, orthology assembly and phylogenetic inference, see
Ringelberg et al. (2022). Here a brief overview is provided.
Hybrid capture and sequencing yielded a large phylogenomic dataset with little
missing data: the concatenated nucleotide alignment of the 821 single-copy nuclear
genes (a subset of all 997 genes, see below) contains 944,871 sites, 824,713 alignment
patterns (i.e. an indication of the phylogenetic informativeness of the alignment, de-
termined by RAxML) and only 11.88% gaps. e ten nuclear species trees that were
inferred using dierent phylogenetic methods are well-supported in terms of gene tree
congruence measures (Figs 2–12) and largely congruent with each other. e few topo-
logical dierences between dierent phylogenies typically involve only small numbers
of species within relatively recent radiations, or deeper putative polytomies such as
along the backbone of the ingoid clade, characterised by lack of phylogenetic signal
across almost all genes (Koenen et al. 2020b), or the backbone of the Archidendron
clade (Fig. 8), characterised by both lack of signal and high conict amongst gene trees.
ese minor topological dierences do not aect any of the ndings of generic non-
monophyly discussed below.
e plastid phylogeny (Suppl. material 3) diers more substantially from the
nuclear species trees, reecting the fact that nuclear and chloroplast genomes have
unique and sometimes conicting evolutionary histories (Bruun-Lund et al. 2017;
Lee-Yaw et al. 2019; Rose et al. 2021). Cytonuclear discordance aects the mono-
phyly of Senegalia Raf. (Terra et al. 2022), Archidendron F. Muell. (Brown et al.
2022), Dimorphandra Schott, the placement of Desmanthus balsensis J.L. Con-
treras (Hughes et al. 2022b) and whether Zygia inundata (Ducke) H.C. Lima ex
Phylogenomics of Caesalpinioideae: generic re-delimitation 13
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Arcoa gonavensis Gardner and Knees 7026 (E)
Tetrapterocarpon geay i Koenen 231 (G, K)
Ceratonia siliqua Wieringa 3477 (WAG)
Acrocarpus fraxinifolius Manos 1416 (DUKE)
Umtiza listeriana 6th International Legume Conference 10 (JRAU)
Gymnocladus dioicus Jongkind and Wieringa 4426 (WAG)
Gleditsia chinensis Koenen 604 (Z)
Cassia cowanii var. guianensis Redden 3277 (US)
Senna cushina Hughes 3121 (Z)
Senna leandrii Koenen 245 (G, K)
Senna mollissima Hughes 3150 (Z)
Senna rugosa de Queiroz 15592 (HUEFS)
Senna lasseigniana Hughes 3086 (Z)
Senna velutina Wood 26598 (K)
Batesia floribunda Grenand 3032 (CAY)
Recordoxylon speciosum Redden 5983 (US)
Melanoxylon brauna Lopes and Andrade 113 (K)
Chamaecrista adiantifolia Iganci 861 (RB)
Chamaecrista viscosa Wood 26658 (K)
Chamaecrista ramosa Lewis 3845 (K)
Chamaecrista lineata Bradley 32006 (US)
Cordeauxia edulis Kuchar 17803 (K)
Stuhlmannia moavi Keraudren and Aymonin 25628 (MO, P)
Cenostigma pluviosum var. maraniona Hughes 3105 (MT)
Libidibia glabrata Lewis and Lozano 3073 (K)
Balsamocarpon brevifolium Eggli and Leuenberger 2986 (Z)
Hoffmannseggia arequipensis Hughes 2342 (FHO)
Zuccagnia punctata Fortunato 5545 (MO, BAB)
Arquita trichocarpa Gagnon 2018 (MT)
Pomaria jamesii Gagnon 2010 020 (MT)
Erythrostemon mexicanus Gagnon 2010 015 (MT)
Erythrostemon coluteifolius Gagnon 207 (MT)
Hererolandia pearsonii Kolberg and Loots HK 1399 (K)
Lophocarpinia aculeatifolia Vogt 1321 (G)
Haematoxylum brasiletto Gagnon 2010 013 (MT)
Caesalpinia cassioides Pennington 789 (K)
Denisophytum madagascariense Bruneau et al. 1348 (MT)
Paubrasilia echinata Filgueiras 3391 (NY)
Tara spinosa Eastwood 36 (FHO)
Coulteria platyloba MacQueen 178 (FHO)
Gelrebia rostrata 6th International Legume Conference 5 (JRAU)
Guilandina bonduc Herendeen and Mbago 9 XII 97 3 (US)
Moullava spicata Gillis 9504 (MO)
Biancaea decapetala Hughes 2227 (FHO)
Pterolobium stellatum Herendeen and Mbago 17 XII 97 9 (F)
Caesalpinia crista Herendeen 1 V 99 3 (US)
Mezoneuron kauaiensis Lorence and Wagner 8904 (PTBG)
2
C
aesalpinia cassioides
P
ennington 789
(
K
)
C
aesalpinia
c
r
ista Herendeen 1 V 99 3 (U
S
)
Arcoa gonavensis Gardner and Knees 7026 (E)
Tetrapterocarpon geay i Koenen 231 (G, K)
Ceratonia siliqua Wieringa 3477 (WAG)
Acrocarpus fraxinifolius Manos 1416 (DUKE)
Umtiza listeriana 6th International Legume Conference 10 (JRAU)
Gymnocladus dioicus Jongkind and Wieringa 4426 (WAG)
Gleditsia chinensis Koenen 604 (Z)
Senna cushina Hughes 3121 (Z)
Senna leandrii Koenen 245 (G, K)
Senna mollissima Hughes 3150 (Z)
Senna rugosa de Queiroz 15592 (HUEFS)
Senna lasseigniana Hughes 3086 (Z)
Senna velutina Wood 26598 (K)
Batesia floribunda Grenand 3032 (CAY)
Recordoxylon speciosum Redden 5983 (US)
Melanoxylon brauna Lopes and Andrade 113 (K)
Chamaecrista adiantifolia Iganci 861 (RB)
Chamaecrista viscosa Wood 26658 (K)
Chamaecrista ramosa Lewis 3845 (K)
Chamaecrista lineata Bradley 32006 (US)
Cordeauxia edulis Kuchar 17803 (K)
Stuhlmannia moavi Keraudren and Aymonin 25628 (MO, P)
Libidibia glabrata Lewis and Lozano 3073 (K)
Balsamocarpon brevifolium Eggli and Leuenberger 2986 (Z)
Hoffmannseggia arequipensis Hughes 2342 (FHO)
Zuccagnia punctata Fortunato 5545 (MO, BAB)
Arquita trichocarpa Gagnon 2018 (MT)
Pomaria jamesii Gagnon 2010 020 (MT)
Erythrostemon mexicanus Gagnon 2010 015 (MT)
Erythrostemon coluteifolius Gagnon 207 (MT)
Hererolandia pearsonii Kolberg and Loots HK 1399 (K)
Lophocarpinia aculeatifolia Vogt 1321 (G)
Haematoxylum brasiletto Gagnon 2010 013 (MT)
Caesalpinia cassioides Pennington 789 (K)
Denisophytum madagascariense Bruneau et al. 1348 (MT)
Paubrasilia echinata Filgueiras 3391 (NY)
Tara spinosa Eastwood 36 (FHO)
Coulteria platyloba MacQueen 178 (FHO)
Gelrebia rostrata 6th International Legume Conference 5 (JRAU)
Guilandina bonduc Herendeen and Mbago 9 XII 97 3 (US)
Moullava spicata Gillis 9504 (MO)
Biancaea decapetala Hughes 2227 (FHO)
Pterolobium stellatum Herendeen and Mbago 17 XII 97 9 (F)
Caesalpinia crista Herendeen 1 V 99 3 (US)
Mezoneuron kauaiensis Lorence and Wagner 8904 (PTBG)
Cassia cowanii var. guianensis Redden 3277 (US)
Cenostigma pluviosum var. maraniona Hughes 3105 (MT)
(continued in Figure 3)
Genus non−monophyletic
0.71
0.25
0.69
0.7
0.19
0.32
0.17
0.48
0.07
0.18
0.47
0.53
0.64
0.89
0.7
0.72
0.8
0.26
0.35
0.33
0.82
0.5
0.81
0.68
0.68
0.72
0.26
0.68
0.06 0.29
0.5
0.13 0.15
0.05 0.26
0
0.02
0.01
0.01
0.03
0.03
0.48
0.02
0.05
0.49
0
0.12
0.08
0.20
Figure 2. Phylogeny of Caesalpinioideae, part 1 (continued in Figs 3–12). Left part of gure shows complete
Caesalpinioideae phylogeny with highlighted in red the part shown in detail on the right. Depicted phylog-
eny is the ASTRAL (Zhang et al. 2018) phylogeny based on 821 single-copy nuclear gene trees, with branch
lengths expressed in coalescent units and terminal branches assigned an arbitrary uniform length for visual
clarity. Genera resolved as (potentially) non-monophyletic are highlighted and clades recognised by Koenen et
al. (2020b) are labelled. Support for relationships is based on gene tree conict: pie charts show the fractions
of supporting and conicting gene trees per node calculated using PhyParts (Smith et al. 2015), with blue
representing supporting gene trees, green gene trees supporting the most common alternative topology, red
gene trees supporting further alternative topologies and grey gene trees uninformative for this node. Numbers
above nodes are Extended Quadripartition Internode Certainty scores calculated with QuartetScores (Zhou
et al. 2020). Numbers below nodes are the outcome of ASTRAL’s polytomy test (Sayyari and Mirarab 2018),
which tests for each node whether the polytomy null model can be rejected. Only non-signicant (i.e. > 0.05)
scores are shown, i.e. only for nodes that are better regarded as polytomies according to the test.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
14
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Schizolobium parahyba Klitgaard 694 (K)
Bussea perrieri Randrianasolo 527 (WAG)
Peltophorum dubium Hughes 2436 (FHO)
Peltophorum africanum Koenen 601 (Z)
Parkinsonia andicola Hughes 2619 (FHO)
Heteroflorum sclerocarpum Hughes 1849 (FHO)
Conzattia multiflora Hughes 2071 (FHO)
Colvillea racemosa Bruneau 1403 (MT)
Delonix decaryi Koenen 238 (G, K)
Delonix edule Willing s.n. (K)
Moldenhawera floribunda Klitgaard 30 (K)
Diptychandra aurantiaca Wood 26513 (K)
Arapatiella psilophylla de Lima et al. 7906 (RB)
Jacqueshuberia brevipes Redden 1240 (US)
Tachigali guianensis Mori 22791 (NY)
Tachigali bracteolata Mori 24793 (NY)
Tachigali paniculata Henkel 657 (NY)
Tachigali va squezii Neill 13998 (MO)
Tachigali odoratissima Morim 562 (RB)
Dimorphandra gardneriana Hughes 2409 (FHO)
Dimorphandra macrostachya Iganci 877 (RB)
Dimorphandra davisii Luckow 4593 (BH)
Mora gonggrijpii Breteler 13792 (WAG)
Burkea africana Smith 6 (WAG)
Stachyothyrsus staudtii van Andel 4054 (WAG)
Dinizia jueirana−facao Folli 4889 (HUEFS, K)
Campsiandra comosa Iganci 856 (RB)
Pachyelasma tessmannii Wieringa 5229 (WAG)
Erythrophleum ivorense Wieringa 5487 (WAG)
Erythrophleum teysmannii Smitinand 10468 (K)
2
D
i
mo
r
p
h
an
d
r
a gar
d
ne
r
i
ana Hughes 2409 (FH
O
)
Di
mo
r
p
h
an
d
r
a macros
t
ac
h
y
a I
g
anci 877
(
RB
)
Di
mo
r
p
h
an
d
r
a
d
a
v
i
s
ii
Lu
c
k
o
w
4593
(
BH
)
Schizolobium parahyba Klitgaard 694 (K)
Bussea perrieri Randrianasolo 527 (WAG)
Peltophorum dubium Hughes 2436 (FHO)
Peltophorum africanum Koenen 601 (Z)
Parkinsonia andicola Hughes 2619 (FHO)
Heteroflorum sclerocarpum Hughes 1849 (FHO)
Conzattia multiflora Hughes 2071 (FHO)
Colvillea racemosa Bruneau 1403 (MT)
Delonix decaryi Koenen 238 (G, K)
Delonix edule Willing s.n. (K)
Moldenhawera floribunda Klitgaard 30 (K)
Diptychandra aurantiaca Wood 26513 (K)
Arapatiella psilophylla de Lima et al. 7906 (RB)
Jacqueshuberia brevipes Redden 1240 (US)
Tachigali guianensis Mori 22791 (NY)
Tachigali bracteolata Mori 24793 (NY)
Tachigali paniculata Henkel 657 (NY)
Tachigali va squezii Neill 13998 (MO)
Tachigali odoratissima Morim 562 (RB)
Dimorphandra gardneriana Hughes 2409 (FHO)
Dimorphandra macrostachya Iganci 877 (RB)
Dimorphandra davisii Luckow 4593 (BH)
Mora gonggrijpii Breteler 13792 (WAG)
Burkea africana Smith 6 (WAG)
Stachyothyrsus staudtii van Andel 4054 (WAG)
Dinizia jueirana−facao Folli 4889 (HUEFS, K)
Campsiandra comosa Iganci 856 (RB)
Pachyelasma tessmannii Wieringa 5229 (WAG)
Erythrophleum ivorense Wieringa 5487 (WAG)
Erythrophleum teysmannii Smitinand 10468 (K)
Mimosoid clade (continued in Figure 4)
Genus non−monophyletic
0.27
0.01
0.05
0.14
0.44
0.01
0.81
0.29
0.55
0.09
0.09
0.21
0.77
0.59
0.36
0.17
0.2
0.15
0.63
0.71
0.79
0.28
0.4
0.57
0.68
0.03
0
0.07
0.76
0.01
0.47
Figure 3. Phylogeny of Caesalpinioideae (continued). See Figure 2 for caption.
Barneby & J.W. Grimes and Z. sabatieri Barneby & J.W. Grimes form the sister
clade of Inga or a grade subtending Inga.
Hereafter the ASTRAL phylogeny based on the subset of 821 single-copy nuclear
gene trees is used as the ‘reference’ Caesalpinioideae backbone phylogeny (Figs 2–12).
We use this particular tree over the plastome phylogeny because the nuclear dataset is
Phylogenomics of Caesalpinioideae: generic re-delimitation 15
based on hundreds of independent loci and contains considerably more sites, taxa and
fewer gaps, while the plastome phylogeny is based on a single non-recombining locus.
e nuclear trees, therefore, likely better represent an approximation of the true evolu-
tionary history of Caesalpinioideae than the phylogeny based on maternally inherited
plastid data. Of the various nuclear trees, we select the ASTRAL phylogeny because we
nd extensive conict amongst individual gene trees in certain parts of the phylogeny
(Figs 2–12), which violates the central assumption of the concatenation model (Jiang et
al. 2020) and because the multi-species coalescent model has been shown to consistently
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Pentaclethra macroloba Boyle 6720 (K)
Pentaclethra macrophylla Galeuchet & Balthazar 10 (Z)
Tetrapleura tetraptera Koenen 155 (WAG)
Adenanthera pavonina Ambriansyah and Arifin AA295 (K)
Amblygonocarpus andongensis Sokpon 1451 (WAG)
Pseudoprosopis sericea Jongkind 9513 (WAG)
Pseudoprosopis gilletii Wieringa 6021 (WAG)
Pseudoprosopis euryphylla Lock & Frison 88/83 (K)
Xylia evansii Jongkind 9064 (WAG)
Calpocalyx dinklagei Wieringa 6094 (WAG)
Calpocalyx heitzii van Valkenburg 2877 (WAG)
Xylia hoffmannii Koenen 402 (Z)
Xylia torreana Maurin et al. RBN171 (JRAU)
Sympetalandra unijuga Sidiyasa 1320 (K)
Sympetalandra schmutzii Schmutz 3764 (MO)
Chidlowia sanguinea Wieringa 4338 (WAG)
Aubrevillea kerstingii Nimba Botanic Team JR957 (WAG)
Piptadeniastrum africanum Koenen 152 (WAG)
Entada pervillei Koenen 302 (G, K)
Entada rheedei Koenen 496 (Z)
Entada sp. van Beusekom et al. 4706
Entada polystachya Amaral Santos 3326 (CEN)
Entada tuberosa Koenen 417 (G, K)
Entada africana van der Maesen 7144 (WAG)
Entada arenaria Bamps 8098 (WAG)
Elephantorrhiza elephantina Komape, Mabe, and Siebert 198 (JRAU)
Elephantorrhiza burkei van der Bank 15 (JRAU)
Prosopis africana Essou 2110 (WAG)
Plathymenia reticulata de Queiroz 15688 (HUEFS)
Fillaeopsis discophora Wieringa 5498 (WAG)
Newtonia hildebrandtii Maurin 2457 (JRAU)
5
X
y
l
i
a
e
v
a
nsii Jongkind 9064
(
W
A
W
W
G
)
C
alpocalyx dinklagei Wie
r
inga 6094
(
W
A
W
W
G)
C
alpocal
y
x heitzii
v
an
V
al
V
V
k
en
b
u
rg 2877
(
W
A
W
W
G)
X
y
lia ho
ff
mannii
K
oenen 402
(
Z
)
X
y
l
i
a torreana Ma
u
r
in et al. RBN171
(
J
R
A
U)
E
nta
d
a p
e
r
v
i
lle
i
K
oenen 302 (G, K)
K
K
Entada rheede
i
K
oenen 496
(
Z
)
E
nta
d
a
s
p
.
v
an
B
eus
e
k
om et a
l
. 470
6
E
nta
d
a po
ly
sta
c
h
y
a
A
m
a
r
al Santos 3326 (CEN
)
E
nta
d
a tu
b
erosa
K
oenen 417 (G, K)
E
ntada a
f
r
i
cana
v
a
n der Maesen 7144
(
W
A
W
W
G
)
E
nta
d
a aren
a
r
i
a Bamps 8098
(
W
A
W
W
G
)
P
rosopis a
f
r
i
cana Essou 2110
(
W
A
W
W
G)
Pentaclethra macroloba Boyle 6720 (K)
Pentaclethra macrophylla Galeuchet & Balthazar 10 (Z)
Tetrapleura tetraptera Koenen 155 (WAG)
Adenanthera pavonina Ambriansyah and Arifin AA295 (K)
Amblygonocarpus andongensis Sokpon 1451 (WAG)
Pseudoprosopis sericea Jongkind 9513 (WAG)
Pseudoprosopis gilletii Wieringa 6021 (WAG)
Pseudoprosopis euryphylla Lock & Frison 88/83 (K)
Xylia evansii Jongkind 9064 (WAG)
Calpocalyx dinklagei Wieringa 6094 (WAG)
Calpocalyx heitzii van Valkenburg 2877 (WAG)
Xylia hoffmannii Koenen 402 (Z)
Xylia torreana Maurin et al. RBN171 (JRAU)
Sympetalandra unijuga Sidiyasa 1320 (K)
Sympetalandra schmutzii Schmutz 3764 (MO)
Chidlowia sanguinea Wieringa 4338 (WAG)
Aubrevillea kerstingii Nimba Botanic Team JR957 (WAG)
Piptadeniastrum africanum Koenen 152 (WAG)
Entada pervillei Koenen 302 (G, K)
Entada rheedei Koenen 496 (Z)
Entada polystachya Amaral Santos 3326 (CEN)
Entada tuberosa Koenen 417 (G, K)
Entada africana van der Maesen 7144 (WAG)
Entada arenaria Bamps 8098 (WAG)
Elephantorrhiza elephantina Komape, Mabe, and Siebert 198 (JRAU)
Elephantorrhiza burkei van der Bank 15 (JRAU)
Prosopis africana Essou 2110 (WAG)
Plathymenia reticulata de Queiroz 15688 (HUEFS)
Fillaeopsis discophora Wieringa 5498 (WAG)
Newtonia hildebrandtii Maurin 2457 (JRAU)
Entada sp. van Beusekom et al. 4706
core mimosoids (continued in Figure 5)
Genus non−monophyletic
Xylia clade
Entada
clade
0.44
0.31
0.61
0.17
0.77
0.8
0.53
0.62
0.65
0.86
0.03
0.57
0.67
0.58
0.57
0.61
0.9
0.51
0.52
−0.01
−0.01
−0.01
−0.01
−0.01
−0.01
−0.01
0.7
0.14
0.74
0.05
0.11
0.563
Figure 4. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
16
outperform the concatenation model on a range of phylogenomic datasets (Jiang et al.
2020). Our analyses reveal that dierent approaches to orthology assessment have a very
minor impact on the nal Caesalpinioideae phylogeny, likely because the vast majority
of nuclear genes in our dataset are single-copy (i.e. 821 of 997) (see Ringelberg et al.
2022 for details). Nevertheless, how to deal with multi-copy genes is a contentious topic
in phylogenetics (Yang and Smith 2014; Moore et al. 2018; Karimi et al. 2019) and we,
therefore, focus on the ASTRAL phylogeny based on just the 821 single-copy genes.
e resultant ASTRAL phylogeny is, in general, robustly supported across the ma-
jority of nodes using measures of gene tree support and conict (Figs 2–12). However,
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Cylicodiscus gabunensis Sosef 645A (WAG)
Indopiptadenia oudhensis Adhikari, Poulsen, and Parmar BAG31 (E)
Prosopis cineraria Hafisullah and Dilawar 266 (Z)
Prosopis farcta Kerimov 31 (NY)
Xerocladia viridiramis Kolberg and Tholkes HK2493 (WIND)
Prosopis ferox Hughes 2618 (FHO)
Prosopis strombulifera Kiesling 4828 (NY)
Prosopis argentina Guaglianone 1338 (NY)
Prosopis kuntzei Hughes 2458 (FHO)
Prosopis juliflora Hughes 1703 (FHO)
Prosopis laevigata Hughes 2058 (FHO)
Prosopis ruscifolia Fortunato 6773 (NY)
Neptunia oleracea Koenen 283 (Z)
Lemurodendron capuronii Koenen 435 (Z)
Leucaena trichandra Hughes 1128 (FHO)
Schleinitzia megaladenia Ramos & Edaño 46708 (P)
Schleinitzia novoguineensis Chaplin 57 84 (FHO)
Schleinitzia insularum Rinehart 17441 (K)
Desmanthus balsensis Hughes 1825 (FHO)
Kanaloa kahoolawensis Lorence 7380 (PTBG)
Desmanthus leptophyllus Hughes 2035 (FHO)
Desmanthus virgatus Wood 26551 (K)
Desmanthus acuminatus Hughes 2314 (FHO)
Mimozyganthus carinatus Hughes 2476 (FHO)
Piptadeniopsis lomentifera Luckow 4505 (BH)
Prosopidastrum globosum Luckow s.n. (BH)
Calliandropsis nervosa Hughes 1784 (K)
Dichrostachys cinerea Maurin 256 (JRAU)
Dichrostachys myriophylla Koenen 301 (G, K)
Gagnebina commersoniana Koenen 374 (G, K)
Dichrostachys paucifoliolata Luckow 4157 (BH)
Alantsilodendron glomeratum Koenen 257 (G, K)
Dichrostachys unijuga Koenen 242 (G, K)
Dichrostachys tenuifolia Labat 3579 (P)
Alantsilodendron villosum Koenen 409 (G, K)
Dichrostachys richardiana Koenen 282 (G, K)
Alantsilodendron pilosum Koenen 203 (Z)
2
P
rosop
i
s c
i
n
e
r
a
r
i
a Ha
f
isullah and Dil
a
w
ar 266
(
Z
)
P
rosop
i
s
f
arc
t
a
K
e
r
i
m
o
v 31
(
NY
)
P
rosop
i
s
f
er
o
x Hughes 2618
(
FH
O)
P
rosop
i
s strom
b
u
li
f
e
r
a Kiesling 4828
(
NY
)
Prosopis argentina Guaglianone 1338 (NY
)
Proso
p
is kunt
z
e
i Hughes 2458 (FHO)
Proso
p
is
j
uli
f
l
o
r
a
Hughes 1703
(
FH
O)
Prosopis la
e
vigata Hughes 2058
(
FH
O)
P
rosop
i
s
r
usc
i
f
o
li
a
F
o
r
t
unato 6773
(
NY
)
Desmanthus balsensis Hughes 1825 (FHO
)
D
esmanthus le
p
to
p
hyllus Hughes 2035 (FHO
)
Desmanthus virgatus Wood 26551 (K
)
Desmanthus acuminatus Hu
g
hes 2314 (FHO
)
Dichrostac
h
y
s cinerea Maurin 256 (JR
A
U)
Dichrosta
c
hys myriophylla
K
oenen 301 (G, K
)
G
agnebina commersoniana
K
o
enen 374
(G
, K
)
Dichrosta
c
h
ys pauc
i
f
o
liolata Lu
c
k
o
w 4157
(
BH
)
Al
ants
il
o
d
en
d
ron g
l
om
e
r
at
um
K
o
enen 257 (G, K
)
Di
c
h
rosta
c
h
ys un
ij
uga
K
oenen 242
(G
, K
)
D
i
c
hr
ostac
h
y
s t
e
n
u
i
f
o
lia Labat 3579
(
P
)
Al
ants
il
o
d
en
d
ron v
ill
osum
K
o
enen 409
(G
, K
)
Di
c
h
rosta
c
h
y
s
r
i
c
h
ar
di
ana
K
oenen 282 (G, K
)
Alantsilodendron
p
ilosum
K
oenen 203 (Z
)
Cylicodiscus gabunensis Sosef 645A (WAG)
Indopiptadenia oudhensis Adhikar i, Poulsen, and Parmar BAG31 (E)
Prosopis cineraria Hafisullah and Dilawar 266 (Z)
Prosopis farcta Kerimov 31 (NY)
Xerocladia viridiramis Kolberg and Tholkes HK2493 (WIND)
Prosopis ferox Hughes 2618 (FHO)
Prosopis strombulifera Kiesling 4828 (NY)
Prosopis argentina Guaglianone 1338 (NY)
Prosopis kuntzei Hughes 2458 (FHO)
Prosopis juliflora Hughes 1703 (FHO)
Prosopis laevigata Hughes 2058 (FHO)
Prosopis ruscifolia Fortunato 6773 (NY)
Neptunia oleracea Koenen 283 (Z)
Lemurodendron capuronii Koenen 435 (Z)
Leucaena trichandra Hughes 1128 (FHO)
Schleinitzia megaladenia Ramos & Edaño 46708 (P)
Schleinitzia novoguineensis Chaplin 57 84 (FHO)
Schleinitzia insularum Rinehart 17441 (K)
Desmanthus balsensis Hughes 1825 (FHO)
Kanaloa kahoolawensis Lorence 7380 (PTBG)
Desmanthus leptophyllus Hughes 2035 (FHO)
Desmanthus virgatus Wood 26551 (K)
Desmanthus acuminatus Hughes 2314 (FHO)
Mimozyganthus carinatus Hughes 2476 (FHO)
Piptadeniopsis lomentifera Luckow 4505 (BH)
Prosopidastrum globosum Luckow s.n. (BH)
Calliandropsis nervosa Hughes 1784 (K)
Dichrostachys cinerea Maurin 256 (JRAU)
Dichrostachys myriophylla Koenen 301 (G, K)
Gagnebina commersoniana Koenen 374 (G, K)
Dichrostachys paucifoliolata Luckow 4157 (BH)
Alantsilodendron glomeratum Koenen 257 (G, K)
Dichrostachys unijugaKoenen 242 (G, K)
Dichrostachys tenuifolia Labat 3579 (P)
Alantsilodendron villosum Koenen 409 (G, K)
Dichrostachys richardiana Koenen 282 (G, K)
Alantsilodendron pilosum Koenen 203 (Z)
(continued in Figure 6)
Genus non−monophyletic Genus possibly non−monophyletic
Dichrostachys clade
−0.01
0
0.78
0.1
0.18
0.09
0.76
0.51
0.64
0.18
0.03
0.2
0.47
0.71
0.14
0.38
0.84
0.87
0.52
−0.01
−0.04
0
0.07
0.44
0.02
0.02
0
0.01
0.05
0
0.12
0.51
0.02
0.87
0.03
0.74
0
0.676
0.598
Figure 5. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Phylogenomics of Caesalpinioideae: generic re-delimitation 17
there are also some specic parts of the phylogeny which show high levels of gene tree
conict and/or lack of phylogenetic signal across large fractions of genes, which appears
to be a feature of most phylogenies based on large phylogenomic datasets (Salichos and
Rokas 2013; Wang et al. 2019; Jiang et al. 2020; Koenen et al. 2020a,b; Yang et al.
2020). In most cases, the primary source of gene tree conict is limited signal in indi-
vidual gene trees rather than the presence of strongly-supported alternative topologies
amongst the gene trees (Figs 2–12, Koenen et al. 2020b), suggesting that the conict
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Vachellia tortilis Koenen 603 (Z)
Vachellia erioloba living collection Botanical Garden Zurich
Vachellia viguieri Koenen 199 (Z)
Vachellia nilotica Eastwood 117 (FHO)
Vachellia farnesiana living collection Botanical Garden Zurich
Anadenanthera colubrina de Queiroz 15685 (HUEFS)
Parkia ulei Poncy s.n. (K)
Parkia panurensis Iganci 842 (RB)
Parkia igneiflora Iganci 885 (RB)
Parkia pendula Simon 1194 (CEN)
Parkia bahiae de Queiroz 15699 (HUEFS)
Parkia timoriana Murphy 351 (NY)
Parkia bicolor Wieringa 6265 (WAG)
Lachesiodendron viridiflorum de Queiroz 15614 (HUEFS)
Stryphnodendron paniculatum Simon 1058 (CEN)
Stryphnodendron adstringens de Queiroz 15580 (HUEFS)
Stryphnodendron pulcherrimum de Queiroz 15482 (HUEFS)
Pseudopiptadenia psilostachya Simon 1245 (CEN)
Pseudopiptadenia contorta de Queiroz 15582 (HUEFS)
Stryphnodendron duckeanum Simon 1606 (CEN)
Pityrocarpa moniliformis Wood 26516 (K)
Pseudopiptadenia schumanniana de Lima 7903 (RB)
Parapiptadenia zehntneri de Queiroz 15692 (HUEFS)
Parapiptadenia excelsa Hughes 2451 (FHO)
Piptadenia uaupensis Mori & Ishikawa 20836 (K)
Piptadenia robusta Luckow 4633 (BH)
Piptadenia buchtienii Hughes 2427 (FHO)
Adenopodia scelerata Jongkind 10602 (WAG)
Adenopodia patens Sandoval MS343 (K)
Mimosa myriadenia Iganci 835 (RB)
Mimosa revoluta Hughes 3051 (Z)
Mimosa hondurana Simon 858 (MEXU)
Mimosa hexandra Wood 26499 (K)
Mimosa tenuiflora de Queiroz 15498 (HUEFS)
Mimosa ceratonia de Queiroz 15484 (HUEFS)
Mimosa grandidieri Koenen 207 (Z)
Mimosa rubicaulis subsp. himalayana Thomas SM 24 1 (K)
Mimosa invisa Simon 715 (FHO)
Mimosa speciosissima Simon 753 (FHO)
Mimosa pigra Simon 820 (MEXU)
Mimosa pudica Simon 1480 (CEN)
Mimosa tequilana Simon 813 (MEXU)
Mimosa tricephala Simon 849 (MEXU)
Mimosa dolens Simon 879 (FHO)
2
S
t
r
y
phnodendron paniculatum Simon 1058 (CEN)
St
r
y
p
h
no
d
en
d
ron a
d
s
t
r
ingens de Queiroz 15580 (HUEFS)
St
r
y
p
h
no
d
en
d
ron pu
l
c
h
e
r
r
i
m
um de Queiroz 15482 (HUEFS)
Pseudop
i
ptaden
i
a ps
i
losta
c
h
y
a
S
imon 1245 (
C
EN)
Pseudo
p
i
p
tadenia conto
r
t
a de Queiroz 15582
(
HUEFS
)
St
r
y
phnodendron duc
k
ea
n
um Simon 1606 (CEN)
Pseudopiptadenia schumanniana de Lima 7903 (RB)
Vachellia tortilis Koenen 603 (Z)
Vachellia erioloba living collection Botanical Garden Zurich
Vachellia viguieri Koenen 199 (Z)
Vachellia nilotica Eastwood 117 (FHO)
Vachellia farnesiana living collection Botanical Garden Zurich
Anadenanthera colubrina de Queiroz 15685 (HUEFS)
Parkia ulei Poncy s.n. (K)
Parkia panurensis Iganci 842 (RB)
Parkia igneiflora Iganci 885 (RB)
Parkia pendula Simon 1194 (CEN)
Parkia bahiae de Queiroz 15699 (HUEFS)
Parkia timoriana Murphy 351 (NY)
Parkia bicolor Wieringa 6265 (WAG)
Lachesiodendron viridiflorum de Queiroz 15614 (HUEFS)
Stryphnodendron paniculatum Simon 1058 (CEN)
Stryphnodendron adstringens de Queiroz 15580 (HUEFS)
Stryphnodendron pulcherrimum de Queiroz 15482 (HUEFS)
Pseudopiptadenia psilostachyaSimon 1245 (CEN)
Pseudopiptadenia contorta de Queiroz 15582 (HUEFS)
Stryphnodendron duckeanum Simon 1606 (CEN)
Pityrocarpa moniliformis Wood 26516 (K)
Pseudopiptadenia schumanniana de Lima 7903 (RB)
Parapiptadenia zehntneri de Queiroz 15692 (HUEFS)
Parapiptadenia excelsa Hughes 2451 (FHO)
Piptadenia uaupensis Mori & Ishikawa 20836 (K)
Piptadenia robusta Luckow 4633 (BH)
Piptadenia buchtienii Hughes 2427 (FHO)
Adenopodia scelerata Jongkind 10602 (WAG)
Adenopodia patens Sandoval MS343 (K)
Mimosa myriadenia Iganci 835 (RB)
Mimosa revoluta Hughes 3051 (Z)
Mimosa hondurana Simon 858 (MEXU)
Mimosa hexandra Wood 26499 (K)
Mimosa tenuiflora de Queiroz 15498 (HUEFS)
Mimosa ceratonia de Queiroz 15484 (HUEFS)
Mimosa grandidieri Koenen 207 (Z)
Mimosa invisa Simon 715 (FHO)
Mimosa speciosissima Simon 753 (FHO)
Mimosa pigra Simon 820 (MEXU)
Mimosa pudica Simon 1480 (CEN)
Mimosa tequilana Simon 813 (MEXU)
Mimosa tricephala Simon 849 (MEXU)
Mimosa dolens Simon 879 (FHO)
Mimosa rubicaulis subsp. himalayana Thomas SM 24 1 (K)
ingoid clade (continued in Figure 7)
Genus non−monophyletic
Parkia clade
Stryphno−
dendron
clade
M
i
m
o
s
a
c
l
a
d
e
−0.12
−0.15
0.16
0.33
0.41
0.83
0.33
0.27
0.06
0.01
0.13
0.09
0.21
0.58
0.06
0.53
0.74
0.6
0.21
0.39
0.29
0.53
0.62
0.26
0.73
0.07
0.04
0.81
0.41
0.1
0.77
−0.15
−0.04
0.55
0.27
0.02
0.02
0.02
0.03
0.05
0.42
0.08
0.05
0.02
Figure 6. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
18
often has methodological rather than biological causes and implying that the presence
of conict per se is no reason for doubts about the recovered Caesalpinioideae topology.
However, some parts of the phylogeny with high levels of gene tree conict or lack of
signal may be better viewed as potential polytomies, including the previously identied
putative hard polytomy subtending a set of six or seven lineages along the backbone of
the ingoid clade (Koenen et al. 2020b) and a putative polytomy across the backbone of
the large Archidendron clade (see Appendix 1). ese parts of the phylogeny showing
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Senegalia ataxacantha Jongkind 10603 (WAG)
Senegalia nigrescens Barnes 536 (FHO)
Parasenegalia visco Fortunato 7645 (SI)
Mariosousa sericea Chase 18949 (K)
Pseudosenegalia feddeana Atahuachi 1146 (FHO, LPB)
Albizia leonardii Zanoni 34986 (NY)
Senegalia bahiensis de Queiroz 15499 (HUEFS)
Senegalia sakalava Koenen 215 (Z)
Senegalia pentagona Jongkind 10670 (WAG)
Senegalia borneensis Ambriansyah AA1679 (L)
Acaciella villosa Hughes 2635 (FHO)
Afrocalliandra gilbertii Gillett and Hemming 24799 (PRE)
Afrocalliandra redacta Germishuizen 5585 (PRE)
Calliandra hygrophila de Queiroz 15542 (HUEFS)
Calliandra viscidula de Queiroz 15541 (HUEFS)
Calliandra haematomma Kass 2008 1 (BH)
Calliandra parviflora Wood 26606 (K)
Calliandra haematocephala Hughes 2604 (FHO)
Calliandra bella de Queiroz 15696 (HUEFS)
Calliandra sessilis de Queiroz 15608 (HUEFS)
Zapoteca nervosa Garcia 665 (NY)
Zapoteca amazonica Graham 270 (K)
Zapoteca caracasana Hughes 3071 (Z)
Zapoteca aculeata Delinks 332 (NY)
Viguieranthus glaber Koenen 325 (Z)
Faidherbia albida Maurin 3495 (JRAU)
Sanjappa cynometroides Krishnaraj 71501 (TBGT)
Calliandra sp. nov. Poilane 9150 (P)
Thailentadopsis tenuis Larsen & Larsen 33960 (K)
Thailentadopsis nitida Kostermans 28234 (K)
Hesperalbizzia occidentalis Hughes 1296 (FHO)
Lysiloma latisiliquum Pennington 9197 (K)
Lysiloma candidum Marazzi 300 (ASU)
Cojoba rufescens Castroviejo 14683 (K)
Cojoba arborea Simon 1545 (CEN)
Cojoba filipes Colella 1331 (NY)
Cojoba zanonii Zanoni 36337 (NY)
Havardia campylacantha Hughes 1404 (K)
Sphinga acatlensis Hughes 2112 (FHO)
Painteria leptophylla Te norio and Manriquez 4067 (MEXU)
Painteria elachistophylla Guzman Cruz UG2169 (K)
Ebenopsis confinis Hughes 1539 (FHO)
Havardia pallens Hughes 2138 (FHO)
Pithecellobium keyense Chase 8958 (K)
Pithecellobium dulce Marazzi 309 (ASU)
Pithecellobium excelsum Hughes 3101 (Z)
Pithecellobium macrandrium Aguilar 1894 (NY)
Pithecellobium hymenaeifolium Arvigo 216 (NY)
2
S
enegalia ataxacantha Jongkind 10603 (
W
A
W
W
G
)
S
enegalia nigrescens Ba
r
n
es 536 (FH
O)
A
lbizia leonardii Zanoni 34986
(
NY
)
S
enegalia bahiensis de
Q
ueiroz 15499 (HUEF
S
)
S
enegalia sakal
a
v
a
K
oenen 215 (Z)
K
K
S
enegalia pentagona Jongkind 10670 (
W
A
W
W
G
)
S
ene
g
alia bo
r
neens
i
s Am
b
r
i
ans
y
ah AA1679
(
L
)
C
allian
d
r
a
h
y
grophila de
Q
ueiroz 15542 (HUEF
S
)
Callian
d
r
a viscidula de Queiroz 15541 (HUEFS)
Callian
d
r
a
haematomma Kass 2008 1
(
BH
)
C
alliand
r
a
pa
r
vi
f
l
o
r
a
W
o
od 26606
(
K
)
C
allian
d
r
a haematocephala Hughes 2604 (FH
O
)
C
allian
d
r
a bella de
Q
ueiroz 15696 (HUEF
S)
C
allian
d
r
a sessilis de Queiroz 15608 (HUEFS)
Calliand
r
a
s
p
.
n
o
v
.
P
oilane 9150
(
P
)
H
a
v
a
rd
i
a cam
p
y
lacantha Hughes 1404
(
K
)
Sphinga acatlensis Hughes 2112 (FHO
)
P
ai
nte
r
i
a leptop
h
yll
a
T
eno
T
T
r
i
o and Man
r
i
quez 4067
(
MEXU
)
P
a
i
nte
r
i
a elach
i
sto
p
h
y
lla
G
uzman
C
r
uz U
G
2169 (K
)
Ebenopsis confinis Hu
g
hes 1539 (FHO)
H
a
v
a
rdia pallens Hughes 2138 (FH
O)
Senegalia ataxacantha Jongkind 10603 (WAG)
Senegalia nigrescens Barnes 536 (FHO)
Parasenegalia visco Fortunato 7645 (SI)
Mariosousa sericea Chase 18949 (K)
Pseudosenegalia feddeana Atahuachi 1146 (FHO, LPB)
Albizia leonardii Zanoni 34986 (NY)
Senegalia bahiensis de Queiroz 15499 (HUEFS)
Senegalia sakalava Koenen 215 (Z)
Senegalia pentagona Jongkind 10670 (WAG)
Senegalia borneensis Ambriansyah AA1679 (L)
Acaciella villosa Hughes 2635 (FHO)
Afrocalliandra gilbertii Gillett and Hemming 24799 (PRE)
Afrocalliandra redacta Germishuizen 5585 (PRE)
Calliandra hygrophila de Queiroz 15542 (HUEFS)
Calliandra viscidula de Queiroz 15541 (HUEFS)
Calliandra haematomma Kass 2008 1 (BH)
Calliandra parviflora Wood 26606 (K)
Calliandra haematocephala Hughes 2604 (FHO)
Calliandra bella de Queiroz 15696 (HUEFS)
Calliandra sessilis de Queiroz 15608 (HUEFS)
Zapoteca nervosa Garcia 665 (NY)
Zapoteca amazonica Graham 270 (K)
Zapoteca caracasana Hughes 3071 (Z)
Zapoteca aculeata Delinks 332 (NY)
Viguieranthus glaber Koenen 325 (Z)
Faidherbia albida Maurin 3495 (JRAU)
Sanjappa cynometroides Krishnaraj 71501 (TBGT)
Thailentadopsis tenuis Larsen & Larsen 33960 (K)
Thailentadopsis nitida Kostermans 28234 (K)
Hesperalbizzia occidentalis Hughes 1296 (FHO)
Lysiloma latisiliquum Pennington 9197 (K)
Lysiloma candidum Marazzi 300 (ASU)
Cojoba rufescens Castroviejo 14683 (K)
Cojoba arborea Simon 1545 (CEN)
Cojoba filipes Colella 1331 (NY)
Cojoba zanonii Zanoni 36337 (NY)
Sphinga acatlensis Hughes 2112 (FHO)
Painteria leptophylla Te norio and Manriquez 4067 (MEXU)
Painteria elachistophylla Guzman Cruz UG2169 (K)
Ebenopsis confinis Hughes 1539 (FHO)
Pithecellobium keyense Chase 8958 (K)
Pithecellobium dulce Marazzi 309 (ASU)
Pithecellobium excelsum Hughes 3101 (Z)
Pithecellobium macrandrium Aguilar 1894 (NY)
Pithecellobium hymenaeifolium Arvigo 216 (NY)
Havardia campylacantha Hughes 1404 (K)
Havardia pallens Hughes 2138 (FHO)
Calliandra sp. nov. Poilane 9150 (P)
(continued in Figure 8)
Genus non−monophyletic Genus possibly non−monophyletic
Calli−
andr
a
clade
Zapoteca clade
Cojoba clade
Pithecellobium
clade
−0.07
−0.07
−0.07
0.07
0.16
0.67
0.07
0.36
0
0.3
0.48
0
0.61
0.22
0.56
0.28
0.5
0.65
0.52
0.08
0.8
0.86
0.34
0.77
0.81
0.92
0.83
0.65
0.03
0
0
0.03
0.03
0.21
0.01
0.31
0.01
0.47
0.03
0.36
0.07
0.06
0.19
0.03
0.72
0.01
0.02
0.01
0.826
Figure 7. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Phylogenomics of Caesalpinioideae: generic re-delimitation 19
high gene tree conict aect only a few decisions about generic delimitation, most nota-
bly across the grade comprising Senegalia and allies (Fig. 7; Terra et al. 2022) and across
the backbone of the Archidendron clade (Fig. 8; Brown et al. 2022).
All the informally named clades of Koenen et al. (2020b; Fig. 1) are here conrmed
with robust support in this new phylogeny (Figs 2–12), including the mimosoid clade
that is robustly supported and subtended by a long branch (Fig. 4). Our results conrm
placement of Chidlowia and Sympetalandra within the mimosoid clade and Dinizia
outside the mimosoid clade, with high support (Fig. 4). Higher-level relationships that
Figure 8. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Wallaceodendron celebicum Flynn 7173 (NY)
Falcataria moluccana Ambri and Arifin W826A (K)
Serianthes nelsonii Moore 1241 (L)
Serianthes calycina Barrabé 1158 (NOU)
Archidendropsis granulosa McKee 38353 (L)
Pararchidendron pruinosum Jobson 1039 (BH)
Archidendron ptenopum Takeuchi and Ama 15334 (L)
Archidendron kanisii Ford and Holmes AF3669 (L)
Archidendron grandiflorum Clarkson 6233 (L)
Archidendron lucidum Wang and Lin 2534 (L)
Archidendron triplinervium Church et al. 1171 (L)
Archidendron ellipticum subsp. ellipticum Kalat ARK 42 (L)
Archidendron clypearia Wieringa 1849 (WAG)
Archidendron quocense Newman 2094 (E)
Archidendron jiringa Annable 3321 (NY)
Archidendron bubalinum Latiff and Zainudin ALM3503 (L)
Archidendropsis xanthoxylon Hyland 9229 (L)
Paraserianthes lophantha subsp. lophantha van Slageren & Newton MSRN648 (K)
Acacia alata var. biglandulosa Murphy 464 (MELU)
Acacia lycopodiifolia Murphy 339 (MELU)
Acacia rostellifera Murphy 466 (MELU)
Acacia ampliceps Murphy 323 (MELU)
Acacia victoriae Ariati 260 (MELU)
Acacia pyrifolia Murphy 337 (MELU)
Acacia murrayana Ariati 110 (MELU)
Acacia platycarpa Murphy 327 (MELU)
Acacia deanei subsp. paucijuga Murphy 599 (MELU)
Acacia pycnantha Murphy 670 (MELU)
Acacia oswaldii Murphy 573 (MELU)
Acacia montana Murphy 672 (MELU)
Acacia verniciflua Karunajeewa 1012 (MEL)
Acacia ausfeldii Karunajeewa 1149 (MEL)
Acacia longifolia Koenen 182 (Z)
Acacia triptera Karunajeewa 1446 (MEL)
Acacia auriculiformis Brown 154 (MEL)
Acacia colei var. colei Murphy 326 (MELU)
Acacia tumida Murphy 306 (MELU)
Acacia sibirica Murphy 486 (MEL)
Cedrelinga cateniformis Pennington 17761 (K)
Albizia carbonaria Daza 16353 (K)
Pseudosamanea cubana Leon 12095 (NY)
Pseudosamanea guachapele Hughes 1198 (FHO)
2
A
rch
i
dendrops
i
s g
r
a
n
u
l
osa
M
c
K
ee 38353
(
L
)
Arch
i
dendron ptenopum
T
a
T
T
k
e
uchi and Ama 15334
(
L
)
Arch
i
dendron kan
i
s
ii
F
ord and Holmes AF3669
(
L
)
Arch
i
dendron
g
r
andi
f
lo
r
u
m
C
la
r
kson 6233
(
L
)
Arch
i
dendron luc
i
dum
W
an
g
and Lin 2534
(
L
)
A
rch
i
dendron t
r
i
pl
i
ne
r
v
ium
C
hurch et al. 1171 (L)
Arch
i
dendron ell
i
pt
i
cum subs
p
. ellipticum Kalat ARK 42
(
L
)
Arch
i
dendron cl
y
pea
r
i
a W
ie
r
i
nga 1849
(
W
A
W
W
G
)
Arch
i
dendron quocense N
e
wman 2094
(
E
)
A
rch
i
dendron
ji
r
i
nga Anna
b
le 3321 (NY)
A
rchidendron
b
ubal
i
n
um Latiff and Zai
n
u
din ALM3503
(
L
)
A
rchidendropsis xanth
o
x
y
lon H
y
land 9229 (L)
A
lb
i
z
i
a carbona
r
ia Daza 16353
(
K
)
Wallaceodendron celebicum Flynn 7173 (NY)
Falcataria moluccana Ambri and Arifin W826A (K)
Serianthes nelsonii Moore 1241 (L)
Serianthes calycina Barrabé 1158 (NOU)
Archidendropsis granulosa McKee 38353 (L)
Pararchidendron pruinosum Jobson 1039 (BH)
Archidendron ptenopum Takeuchi and Ama 15334 (L)
Archidendron kanisii Ford and Holmes AF3669 (L)
Archidendron grandiflorum Clarkson 6233 (L)
Archidendron lucidum Wang and Lin 2534 (L)
Archidendron triplinervium Church et al. 1171 (L)
Archidendron clypearia Wieringa 1849 (WAG)
Archidendron quocense Newman 2094 (E)
Archidendron jiringa Annable 3321 (NY)
Archidendron bubalinum Latiff and Zainudin ALM3503 (L)
Archidendropsis xanthoxylon Hyland 9229 (L)
Acacia lycopodiifolia Murphy 339 (MELU)
Acacia rostellifera Murphy 466 (MELU)
Acacia ampliceps Murphy 323 (MELU)
Acacia victoriae Ariati 260 (MELU)
Acacia pyrifolia Murphy 337 (MELU)
Acacia murrayana Ariati 110 (MELU)
Acacia platycarpa Murphy 327 (MELU)
Acacia pycnantha Murphy 670 (MELU)
Acacia oswaldii Murphy 573 (MELU)
Acacia montana Murphy 672 (MELU)
Acacia verniciflua Karunajeewa 1012 (MEL)
Acacia ausfeldii Karunajeewa 1149 (MEL)
Acacia longifolia Koenen 182 (Z)
Acacia triptera Karunajeewa 1446 (MEL)
Acacia auriculiformis Brown 154 (MEL)
Acacia tumida Murphy 306 (MELU)
Acacia sibirica Murphy 486 (MEL)
Cedrelinga cateniformis Pennington 17761 (K)
Albizia carbonaria Daza 16353 (K)
Pseudosamanea cubana Leon 12095 (NY)
Pseudosamanea guachapele Hughes 1198 (FHO)
Acacia alata var. biglandulosa Murphy 464 (MELU)
Acacia colei var. colei Murphy 326 (MELU)
Archidendron ellipticum subsp. ellipticum Kalat ARK 42 (L)
Paraserianthes lophantha subsp. lophantha van Slageren & Newton MSRN648 (K)
Acacia deanei subsp. paucijuga Murphy 599 (MELU)
(continued in Figure 9)
Genus non−monophyletic Genus possibly non−monophyletic
Archidendron
clade
0.2
0.5
0.18
0.1
0.61
0.13
0.11
0.54
0.51
0.06
0.51
0.25
0.78
0.13
0.49
0.02
0.15
0.39
−0.07
−0.07
−0.02
−0.02
−0.01
0
−0.02
0.25
0.01
0.02
0.07
0.05
0.01
0.24
0.01
−0.01
0.02
0.02
0.11
0
0.01
−0.05
0.29
0.01
0.959
0.955
0.205
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
20
form the basis for the clade- and tribal-based classication of Caesalpinioideae pre-
sented in “Advances in Legume Systematics 14, Part 2”, are not further discussed here.
Generic non-monophyly
Twenty-two genera were recovered as non-monophyletic or were nested within anoth-
er genus and, therefore, likely require generic re-delimitation (Figs 2–12; Appendix 1).
In addition, based on our results, the taxonomic status of Gagnebina Neck. ex DC.,
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Albizia edwallii Dalmaso 272 (RB)
Albizia coripatensis Hughes 2433 (FHO)
Albizia burkartiana Stival−Santos 678 (RB)
Albizia berteroana Jiménez Rodríguez 1107 (NY)
Albizia xerophytica Hughes 1435 (K)
Albizia adinocephala Hughes 1070 (FHO)
Albizia tomentosa Hughes 648 (K)
Albizia sinaloensis Hughes 1576 (K)
Albizia niopoides Simon 1601 (CEN)
Albizia decandra Vilhena 231 (NY)
Albizia multiflora Hughes 3090 (Z)
Albizia glabripetala Lewis 1652 (K)
Albizia inundata Wood 26530 (K)
Albizia subdimidiata var. minor Gorts 341 (K)
Albizia subdimidiata var. subdimidiata Ferreira 210 (K)
Punjuba callejasii Daly 5935 (NY)
Punjuba racemiflora Jimenez and Soares 3626 (USJ)
Punjuba lehmannii Escobar 7465 (NY)
Punjuba killipii Palodorios 6252 (NY)
Jupunba macradenia Lourteig 3021 (NY)
Balizia leucocalyx Aguilar 1939 (NY)
Balizia pedicellaris de Queiroz 15529 (HUEFS)
Balizia elegans Iganci 870 (RB)
Balizia sp. nov. Morim 577 (RB)
Albizia obliquifoliolata Wieringa 6519 (WAG)
Albizia rhombifolia Deighton 3618 (K)
Hydrochorea gonggrijpii Tillett 45696 (K)
Hydrochorea marginata subsp. panurensis Morim 563 (RB)
Hydrochorea corymbosa (1) Bonadeu 655 (RB)
Hydrochorea corymbosa (2) Iganci 862 (RB)
Jupunba langsdorffii Ribeiro 728 (RB)
Jupunba oxyphyllidia Yonker 6157 (NY)
Jupunba idiopoda Quesada 1718 (NY)
Jupunba nipensis Mayo 19662 (NY)
Jupunba aspleniifolia Ekman 6383 (NY)
Jupunba abbottii Zanoni 21220 (NY)
Jupunba oppositifolia Liegier 16014 (NY)
Jupunba laeta Mori 25147 (NY)
Jupunba cochleata Bonadeu 673 (RB)
Jupunba filamentosa de Lima 7487 (RB)
Jupunba rhombea Iganci 261 (RB)
Jupunba villosa Borges 423 (RB)
Jupunba brachystachya de Lima 7438 (RB)
Jupunba trapezifolia var. micradenia Simon 1600 (CEN)
Jupunba barbouriana Iganci 847 (RB)
Jupunba commutata Maguire 46145 (NY)
Jupunba microcalyx Iganci 855 (RB)
Jupunba leucophylla Iganci 839 (RB)
Jupunba floribunda Iganci 883 (RB)
Jupunba longipedunculata Cardona 2682 (NY)
1
Alb
i
z
i
a ed
w
allii Dalmaso 272
(
RB
)
Alb
i
z
i
a co
r
ipatensis Hughes 2433 (FH
O)
Alb
i
z
i
a
b
u
r
k
a
r
tiana
S
t
i
v
al−
S
antos 678 (RB)
Alb
i
z
i
a be
r
t
eroana Jim
é
nez Ro
d
r
í
guez 1107 (NY
)
A
lb
i
z
i
a
x
erop
h
ytica Hu
g
hes 1435 (K)
A
lbizia adinocephala Hughes 1070 (FH
O)
A
lbizia tomentosa Hughes 648
(
K
)
A
lbizia sinaloensis Hughes 1576
(
K
)
Albizia niopoides
S
imon 1601 (
C
EN)
Alb
i
z
i
a decan
d
r
a Vilhena 231
(
NY
)
A
lb
i
z
i
a
m
u
lti
f
l
o
r
a
Hughes 3090
(
Z
)
Alb
i
z
i
a gla
b
r
i
petala
L
e
wis 1652
(
K
)
Alb
i
z
i
a
i
n
un
d
ata
W
ood 26530
(
K
)
A
lbizia subdimidiata
v
a
r
. minor Go
r
t
s 341 (K)
A
lbizia subdimidiata
v
ar. subdimidiata F
e
rrei
r
a
210 (K)
J
upun
b
a mac
r
aden
i
a Lou
r
teig 3021
(
NY
)
Balizia leucocalyx A
g
uilar 1939
(
NY
)
Balizia pedicella
r
is de Queiroz 15529 (HUEFS)
B
alizia elegans Iganci 870
(
RB
)
Bal
i
z
i
a s
p
.
n
o
v. Mo
r
i
m 577
(
RB
)
Alb
i
z
i
a
o
b
l
i
qu
i
f
ol
i
olata W
ie
r
i
nga 6519
(
W
A
W
W
G
)
Alb
i
z
i
a rhomb
i
f
o
lia Dei
g
hton 3618 (K)
J
upunba langsdorffii Ribeiro 728
(
RB
)
J
upun
b
a
o
x
yp
h
y
ll
i
d
i
a
Y
on
Y
Y
k
e
r 6157
(
NY
)
J
upunba idiopoda
Q
uesada 1718 (NY)
J
upunba n
i
pens
i
s
M
a
y
o 19662
(
NY
)
J
upunba asplen
ii
f
o
lia Ekman 6383
(
NY
)
J
u
pun
b
a a
b
bottii Zanoni 21220
(
NY
)
J
u
punba oppos
i
t
i
f
o
lia Lie
g
ier 16014
(
NY
)
J
upun
b
a
l
aeta
M
o
r
i
25147
(
NY
)
J
upunba cochleata Bonadeu 673
(
RB
)
J
upunba filamentosa de Lima 7487
(
RB
)
J
upunba rhombea Iganci 261
(
RB
)
J
upunba villosa Bor
g
es 423
(
RB
)
J
upun
b
a
b
r
ac
h
y
s
t
a
c
h
y
a
de Lima 7438
(
RB
)
J
upun
b
a
t
r
a
pez
i
f
ol
i
a
v
a
r
. m
i
c
r
adenia
S
imon 1600 (
C
EN
)
J
u
pun
b
a
b
ar
b
ou
r
iana Iganci 847
(
RB
)
J
u
pun
b
a com
m
u
tata Maguire 46145
(
NY
)
J
u
punba microcalyx Iganci 855
(
RB
)
J
u
pun
b
a
l
euco
p
h
ylla Iganci 839
(
RB
)
J
upunba flo
r
i
b
u
nda Iganci 883
(
RB
)
J
upunba longipedunculata Cardona 2682 (NY)
Albizia edwallii Dalmaso 272 (RB)
Albizia coripatensis Hughes 2433 (FHO)
Albizia burkartiana Stival−Santos 678 (RB)
Albizia berteroana Jiménez Rodríguez 1107 (NY)
Albizia xerophytica Hughes 1435 (K)
Albizia adinocephala Hughes 1070 (FHO)
Albizia tomentosa Hughes 648 (K)
Albizia sinaloensis Hughes 1576 (K)
Albizia niopoides Simon 1601 (CEN)
Albizia decandra Vilhena 231 (NY)
Albizia multiflora Hughes 3090 (Z)
Albizia glabripetala Lewis 1652 (K)
Albizia inundata Wood 26530 (K)
Punjuba callejasii Daly 5935 (NY)
Punjuba racemiflora Jimenez and Soares 3626 (USJ)
Punjuba lehmannii Escobar 7465 (NY)
Punjuba killipii Palodorios 6252 (NY)
Jupunba macradenia Lourteig 3021 (NY)
Balizia leucocalyx Aguilar 1939 (NY)
Balizia pedicellaris de Queiroz 15529 (HUEFS)
Balizia elegans Iganci 870 (RB)
Albizia obliquifoliolata Wieringa 6519 (WAG)
Albizia rhombifolia Deighton 3618 (K)
Hydrochorea gonggrijpii Tillett 45696 (K)
Hydrochorea corymbosa (1) Bonadeu 655 (RB)
Hydrochorea corymbosa (2) Iganci 862 (RB)
Jupunba langsdorffii Ribeiro 728 (RB)
Jupunba oxyphyllidia Yo nker 6157 (NY)
Jupunba idiopoda Quesada 1718 (NY)
Jupunba nipensis Mayo 19662 (NY)
Jupunba aspleniifolia Ekman 6383 (NY)
Jupunba abbottii Zanoni 21220 (NY)
Jupunba oppositifolia Liegier 16014 (NY)
Jupunba laeta Mori 25147 (NY)
Jupunba cochleata Bonadeu 673 (RB)
Jupunba filamentosa de Lima 7487 (RB)
Jupunba rhombea Iganci 261 (RB)
Jupunba villosa Borges 423 (RB)
Jupunba brachystachya de Lima 7438 (RB)
Jupunba barbouriana Iganci 847 (RB)
Jupunba commutata Maguire 46145 (NY)
Jupunba microcalyx Iganci 855 (RB)
Jupunba leucophylla Iganci 839 (RB)
Jupunba floribunda Iganci 883 (RB)
Jupunba longipedunculata Cardona 2682 (NY)
Albizia subdimidiata var. minor Gorts 341 (K)
Albizia subdimidiata var. subdimidiata Ferreira 210 (K)
Jupunba trapezifolia var. micradenia Simon 1600 (CEN)
Hydrochorea marginata subsp. panurensis Morim 563 (RB)
Balizia sp. nov. Morim 577 (RB)
(continued in Figure 10)
Genus non−monophyletic
Jupunba
clade
−0.34
0.21
0.27
0.38
0.02
0.06
0.46
0.12
0.08
0.42
0.01
0.03
0.06
0.15
0.14
0.19
0.44
0.12
0.05
0.08
0.17
0.13
0.35
0.33
0.55
0.19
−0.07
0.01
0
0
0.01
0.01
0.09
0
0.01
00.13
0.02
0.02
0.03
0.02
0
0.04
0.01
0.46
0.01
0.06
0.01
0.14
0.05
0.204
0.131
0.054
0.336
0.777
Figure 9. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Phylogenomics of Caesalpinioideae: generic re-delimitation 21
Sphinga Barneby & J.W. Grimes and Ebenopsis Britton & Rose, each represented here
by a single taxon and nested in clades with complex generic relationships, require ad-
ditional species sampling. Furthermore, although Archidendron species form a clade
(Fig. 8), the genus is not supported as monophyletic in a substantial fraction of the in-
dividual gene trees (Fig. 8), nor in the plastid tree (Suppl. material 3) (see Brown et al.
2022). Overall, our results therefore show that 14(–17)% of the 152 Caesalpinioideae
genera require re-delimitation and taxonomic updating. Only two of these genera are
non-mimosoid Caesalpinioideae: Dimorphandra Schott and Caesalpinia. Almost all
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Samanea saman Hughes 421 (FHO)
Chloroleucon mangense var. mangense Lozano 1166 (K)
Chloroleucon tenuiflorum de Queiroz 15514 (HUEFS)
Leucochloron bolivianum Hughes 2608 (FHO)
Enterolobium contortisiliquum de Queiroz 15579 (HUEFS)
Enterolobium cyclocarpum MacQueen & Styles 75 (K)
Enterolobium barinense Blanco 157 (NY)
Enterolobium barnebianum Villa 1775 (K)
Enterolobium maximum Nascimento 34 (K)
Enterolobium gummiferum Harley 28284 (K)
Albizia umbellata Jobson 1037 (BH)
Albizia umbellata subsp. umbellata Larsen 33736 (K)
Albizia saponaria Jobson 1041 (BH)
Albizia retusa Hyland 2732 (L)
Albizia adianthifolia Wieringa 6278 (WAG)
Albizia zygia Wieringa 5915 (WAG)
Albizia grandibracteata Koenen 159 (WAG)
Albizia ferruginea Jongkind 10762 (WAG)
Albizia versicolor Maurin 560 (JRAU)
Albizia brevifolia Maurin 826 (JRAU)
Albizia anthelmintica Maurin 363 (JRAU)
Albizia viridis Du Puy M251 (K)
Albizia atakataka Koenen 229 (Z)
Albizia polyphylla Koenen 256 (Z)
Albizia mahalao Koenen 216 (Z)
Albizia bernieri Koenen 354 (Z)
Albizia boivinii Koenen 270 (Z)
Albizia obbiadensis Thulin 4163 (UPS)
Albizia aurisparsa Koenen 230 (Z)
Albizia sahafariensis Koenen 405 (Z)
Albizia masikororum Koenen 237 (Z)
1
Leucochloron bol
i
v
i
a
n
um Hughes 2608 (FH
O
)
Albizia umbellata Jobson 1037 (BH)
Alb
i
z
i
a umbellata subs
p
.
umbellata Larsen 33736
(
K
)
Alb
i
z
i
a sapon
a
r
i
a Jobson 1041
(
BH
)
Albizia retusa H
y
land 2732
(
L
)
Alb
i
z
i
a ad
i
anth
i
f
o
l
i
a W
i
e
r
i
n
g
a 6278
(
W
A
W
W
G
)
A
lb
i
z
i
a zy
gi
a W
i
e
r
in
g
a 5915
(
W
A
W
W
G)
A
lb
i
z
i
a
g
r
a
nd
ib
r
a
c
t
ea
t
a
K
o
enen 159
(
W
A
W
W
G)
A
lb
i
z
i
a
f
er
r
u
ginea Jongkind 10762
(
W
A
W
W
G)
A
lb
i
z
i
a
v
e
rs
i
color Mau
r
in 560
(
J
R
A
U)
Alb
i
z
i
a b
r
e
vi
f
ol
i
a Mau
r
i
n 826
(
JR
A
U)
Alb
i
z
i
a anthelm
i
nt
i
ca Mau
r
in 363
(
JR
A
U
)
A
lb
i
z
i
a v
i
r
idis Du Pu
y
M251
(
K
)
Alb
i
z
i
a atakataka
K
o
enen 229 (Z
)
A
lb
i
z
i
a pol
y
p
h
yll
a
K
o
enen 256
(
Z
)
A
lb
i
z
i
a mahalao
K
o
enen 216
(
Z
)
A
lb
i
z
i
a be
r
n
i
e
r
i
K
o
enen 354
(
Z
)
Alb
i
z
i
a bo
i
v
i
n
ii
K
oenen 270 (Z
)
Alb
i
z
i
a
o
b
biadensis Thulin 4163 (UP
S
)
A
lb
i
z
i
a au
r
i
sparsa
K
o
enen 230
(
Z
)
A
lb
i
z
i
a saha
f
a
r
i
ens
i
s
K
o
enen 405
(
Z
)
A
lb
i
z
i
a mas
i
k
oro
r
um
K
oenen 237 (Z)
K
K
Samanea saman Hughes 421 (FHO)
Chloroleucon tenuiflorum de Queiroz 15514 (HUEFS)
Leucochloron bolivianum Hughes 2608 (FHO)
Enterolobium contortisiliquum de Queiroz 15579 (HUEFS)
Enterolobium cyclocarpum MacQueen & Styles 75 (K)
Enterolobium barinense Blanco 157 (NY)
Enterolobium barnebianum Villa 1775 (K)
Enterolobium maximum Nascimento 34 (K)
Enterolobium gummiferum Harley 28284 (K)
Albizia umbellata Jobson 1037 (BH)
Albizia saponaria Jobson 1041 (BH)
Albizia retusa Hyland 2732 (L)
Albizia adianthifolia Wieringa 6278 (WAG)
Albizia zygia Wieringa 5915 (WAG)
Albizia grandibracteata Koenen 159 (WAG)
Albizia ferruginea Jongkind 10762 (WAG)
Albizia versicolor Maurin 560 (JRAU)
Albizia brevifolia Maurin 826 (JRAU)
Albizia anthelmintica Maurin 363 (JRAU)
Albizia viridis Du Puy M251 (K)
Albizia atakataka Koenen 229 (Z)
Albizia polyphylla Koenen 256 (Z)
Albizia mahalao Koenen 216 (Z)
Albizia bernieri Koenen 354 (Z)
Albizia boivinii Koenen 270 (Z)
Albizia obbiadensis Thulin 4163 (UPS)
Albizia aurisparsa Koenen 230 (Z)
Albizia sahafariensis Koenen 405 (Z)
Albizia masikororum Koenen 237 (Z)
Chloroleucon mangense var. mangense Lozano 1166 (K)
Albizia umbellata subsp. umbellata Larsen 33736 (K)
Inga clade (continued in Figure 11)
Genus non−monophyletic
Samanea
clade
A
l
b
i
z
i
a
c
l
a
d
e
−0.02
0.02
0.12
0.15
0.55
0.25
0.08
−0.02
0.42
0.35
0.32
0.33
0.14
0.03
0.59
−0.24
0.07
−0.03
0.22
0.01
0.47
0
0.02
−0.01
0
0.01
0.02
0
0.59
0.5
0.01
0.121
0.929
Figure 10. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
22
the non-monophyly issues are, therefore, in the mimosoid clade, where 22(–27)% of
the 90 genera will require name changes.
Appendix 1 lists all (potentially) non-monophyletic genera with notes and point-
ers to papers in this Special Issue that discuss these genera and, in many cases, propose
nomenclatural changes that resolve many of the non-monophyly issues revealed in
our analyses. In some cases, it is clear that formal taxonomic re-circumscription must
await more densely-sampled phylogenies and detailed morphological analyses. It is
also important to note that, unless explicitly stated otherwise, the reported generic
non-monophyly is recovered in all trees (i.e. the nuclear ASTRAL, RAxML and Phy-
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Blanchetiodendron blanchetii de Queiroz 15616 (HUEFS)
Leucochloron limae Chase 8250 (K)
Abarema diamantina Guerra 148 (ICN)
Abarema cochliacarpos de Queiroz 15538 (HUEFS)
Robrichia oldemanii Bonadeu 706 (NY)
Robrichia schomburgkii Maguire 56534 (K)
Albizia dinklagei Jongkind 7359 (WAG)
Albizia altissima Jongkind 10709 (WAG)
Albizia leptophylla Brummitt 14035 (K)
Albizia eriorhachis Breteler 507 (WAG)
Zygia ocumarensis Stergios 14780 (NY)
Macrosamanea kegelii Prevost 1721 (NY)
Macrosamanea spruceana Steyermark 87793 (NY)
Macrosamanea duckei Simon 1646 (CEN)
Macrosamanea amplissima Bonadeu 663 (RB)
Macrosamanea prancei da Silva 183 (NY)
Macrosamanea discolor Wurdack 42732 (K)
Macrosamanea simabifolia Iganci 881 (RB)
Zygia claviflora Iganci 841 (RB)
Zygia racemosa Simon 1658 (CEN)
Zygia basijuga Wurdack 1937 (NY)
Zygia bisingula Ortega Mendoza 2561 (NY)
Zygia ramiflora de Lima 2751 (NY)
Zygia inaequalis Iganci 832 (RB)
Zygia conzattii Ortega 596 (K)
Zygia unifoliolata Wendt 4388 (K)
Zygia rhytidocarpa Yuncker 8553 (NY)
Zygia latifolia var. communis Simon 1649 (CEN)
Zygia ampla Prance 26527 (NY)
Zygia longifolia MacQueen 609 (K)
Zygia cataractae Bonadeu 647 (RB)
Zygia morongii Krapovickas 23604 (NY)
Zygia obolingoides Krukoff 10969 (NY)
Zygia sp. Coley and Kursar Tip917 (UT)
1
L
eucochloron limae
C
hase 8250 (K)
Albizia dinkla
g
ei Jon
g
kind 7359
(
W
A
W
W
G)
Albizia altissima Jongkind 10709
(
W
A
W
W
G
)
Alb
i
z
i
a leptop
h
yll
a
B
r
u
mmitt 14035
(
K
)
Alb
i
z
i
a
e
r
i
orhachis Breteler 507
(
W
A
W
W
G
)
Zygia ocumarensis
S
tergios 14780 (NY)
Zy
g
ia c
l
a
vifl
o
r
a
I
g
anci 841 (RB
)
Zyg
i
a
r
acemosa
S
imon 1658 (
C
EN
)
Zyg
i
a bas
ij
uga
W
u
rdack 1937
(
NY
)
Zygia bisingula
O
r
t
ega Mendoza 2561 (NY)
Z
y
gi
a
r
a
miflo
r
a
de Lima 2751
(
NY
)
Zygia inaequalis Iganci 832
(
RB
)
Zygia conzattii O
r
t
ega 596
(
K
)
Zyg
i
a un
i
f
o
l
i
olata
W
endt 4388
(
K
)
Zyg
i
a r
h
y
t
i
doca
r
pa
Y
unc
Y
Y
k
er 8553
(
NY
)
Zyg
i
a lat
i
f
o
l
i
a
v
a
r
.
com
m
unis
S
imon 1649 (
C
EN)
Zyg
i
a ampla
P
r
ance 26527
(
NY
)
Zyg
i
a long
i
f
o
lia Mac
Q
ueen 609 (K)
Zyg
i
a cat
a
r
actae Bonadeu 647
(
RB
)
Zyg
i
a morong
ii
K
r
ap
o
vickas 23604
(
NY
)
Z
yg
i
a obol
i
ngo
i
des K
r
u
k
o
ff 10969
(
NY
)
Z
yg
i
a s
p
.
Col
e
y
an
d
K
ursar Tip917
(
UT
)
Blanchetiodendron blanchetii de Queiroz 15616 (HUEFS)
Leucochloron limae Chase 8250 (K)
Abarema diamantina Guerra 148 (ICN)
Abarema cochliacarpos de Queiroz 15538 (HUEFS)
Robrichia oldemanii Bonadeu 706 (NY)
Robrichia schomburgkii Maguire 56534 (K)
Albizia dinklagei Jongkind 7359 (WAG)
Albizia altissima Jongkind 10709 (WAG)
Albizia leptophylla Brummitt 14035 (K)
Albizia eriorhachis Breteler 507 (WAG)
Zygia ocumarensis Stergios 14780 (NY)
Macrosamanea kegelii Prevost 1721 (NY)
Macrosamanea spruceana Steyermark 87793 (NY)
Macrosamanea duckei Simon 1646 (CEN)
Macrosamanea amplissima Bonadeu 663 (RB)
Macrosamanea prancei da Silva 183 (NY)
Macrosamanea discolor Wurdack 42732 (K)
Macrosamanea simabifolia Iganci 881 (RB)
Zygia claviflora Iganci 841 (RB)
Zygia racemosa Simon 1658 (CEN)
Zygia basijuga Wurdack 1937 (NY)
Zygia bisingula Ortega Mendoza 2561 (NY)
Zygia ramiflora de Lima 2751 (NY)
Zygia inaequalis Iganci 832 (RB)
Zygia conzattii Ortega 596 (K)
Zygia unifoliolata Wendt 4388 (K)
Zygia rhytidocarpa Yuncker 8553 (NY)
Zygia ampla Prance 26527 (NY)
Zygia longifolia MacQueen 609 (K)
Zygia cataractae Bonadeu 647 (RB)
Zygia morongii Krapovickas 23604 (NY)
Zygia obolingoides Krukoff 10969 (NY)
Zygia latifolia var. communis Simon 1649 (CEN)
Zygia sp. Coley and Kursar Tip917 (UT)
(continued in Figure 12)
Genus non−monophyletic
Inga
clade
−0.06
0.01
0.02
0.17
0.15
0.5
0.3
0.03
0.47
−0.06
−0.06
−0.06
−0.06
0
0.11
0
0.08
0.02 0.02
0.01
0.01
0.01
0.02
0
0.01
0.09
0
0.02
0.11 −0.01
0.01 0.01
0.39
0
0.471
0.095
0.063
0.424
Figure 11. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Phylogenomics of Caesalpinioideae: generic re-delimitation 23
loBayes species trees and chloroplast phylogeny) with high support values expressed
and assessed in terms of numbers or fractions of supporting or conicting genes.
Character evolution
Armature, types of inorescence heteromorphy and pod dehiscence type each show
high levels of homoplasy (Figs 13–15, Table S2) with all types of armature, oral het-
eromorphy and pod dehiscence hypothesised to have evolved multiple times.
5
Mimosoid
clade
core
mimosoids
ingoid
clade
Zygia inundata Poncy 361 (NY)
Zygia sabatieri Sabatier 4838 (K)
Inga huberi Coley and Kursar TAKPDC1755 (UT)
Inga tenuistipula Dexter 110 (E)
Inga stipularis Coley and Kursar TAKPDC1856 (UT)
Inga heterophylla Dexter 345 (E, MOL)
Inga brevipes Coley and Kursar TAKPDC1694 (UT)
Inga umbellifera BCI 103
Inga alba Coley and Kursar TAKPDC1677 (UT)
Inga laurina Dexter 398 (E)
Inga cinnamomea Dexter 465 (E, MOL)
Inga longiflora Coley and Kursar TAKPDC1788 (UT)
Inga punctata BCI 8580
Inga leiocalycina Dexter 355 (E, MOL)
Inga setosa Dexter 343 (E, MOL)
Inga sapindoides BCI 97
Inga edulis Coley and Kursar TAKPDC1719 (UT)
Inga thibaudiana Coley and Kursar TAKPDC1859 (UT)
Inga ruiziana BCI 8589
Inga alata Coley and Kursar TAKPDC1673
Inga pezizifera BCI 8577
Inga marginata BCI 8582
Inga bourgonii Coley and Kursar TAKPDC1688 (UT)
Inga nouragensis Coley and Kursar TAKPDC1819 (UT)
Inga cylindrica Coley and Kursar TAKPDC1713 (UT)
Inga auristellae Coley and Kursar TAKPDC1681 (UT)
0.5
Zyg
i
a
i
n
un
d
ata
P
onc
y
361
(
NY
)
Zyg
i
a sabat
i
e
r
i
S
abatier 4838 (K)
Zygia inundata Poncy 361 (NY)
Zygia sabatieri Sabatier 4838 (K)
Inga huberi Coley and Kursar TAKPDC1755 (UT)
Inga tenuistipula Dexter 110 (E)
Inga stipularis Coley and Kursar TAKPDC1856 (UT)
Inga heterophylla Dexter 345 (E, MOL)
Inga brevipes Coley and Kursar TAKPDC1694 (UT)
Inga umbellifera BCI 103
Inga alba Coley and Kursar TAKPDC1677 (UT)
Inga laurina Dexter 398 (E)
Inga cinnamomea Dexter 465 (E, MOL)
Inga longiflora Coley and Kursar TAKPDC1788 (UT)
Inga punctata BCI 8580
Inga leiocalycina Dexter 355 (E, MOL)
Inga setosa Dexter 343 (E, MOL)
Inga sapindoides BCI 97
Inga edulis Coley and Kursar TAKPDC1719 (UT)
Inga thibaudiana Coley and Kursar TAKPDC1859 (UT)
Inga ruiziana BCI 8589
Inga alata Coley and Kursar TAKPDC1673
Inga pezizifera BCI 8577
Inga marginata BCI 8582
Inga bourgonii Coley and Kursar TAKPDC1688 (UT)
Inga nouragensis Coley and Kursar TAKPDC1819 (UT)
Inga cylindrica Coley and Kursar TAKPDC1713 (UT)
Inga auristellae Coley and Kursar TAKPDC1681 (UT)
Genus non−monophyletic
Inga
clade
(con−
tinued)
0.14
0.31
0.05
0.08
0.09
0.16
0.02
0.03
0.02
0.05
0
0.01
0.01
0.01
0.05
0
0
0.04
0
0.03
0
0
0.02
0
0
0.501
0.305
0.9
0.862
Figure 12. Phylogeny of Caesalpinioideae (continued). See Fig. 2 for caption.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
24
Discussion
Generic non-monophyly
e new Caesalpinioideae phylogeny (Figs 2–12) reveals extensive generic non-
monophyly: 22 genera are non-monophyletic or nested within another genus and
four other genera could likely also be non-monophyletic (Appendix 1). Notably, there
are just two non-monophyletic genera (3% of the 62) across the non-mimosoid Cae-
salpinioideae, while 20 (to 24) mimosoid genera (i.e. 22(–27)% of 90 genera) are
non-monophyletic. e discovery of such a high level of generic non-monophyly in
the mimosoid clade is likely attributable to the denser taxon sampling in mimosoids
than non-mimosoids in our analyses; the greater species-richness of mimosoids, which
account for ca. 75% of the ca. 4,600 Caesalpinioideae species (LPWG 2017), but
only 59% of the 152 genera, indicating that, on average, mimosoid genera are more
species-rich and, therefore, more likely to have monophyly issues than non-mimosoid
Caesalpinioideae genera; the fact that the Caesalpinia Group, the most problematic
clade of non-mimosoid Caesalpinioideae in terms of generic delimitation, was already
largely resolved by Gagnon et al. (2016), further reducing the likelihood of non-
monophyly issues across non-mimosoid Caesalpinioideae; and nally, the continued
legacy of Bentham’s broadly circumscribed mimosoid genera which has still not been
fully resolved. For example, Acacia, which as indicated earlier, was once a pantropical
genus with over 1,400 species (Miller and Seigler 2012) and now comprises seven
genera, yet one of these genera, Senegalia, is here recovered as non-monophyletic
(Fig. 7) and further subdivision of Senegalia seems likely (Terra et al. 2022). Similarly,
Calliandra once had a pantropical distribution until Barneby (1998) restricted it to
the New World (de Souza et al. 2013). However, not all Old World Calliandra species
have yet been assigned to other genera and Calliandra, therefore, also remains non-
monophyletic (Fig. 7). Finally, Albizia, the last mimosoid ‘dustbin genus’ (Barneby
and Grimes 1996; Brown 2008; Koenen et al. 2020b) is here conrmed to be non-
monophyletic in line with previous ndings (Koenen et al. 2020b) (Figs 7–11), but
with two previously unsampled Neotropical species each representing additional evo-
lutionary lineages (Terra et al. 2022; Koenen 2022b). Nevertheless, most African,
Madagascan and Asian Albizia species do form a single clade (Fig. 10; Koenen et al.,
unpublished data), while most Neotropical species are also in a single clade (Aviles et
al. 2022) (Fig. 9, see Appendix 1).
Morphological homoplasy
Given the extensive re-arrangements of genera in Caesalpinioideae over the last two
decades, the question arises why such a signicant fraction of genera is still non-mono-
phyletic in these new phylogenomic analyses. We identify two main reasons for this.
First, extensive morphological homoplasy has misled generic delimitation and second,
lack of pantropical taxonomic synthesis and phylogenetic sampling have resulted in
Phylogenomics of Caesalpinioideae: generic re-delimitation 25
failure to identify clades that span the Old World and New World or, conversely,
amphi-Atlantic genera that are non-monophyletic, i.e. potential trans-continental con-
nections and disconnects.
First, and most importantly, the likely extent of homoplasy of morphology and
functional traits across Caesalpinioideae is only now starting to be revealed using this
new phylogeny (Figs 13–15; de Faria et al. 2022). Here, we reconstructed hypotheses
for the evolutionary trajectories of three trait syndromes – armature, mode of fruit
dehiscence and aspects of oral heteromorphy – to demonstrate the extent of homo-
plasy and to show how the repeated evolution of distinctive types of, for example, fruit
dehiscence has misled generic delimitation.
Fruits are highly diverse across Caesalpinioideae reecting adaptations for hydro-
chory, anemochory, endozoochory, ornithochory, and myrmecochory, as well as sev-
eral forms of mechanical seed dispersal via explosively, elastically and inertly dehiscent
fruits. Here, we show that fruit dehiscence type shows extensive homoplasy across the
mimosoid clade, with repeated evolution of, for example, pods elastically dehiscent
from the apex, craspedia and lomentiform fruits (Fig. 13). It is now clear that repeated,
potentially convergent evolution of fruit types has repeatedly misled generic delimita-
tion and provided the basis for ‘fruit genera’ that have subsequently been shown to be
non-monophyletic.
For example, as pointed out by Barneby (1998), the only character uniting
Bentham’s (1875) broadly circumscribed pantropical Calliandra was the elastically
dehiscent fruit, opening from the apex with the valves recurving, but not laterally
twisting (Fig. 13a–e). Just how misplaced this reliance on fruit type as a generic syna-
pomorphy was, is evident from the long parade of new genera segregated from Cal-
liandra, most of them in the two decades after Barneby (1998) restricted the genus to
just the New World species: Zapoteca H.M. Hern. (Hernández 1986), Viguieranthus
Villiers (Du Puy et al. 2002), ailentadopsis Kostermans (Lewis and Schrire 2003),
Afrocalliandra E.R. Souza & L.P. Queiroz (de Souza et al. 2013) and Sanjappa E.R.
Souza & M.V. Krishnaraj (de Souza et al. 2016). is procession is still incomplete
given that Calliandra is still non-monophyletic (Fig. 7), pending phylogenetic place-
ment of the Asian Calliandra umbrosa (Wall.) Benth. (see de Souza et al. 2016) and
an, as yet, undescribed species (Fig. 7), the last remaining of the species excluded from
Calliandra by Barneby (1998) that have not yet been placed in a segregate genus. It is
clear that the distinctive ‘Calliandra pod’ has evolved at least six times independently
across Caesalpinioideae (Fig. 13) and occurs in at least 12 phylogenetically scattered
genera including Jaqueshuberia Ducke, Bussea Harms, Pseudoprosopis Harms, some
species of Dichrostachys (DC.) Wight & Arn., Alantsilodendron Villiers, Calliandropsis
H.M. Hern. & P. Guinet, Calliandra, Zapoteca, Viguieranthus, Sanjappa, Afrocallian-
dra and a small subset of species of Acacia. Of course, it is possible that more detailed
anatomical investigation of these morphologically and functionally similar fruits will
reveal anatomical dierences that show that the homology of this fruit type is mis-
placed, but the structure of the pod valves and raised sutures of most of these are
remarkably similar (Fig. 13a–e).
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
26
ab
cd
ef
gh
j
kl
i
Pentaclethra macroloba
Pentaclethramacrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada sp.
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa rubicaulis subsp. himalayana
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizialeonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Calliandra sp. nov.
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron ellipticum subsp. ellipticum
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Paraserianthes lophantha subsp. lophantha
Acacia alata var. biglandulosa
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia deanei subsp. paucijuga
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia colei var. colei
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albiziacarbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albiziaedwallii
Albiziacoripatensis
Albiziaburkartiana
Albiziaberteroana
Albiziaxerophytica
Albiziaadinocephala
Albiziatomentosa
Albiziasinaloensis
Albizianiopoides
Albiziadecandra
Albiziamultiflora
Albiziaglabripetala
Albiziainundata
Albiziasubdimidiata var. minor
Albiziasubdimidiata var. subdimidiata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizialeucocalyx
Baliziapedicellaris
Baliziaelegans
Baliziasp. nov.
Albiziaobliquifoliolata
Albiziarhombifolia
Hydrochorea gonggrijpii
Hydrochorea marginata subsp. panurensis
Hydrochorea corymbosa (1)
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba trapezifolia var. micradenia
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon mangense var. mangense
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albiziaumbellata
Albiziaumbellata subsp. umbellata
Albiziasaponaria
Albiziaretusa
Albiziaadianthifolia
Albiziazygia
Albiziagrandibracteata
Albiziaferruginea
Albiziaversicolor
Albiziabrevifolia
Albiziaanthelmintica
Albiziaviridis
Albiziaatakataka
Albiziapolyphylla
Albiziamahalao
Albiziabernieri
Albiziaboivinii
Albiziaobbiadensis
Albiziaaurisparsa
Albiziasahafariensis
Albiziamasikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albiziadinklagei
Albiziaaltissima
Albizialeptophylla
Albiziaeriorhachis
Zygia inundata
Zygia sabatieri
Ingahuberi
Ingatenuistipula
Ingastipularis
Ingaheterophylla
Ingabrevipes
Ingaumbellifera
Ingaalba
Ingalaurina
Ingacinnamomea
Ingalongiflora
Ingapunctata
Ingaleiocalycina
Ingasetosa
Ingasapindoides
Ingaedulis
Ingathibaudiana
Ingaruiziana
Ingaalata
Ingapezizifera
Ingamarginata
Ingabourgonii
Inganouragensis
Ingacylindrica
Ingaauristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia latifolia var. communis
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Zygia sp.
Pentaclethra macroloba
Pentaclethramacrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizialeonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albiziacarbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albiziaedwallii
Albiziacoripatensis
Albiziaburkartiana
Albiziaberteroana
Albiziaxerophytica
Albiziaadinocephala
Albiziatomentosa
Albiziasinaloensis
Albizianiopoides
Albiziadecandra
Albiziamultiflora
Albiziaglabripetala
Albiziainundata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizialeucocalyx
Baliziapedicellaris
Baliziaelegans
Albiziaobliquifoliolata
Albiziarhombifolia
Hydrochorea gonggrijpii
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albiziaumbellata
Albiziasaponaria
Albiziaretusa
Albiziaadianthifolia
Albiziazygia
Albiziagrandibracteata
Albiziaferruginea
Albiziaversicolor
Albiziabrevifolia
Albiziaanthelmintica
Albiziaviridis
Albiziaatakataka
Albiziapolyphylla
Albiziamahalao
Albiziabernieri
Albiziaboivinii
Albiziaobbiadensis
Albiziaaurisparsa
Albiziasahafariensis
Albiziamasikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albiziadinklagei
Albiziaaltissima
Albizialeptophylla
Albiziaeriorhachis
Zygia inundata
Zygia sabatieri
Ingahuberi
Ingatenuistipula
Ingastipularis
Ingaheterophylla
Ingabrevipes
Ingaumbellifera
Ingaalba
Ingalaurina
Ingacinnamomea
Ingalongiflora
Ingapunctata
Ingaleiocalycina
Ingasetosa
Ingasapindoides
Ingaedulis
Ingathibaudiana
Ingaruiziana
Ingaalata
Ingapezizifera
Ingamarginata
Ingabourgonii
Inganouragensis
Ingacylindrica
Ingaauristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Acacia alatavar.biglandulosa
Acacia coleivar.colei
Albiziasubdimidiatavar. minor
Albiziasubdimidiatavar. subdimidiata
Jupunba trapezifoliavar.micradenia
Chloroleucon mangensevar.mangense
Zygia latifoliavar.communis
Mimosa rubicaulissubsp.himalayana
Archidendron ellipticumsubsp.ellipticum
Paraserianthes lophanthasubsp.lophantha
Acacia deaneisubsp.paucijuga
Hydrochorea marginatasubsp.panurensis
Albiziaumbellatasubsp.umbellata
Calliandrasp. nov.
Baliziasp. nov.
Hydrochorea corymbosa
Entadasp.
Zygiasp.
Pod dehiscence type
Indehiscent
Elastically dehiscent
Explosively dehiscent
Inertly dehiscent
Craspedium
Loment
Unknown
Figure 13. Evolution of fruit dehiscence types across the mimosoid clade. Character states were dened as:
indehiscent; inertly dehiscent along one or both sutures; explosively dehiscent, whereby the woody valves twist
and split along both sutures along whole length of pod simultaneously; elastically dehiscent from the apex,
the valves recurving, but not laterally twisting; craspedium, i.e. fruits breaking up into free-falling one-seeded
articles leaving a persistent replum or whole valve breaking away intact from replum (valvately dehiscent);
lomentiform fruit, i.e. the valves readily cracking between the seeds into one-seeded articles, taken here to
include crypto-lomentiform fruits. Branch lengths are not informative in this gure. Photos a–e elastically
dehiscent a Acacia argyraea Tindale b Calliandra prostrata Benth. c Calliandropsis nervosa (Britton & Rose)
H.M. Hern. & P. Guinet d Alantsilodendron mahafalense (R. Vig.) Villiers e Zapoteca portoricensis (Jacq.)
H.M. Hern f–h craspedium f Entada polystachya (L.) DC. g Lysiloma tergeminum Benth. h Mimosa montana
Kunth. var. sandemanii Barneby i–l lomentiform i Albizia moniliformis (DC.) F. Muell. j Albizia subdimid-
iata (Splitg.) Barneby & J.W. Grimes k Albizia pistaciifolia (Willd.) Barneby & J.W. Grimes l Prosopidas-
trum globosum (Gillies ex Hook. & Arn.) Burkart. Photos a Bruce Maslin b, c , e – h Colin Hughes d http://
clubbotatoliara.e-monsite.com/pages/posters-lms-rapports/photos.html i Garry Sankowsky http://www.
rainforestmagic.com.au j Marcelo Simon k Xavier Cornejo l https://www.oramendocina.com.ar.
Phylogenomics of Caesalpinioideae: generic re-delimitation 27
Figure 14. Evolution of types of oral heteromorphy across the mimosoid clade. Character states were de-
ned as: homomorphic, i.e. with no conspicuous modication or variation amongst owers within an inores-
cence (here we include inorescences that can comprise proportions of male and bisexual owers, but no other
more conspicuous variation); heteromorphic 1 = basal owers of the inorescence with showy staminodia; het-
eromorphic 2 = owers dimorphic within an inorescence, the central ower (or owers) enlarged/sessile cf. the
peripheral (sometimes pedicellate) owers. Branch lengths are not informative in this gure. Photos a–h heter-
omorphic 1 a Neptunia plena (L.) Benth. b Dichrostachys cinerea (L.) Wight & Arn. c Dichrostachys myriophylla
Baker d Gagnebina pterocarpa (Lam.) Baill. e Dichrostachys bernieriana Baill. f Dichrostachys akataensis Villiers
g Parkia bahiae H.C. Hopkins h Parkia nitida Miq. i–l heteromorphic 2 i Pseudosamanea guachapele (Kunth)
Harms j Albizia obliquifoliolata De Wild. k Hydrochorea corymbosa (Rich.) Barneby & J.W. Grimes l Albizia
grandibracteata Taub. Photos a , b , g , i Colin Hughes c , k , l Erik Koenen d Melissa Luckow e, f Dave Du Puy
h Giacomo Sellan https://identify.plantnet.org/the-plant-list/observations/1012799991 j Jan Wieringa.
Pentaclethra macroloba
Pentaclethramacrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada sp.
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa rubicaulis subsp. himalayana
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizia leonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Calliandra sp. nov.
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron ellipticum subsp. ellipticum
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Paraserianthes lophantha subsp. lophantha
Acacia alata var. biglandulosa
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia deanei subsp. paucijuga
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia colei var. colei
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albizia carbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albizia edwallii
Albizia coripatensis
Albizia burkartiana
Albizia berteroana
Albizia xerophytica
Albizia adinocephala
Albizia tomentosa
Albizia sinaloensis
Albizia niopoides
Albizia decandra
Albizia multiflora
Albizia glabripetala
Albizia inundata
Albizia subdimidiata var. minor
Albizia subdimidiata var. subdimidiata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizia leucocalyx
Balizia pedicellaris
Balizia elegans
Balizia sp. nov.
Albizia obliquifoliolata
Albizia rhombifolia
Hydrochorea gonggrijpii
Hydrochorea marginata subsp. panurensis
Hydrochorea corymbosa (1)
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba trapezifolia var. micradenia
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon mangense var. mangense
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albizia umbellata
Albizia umbellata subsp. umbellata
Albizia saponaria
Albizia retusa
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia ferruginea
Albizia versicolor
Albizia brevifolia
Albizia anthelmintica
Albizia viridis
Albizia atakataka
Albizia polyphylla
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia obbiadensis
Albizia aurisparsa
Albizia sahafariensis
Albizia masikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albizia dinklagei
Albizia altissima
Albizia leptophylla
Albizia eriorhachis
Zygia inundata
Zygia sabatieri
Inga huberi
Inga tenuistipula
Inga stipularis
Inga heterophylla
Inga brevipes
Inga umbellifera
Inga alba
Inga laurina
Inga cinnamomea
Inga longiflora
Inga punctata
Inga leiocalycina
Ingasetosa
Inga sapindoides
Inga edulis
Inga thibaudiana
Inga ruiziana
Inga alata
Inga pezizifera
Inga marginata
Inga bourgonii
Inga nouragensis
Inga cylindrica
Inga auristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia latifolia var. communis
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Zygia sp.
Pentaclethra macroloba
Pentaclethramacrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizia leonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albizia carbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albizia edwallii
Albizia coripatensis
Albizia burkartiana
Albizia berteroana
Albizia xerophytica
Albizia adinocephala
Albizia tomentosa
Albizia sinaloensis
Albizia niopoides
Albizia decandra
Albizia multiflora
Albizia glabripetala
Albizia inundata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizia leucocalyx
Balizia pedicellaris
Balizia elegans
Albizia obliquifoliolata
Albizia rhombifolia
Hydrochorea gonggrijpii
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albizia umbellata
Albizia saponaria
Albizia retusa
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia ferruginea
Albizia versicolor
Albizia brevifolia
Albizia anthelmintica
Albizia viridis
Albizia atakataka
Albizia polyphylla
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia obbiadensis
Albizia aurisparsa
Albizia sahafariensis
Albizia masikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albizia dinklagei
Albizia altissima
Albizia leptophylla
Albizia eriorhachis
Zygia inundata
Zygia sabatieri
Inga huberi
Inga tenuistipula
Inga stipularis
Inga heterophylla
Inga brevipes
Inga umbellifera
Inga alba
Inga laurina
Inga cinnamomea
Inga longiflora
Inga punctata
Inga leiocalycina
Ingasetosa
Inga sapindoides
Inga edulis
Inga thibaudiana
Inga ruiziana
Inga alata
Inga pezizifera
Inga marginata
Inga bourgonii
Inga nouragensis
Inga cylindrica
Inga auristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Acacia alatavar.biglandulosa
Acacia coleivar.colei
Albizia subdimidiatavar.minor
Albizia subdimidiatavar.subdimidiata
Jupunba trapezifoliavar.micradenia
Chloroleucon mangensevar.mangense
Zygia latifoliavar.communis
Mimosa rubicaulissubsp.himalayana
Archidendron ellipticumsubsp.ellipticum
Paraserianthes lophanthasubsp.lophantha
Acacia deaneisubsp.paucijuga
Hydrochorea marginatasubsp.panurensis
Albizia umbellatasubsp.umbellata
Calliandrasp. nov.
Baliziasp. nov.
Hydrochorea corymbosa
Entadasp.
Zygiasp.
Inflorescence type
Homomorphic
Heteromorphic 1
Heteromorphic 2
Unknown
ab
cd
g
i
kl
ef
j
h
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
28
ere are several other examples of classications and especially genera being
misled by parallel evolution of fruit types. For example, the polyphyly of the genus
Enterolobium Mart. (de Souza et al. 2022a; Figs 10–11) was unexpected because the
two clades of Enterolobium species share the distinctive indehiscent thickened and
curled ‘ear pod’ fruit type. Similarly, it also seems clear that septate lomentiform
fruits with valves readily cracking between the seeds and breaking up into one-seeded
articles have also evolved multiple times (Fig. 13), often within genera (e.g. Capuron
1970; Aviles et al. 2022; Koenen 2022a; Soares et al. 2022) associated with hydro-
chory in species adapted to grow in seasonally inundated habitats and this has im-
pacted on generic delimitation. For example, Barneby and Grimes (1996) separated
their newly-segregated genera Balizia and Hydrochorea Barneby & J.W. Grimes on
fruit types, yet it is clear that Hydrochorea is nested within a paraphyletic Balizia (Fig.
9; Soares et al. 2022) and that the distinctive lomentiform fruits of Hydrochorea are
derived from non-lomentiform indehiscent or follicularly dehiscent pods within this
clade (Aviles et al. 2022; Soares et al. 2022). is prevalence of homoplasy associated
with fruit types across the mimosoid clade matches that seen across other legume
clades (e.g. in subfamily Papilionoideae; Geesink 1984; Hu et al. 2000; Lavin et al.
2001) suggesting that the late developmental stages of the legume pod and associated
legume seed dispersal syndromes are prone to convergent evolution, as previously
suggested (Geesink 1984; Hu et al. 2000).
Of course, homoplasy per se in no way negates the value and importance of mor-
phology for classication, but instead prompts re-evaluation of homology and the util-
ity of specic morphological characters via reciprocal illumination with new molecular
phylogenetic evidence. For example, armature is also homoplasious across Caesalpin-
ioideae with repeated evolution of stipular spines, nodal and internodal prickles, axil-
lary thorns and spinescent shoots (Fig. 15). While armature has been little used as
the basis for dening genera because vegetative characters were generally downplayed
compared to oral and fruit characters (e.g. Bentham 1875; Burkart 1976), the utility
of armature for delimiting some groups within individual clades is increasingly ap-
parent. For example, the four genera segregated from the non-monophyletic Prosopis
s.l. by Hughes et al. (2022a) are diagnosed by dierent types of armature (Fig. 15).
Similarly, armature is an important character distinguishing the segregates of Acacia s.l.
(spinescent stipules in Vachellia, nodal and internodal prickles in Senegalia, unarmed
in Acacia s.s., Parasenegalia, Pseudosenegalia, Mariosousa and Acaciella) and the distri-
bution of prickles (nodal vs. internodal) is discussed in relation to the non-monophyly
of Senegalia (Terra et al. 2022). Similarly, the two major clades of genera that make up
the Caesalpinia Group (Figs 2 and 15) are separated by dierences in armature.
Detailed phylogenetic reconstructions for other characters, based on more rigorous
and detailed anatomical assessment of homology, will undoubtedly be worthwhile, but it is
already clear that the three traits mapped here (Figs 13–15) are not exceptional in terms of
their high levels of homoplasy. Leaves also show evolutionarily labile patterns with numer-
ous repeated transitions from micro- to macrophyllidinous leaves within a large majority
of Caesalpinioideae genera. Even the more prominent leaf type innovations of bipinnate
Phylogenomics of Caesalpinioideae: generic re-delimitation 29
ab
cd
ef
gh
Arcoa gonavensis
Tetrapterocarpon geayi
Ceratonia siliqua
Acrocarpus fraxinifolius
Umtiza listeriana
Gymnocladus dioicus
Gleditsia chinensis
Cassia cowanii var. guianensis
Senna cushina
Senna leandrii
Senna mollissima
Senna rugosa
Senna lasseigniana
Senna velutina
Batesia floribunda
Recordoxylon speciosum
Melanoxylon brauna
Chamaecrista adiantifolia
Chamaecrista viscosa
Chamaecrista ramosa
Chamaecrista lineata
Cordeauxia edulis
Stuhlmannia moavi
Cenostigma pluviosum var. maraniona
Libidibia glabrata
Balsamocarpon brevifolium
Hoffmannseggia arequipensis
Zuccagnia punctata
Arquita trichocarpa
Pomaria jamesii
Erythrostemon mexicanus
Erythrostemon coluteifolius
Hererolandia pearsonii
Lophocarpinia aculeatifolia
Haematoxylum brasiletto
Caesalpinia cassioides
Denisophytum madagascariense
Paubrasilia echinata
Tara spinosa
Coulteria platyloba
Gelrebia rostrata
Guilandina bonduc
Moullava spicata
Biancaea decapetala
Pterolobium stellatum
Caesalpinia crista
Mezoneuron kauaiensis
Schizolobium parahyba
Bussea perrieri
Peltophorum dubium
Peltophorum africanum
Parkinsonia andicola
Heteroflorum sclerocarpum
Conzattia multiflora
Colvillea racemosa
Delonix decaryi
Delonix edule
Moldenhawera floribunda
Diptychandra aurantiaca
Arapatiella psilophylla
Jacqueshuberia brevipes
Tachigali guianensis
Tachigali bracteolata
Tachigali paniculata
Tachigali vasquezii
Tachigali odoratissima
Dimorphandra gardneriana
Dimorphandra macrostachya
Dimorphandra davisii
Mora gonggrijpii
Burkea africana
Stachyothyrsus staudtii
Dinizia jueirana−facao
Campsiandra comosa
Pachyelasma tessmannii
Erythrophleum ivorense
Erythrophleum teysmannii
Pentaclethra macroloba
Pentaclethra macrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada sp.
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa rubicaulis subsp. himalayana
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizia leonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Calliandra sp. nov.
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron ellipticum subsp. ellipticum
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Paraserianthes lophantha subsp. lophantha
Acacia alata var. biglandulosa
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia deanei subsp. paucijuga
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia colei var. colei
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albizia carbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albizia edwallii
Albizia coripatensis
Albizia burkartiana
Albizia berteroana
Albizia xerophytica
Albizia adinocephala
Albizia tomentosa
Albizia sinaloensis
Albizia niopoides
Albizia decandra
Albizia multiflora
Albizia glabripetala
Albizia inundata
Albizia subdimidiata var. minor
Albizia subdimidiata var. subdimidiata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizia leucocalyx
Balizia pedicellaris
Balizia elegans
Balizia sp. nov.
Albizia obliquifoliolata
Albizia rhombifolia
Hydrochorea gonggrijpii
Hydrochorea marginata subsp. panurensis
Hydrochorea corymbosa (1)
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba trapezifolia var. micradenia
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon mangense var. mangense
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albizia umbellata
Albizia umbellata subsp. umbellata
Albizia saponaria
Albizia retusa
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia ferruginea
Albizia versicolor
Albizia brevifolia
Albizia anthelmintica
Albizia viridis
Albizia atakataka
Albizia polyphylla
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia obbiadensis
Albizia aurisparsa
Albizia sahafariensis
Albizia masikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albizia dinklagei
Albizia altissima
Albizia leptophylla
Albizia eriorhachis
Zygia inundata
Zygia sabatieri
Inga huberi
Inga tenuistipula
Inga stipularis
Inga heterophylla
Inga brevipes
Inga umbellifera
Inga alba
Inga laurina
Inga cinnamomea
Inga longiflora
Inga punctata
Inga leiocalycina
Inga setosa
Inga sapindoides
Inga edulis
Inga thibaudiana
Inga ruiziana
Inga alata
Inga pezizifera
Inga marginata
Inga bourgonii
Inga nouragensis
Inga cylindrica
Inga auristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia latifolia var. communis
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Zygia sp.
Arcoa gonavensis
Tetrapterocarpon geayi
Ceratonia siliqua
Acrocarpus fraxinifolius
Umtiza listeriana
Gymnocladus dioicus
Gleditsia chinensis
Senna cushina
Senna leandrii
Senna mollissima
Senna rugosa
Senna lasseigniana
Senna velutina
Batesia floribunda
Recordoxylon speciosum
Melanoxylon brauna
Chamaecrista adiantifolia
Chamaecrista viscosa
Chamaecrista ramosa
Chamaecrista lineata
Cordeauxia edulis
Stuhlmannia moavi
Libidibia glabrata
Balsamocarpon brevifolium
Hoffmannseggia arequipensis
Zuccagnia punctata
Arquita trichocarpa
Pomaria jamesii
Erythrostemon mexicanus
Erythrostemon coluteifolius
Hererolandia pearsonii
Lophocarpinia aculeatifolia
Haematoxylum brasiletto
Caesalpinia cassioides
Denisophytum madagascariense
Paubrasilia echinata
Tara spinosa
Coulteria platyloba
Gelrebia rostrata
Guilandina bonduc
Moullava spicata
Biancaea decapetala
Pterolobium stellatum
Caesalpinia crista
Mezoneuron kauaiensis
Schizolobium parahyba
Bussea perrieri
Peltophorum dubium
Peltophorum africanum
Parkinsonia andicola
Heteroflorum sclerocarpum
Conzattia multiflora
Colvillea racemosa
Delonix decaryi
Delonix edule
Moldenhawera floribunda
Diptychandra aurantiaca
Arapatiella psilophylla
Jacqueshuberia brevipes
Tachigali guianensis
Tachigali bracteolata
Tachigali paniculata
Tachigali vasquezii
Tachigali odoratissima
Dimorphandra gardneriana
Dimorphandra macrostachya
Dimorphandra davisii
Mora gonggrijpii
Burkea africana
Stachyothyrsus staudtii
Dinizia jueirana−facao
Campsiandra comosa
Pachyelasma tessmannii
Erythrophleum ivorense
Erythrophleum teysmannii
Pentaclethra macroloba
Pentaclethra macrophylla
Tetrapleura tetraptera
Adenanthera pavonina
Amblygonocarpus andongensis
Pseudoprosopis sericea
Pseudoprosopis gilletii
Pseudoprosopis euryphylla
Xylia evansii
Calpocalyx dinklagei
Calpocalyx heitzii
Xylia hoffmannii
Xylia torreana
Sympetalandra unijuga
Sympetalandra schmutzii
Chidlowia sanguinea
Aubrevillea kerstingii
Piptadeniastrum africanum
Entada pervillei
Entada rheedei
Entada polystachya
Entada tuberosa
Entada africana
Entada arenaria
Elephantorrhiza elephantina
Elephantorrhiza burkei
Prosopis africana
Plathymenia reticulata
Fillaeopsis discophora
Newtonia hildebrandtii
Cylicodiscus gabunensis
Indopiptadenia oudhensis
Prosopis cineraria
Prosopis farcta
Xerocladia viridiramis
Prosopis ferox
Prosopis strombulifera
Prosopis argentina
Prosopis kuntzei
Prosopis juliflora
Prosopis laevigata
Prosopis ruscifolia
Neptunia oleracea
Lemurodendron capuronii
Leucaena trichandra
Schleinitzia megaladenia
Schleinitzia novoguineensis
Schleinitzia insularum
Desmanthus balsensis
Kanaloa kahoolawensis
Desmanthus leptophyllus
Desmanthus virgatus
Desmanthus acuminatus
Mimozyganthus carinatus
Piptadeniopsis lomentifera
Prosopidastrum globosum
Calliandropsis nervosa
Dichrostachys cinerea
Dichrostachys myriophylla
Gagnebina commersoniana
Dichrostachys paucifoliolata
Alantsilodendron glomeratum
Dichrostachys unijuga
Dichrostachys tenuifolia
Alantsilodendron villosum
Dichrostachys richardiana
Alantsilodendron pilosum
Vachellia tortilis
Vachellia erioloba
Vachellia viguieri
Vachellia nilotica
Vachellia farnesiana
Anadenanthera colubrina
Parkia ulei
Parkia panurensis
Parkia igneiflora
Parkia pendula
Parkia bahiae
Parkia timoriana
Parkia bicolor
Lachesiodendron viridiflorum
Stryphnodendron paniculatum
Stryphnodendron adstringens
Stryphnodendron pulcherrimum
Pseudopiptadenia psilostachya
Pseudopiptadenia contorta
Stryphnodendron duckeanum
Pityrocarpa moniliformis
Pseudopiptadenia schumanniana
Parapiptadenia zehntneri
Parapiptadenia excelsa
Piptadenia uaupensis
Piptadenia robusta
Piptadenia buchtienii
Adenopodia scelerata
Adenopodia patens
Mimosa myriadenia
Mimosa revoluta
Mimosa hondurana
Mimosa hexandra
Mimosa tenuiflora
Mimosa ceratonia
Mimosa grandidieri
Mimosa invisa
Mimosa speciosissima
Mimosa pigra
Mimosa pudica
Mimosa tequilana
Mimosa tricephala
Mimosa dolens
Senegalia ataxacantha
Senegalia nigrescens
Parasenegalia visco
Mariosousa sericea
Pseudosenegalia feddeana
Albizia leonardii
Senegalia bahiensis
Senegalia sakalava
Senegalia pentagona
Senegalia borneensis
Acaciella villosa
Afrocalliandra gilbertii
Afrocalliandra redacta
Calliandra hygrophila
Calliandra viscidula
Calliandra haematomma
Calliandra parviflora
Calliandra haematocephala
Calliandra bella
Calliandra sessilis
Zapoteca nervosa
Zapoteca amazonica
Zapoteca caracasana
Zapoteca aculeata
Viguieranthus glaber
Faidherbia albida
Sanjappa cynometroides
Thailentadopsis tenuis
Thailentadopsis nitida
Hesperalbizzia occidentalis
Lysiloma latisiliquum
Lysiloma candidum
Cojoba rufescens
Cojoba arborea
Cojoba filipes
Cojoba zanonii
Havardia campylacantha
Sphinga acatlensis
Painteria leptophylla
Painteria elachistophylla
Ebenopsis confinis
Havardia pallens
Pithecellobium keyense
Pithecellobium dulce
Pithecellobium excelsum
Pithecellobium macrandrium
Pithecellobium hymenaeifolium
Wallaceodendron celebicum
Falcataria moluccana
Serianthes nelsonii
Serianthes calycina
Archidendropsis granulosa
Pararchidendron pruinosum
Archidendron ptenopum
Archidendron kanisii
Archidendron grandiflorum
Archidendron lucidum
Archidendron triplinervium
Archidendron clypearia
Archidendron quocense
Archidendron jiringa
Archidendron bubalinum
Archidendropsis xanthoxylon
Acacia lycopodiifolia
Acacia rostellifera
Acacia ampliceps
Acacia victoriae
Acacia pyrifolia
Acacia murrayana
Acacia platycarpa
Acacia pycnantha
Acacia oswaldii
Acacia montana
Acacia verniciflua
Acacia ausfeldii
Acacia longifolia
Acacia triptera
Acacia auriculiformis
Acacia tumida
Acacia sibirica
Cedrelinga cateniformis
Albizia carbonaria
Pseudosamanea cubana
Pseudosamanea guachapele
Albizia edwallii
Albizia coripatensis
Albizia burkartiana
Albizia berteroana
Albizia xerophytica
Albizia adinocephala
Albizia tomentosa
Albizia sinaloensis
Albizia niopoides
Albizia decandra
Albizia multiflora
Albizia glabripetala
Albizia inundata
Punjuba callejasii
Punjuba racemiflora
Punjuba lehmannii
Punjuba killipii
Jupunba macradenia
Balizia leucocalyx
Balizia pedicellaris
Balizia elegans
Albizia obliquifoliolata
Albizia rhombifolia
Hydrochorea gonggrijpii
Jupunba langsdorffii
Jupunba oxyphyllidia
Jupunba idiopoda
Jupunba nipensis
Jupunba aspleniifolia
Jupunba abbottii
Jupunba oppositifolia
Jupunba laeta
Jupunba cochleata
Jupunba filamentosa
Jupunba rhombea
Jupunba villosa
Jupunba brachystachya
Jupunba barbouriana
Jupunba commutata
Jupunba microcalyx
Jupunba leucophylla
Jupunba floribunda
Jupunba longipedunculata
Samanea saman
Chloroleucon tenuiflorum
Leucochloron bolivianum
Enterolobium contortisiliquum
Enterolobium cyclocarpum
Enterolobium barinense
Enterolobium barnebianum
Enterolobium maximum
Enterolobium gummiferum
Albizia umbellata
Albizia saponaria
Albizia retusa
Albizia adianthifolia
Albizia zygia
Albizia grandibracteata
Albizia ferruginea
Albizia versicolor
Albizia brevifolia
Albizia anthelmintica
Albizia viridis
Albizia atakataka
Albizia polyphylla
Albizia mahalao
Albizia bernieri
Albizia boivinii
Albizia obbiadensis
Albizia aurisparsa
Albizia sahafariensis
Albizia masikororum
Blanchetiodendron blanchetii
Leucochloron limae
Abarema diamantina
Abarema cochliacarpos
Robrichia oldemanii
Robrichia schomburgkii
Albizia dinklagei
Albizia altissima
Albizia leptophylla
Albizia eriorhachis
Zygia inundata
Zygia sabatieri
Inga huberi
Inga tenuistipula
Inga stipularis
Inga heterophylla
Inga brevipes
Inga umbellifera
Inga alba
Inga laurina
Inga cinnamomea
Inga longiflora
Inga punctata
Inga leiocalycina
Inga setosa
Inga sapindoides
Inga edulis
Inga thibaudiana
Inga ruiziana
Inga alata
Inga pezizifera
Inga marginata
Inga bourgonii
Inga nouragensis
Inga cylindrica
Inga auristellae
Zygia ocumarensis
Macrosamanea kegelii
Macrosamanea spruceana
Macrosamanea duckei
Macrosamanea amplissima
Macrosamanea prancei
Macrosamanea discolor
Macrosamanea simabifolia
Zygia claviflora
Zygia racemosa
Zygia basijuga
Zygia bisingula
Zygia ramiflora
Zygia inaequalis
Zygia conzattii
Zygia unifoliolata
Zygia rhytidocarpa
Zygia ampla
Zygia longifolia
Zygia cataractae
Zygia morongii
Zygia obolingoides
Cassia cowaniivar.guianensis
Cenostigma pluviosumvar.maraniona
Acacia alatavar.biglandulosa
Acacia coleivar.colei
Albizia subdimidiatavar.minor
Albizia subdimidiatavar.subdimidiata
Jupunba trapezifoliavar.micradenia
Chloroleucon mangensevar.mangense
Zygia latifoliavar.communis
Mimosa rubicaulissubsp.himalayana
Archidendron ellipticumsubsp.ellipticum
Paraserianthes lophanthasubsp.lophantha
Acacia deaneisubsp.paucijuga
Hydrochorea marginatasubsp.panurensis
Albizia umbellatasubsp.umbellata
Calliandrasp. nov.
Baliziasp. nov.
Hydrochorea corymbosa
Entadasp.
Zygiasp.
Mimosoid clade
Armature type
Axillary thorns
Internodal prickles
Nodal prickles
Spinescent shoots
Stipular spines
Unarmed
Figure 15. Evolution of dierent types of armature across Caesalpinioideae. Character states were de-
ned as: unarmed; nodal or internodal prickles on stem; stipular spines; nodal axillary thorns including modi-
ed inorescence axes of Chloroleucon; spinescent shoots. Branch lengths are not informative in this gure.
Photos a and b axillary thorns a Parkinsonia andicola (Griseb.) Varjão & Mansano b Prosopis juliora
(Sw.) DC. c, d, h internodal prickles c Senegalia tamarindifolia (L.) Britton & Rose d Mimosa ophthal-
mocentra Mart. ex Benth. e spinescent shoots, Prosopis kuntzei Harms f and g stipular spines f Prosopis
ferox Griseb. g Vachellia cornigera (L.) Seigler & Ebinger h Cylicodiscus gabunensis Harms. All photos
Colin Hughes, except h William Hawthorne.
vs. pinnate leaves, presence of phyllodes and presence or absence of extraoral leaf nectar-
ies (EFNs) are all hypothesised to be homoplasious. Multiple reversals to once-pinnate
leaves within mimosoids (Inga, Calliandra hymenaeodes (Persoon) Benth., Sanjappa cyn-
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
30
ometroides (Bedd.) E.R. Souza & M.V. Krishnaraj and Cojoba rufescens (Benth.) Britton
& Rose), multiple origins of phyllodes (in Acacia pro parte, species of Senna including S.
phyllodinea (R. Br.) Symon and some varieties of S. artemisoides (Gaudich. ex DC.) Randell
and Mimosa species including, for example, M. extranea Benth. and M. phyllodinea Benth.
(Barneby 1991)), and multiple losses of EFNs (Marazzi et al. 2019) need to be hypoth-
esised to account for the phylogenetic distributions of these traits. Floral traits show similar
extensive homoplasy with multiple derivations of dierent types of oral heteromorphy
(Fig. 14), numerous switches between spikes and capitula and repeated evolution of diverse
compound inorescence conformations (Grimes 1999), homoplasious occurrences of dif-
ferent types of anther glands (Luckow and Grimes 1997) and extremely diverse and evo-
lutionarily labile shapes and sizes of polyads, even within some genera (e.g. Hughes 1997).
As indicated above, number of stamens and their connation or not into a staminal tube,
the two androecial traits that underpinned the tribal classication of mimosoids rst es-
tablished by Bentham (1875), are also homoplasious across mimosoids such that the tribal
classication has not stood the test of time and molecular phylogenetics. Plant functional
traits including nodulation (de Faria et al. 2022) and growth forms (Gagnon et al. 2019)
also show high levels of homoplasy. Indeed, it appears that nearly all Caesalpinioideae mor-
phological characters and functional traits are homoplasious, given that collectively we, as
authors familiar with Caesalpinioideae, have been unable to come up with any morpho-
logical characters or functional traits that provide robust synapomorphies subtending larger
subclades within Caesalpinioideae, due to either multiple evolutionary origins or repeated
independent losses or reversals. Perhaps the one exception to this would be the aquatic
habit in Neptunia Lour. spp., which is unique within Caesalpinioideae, although many
mimosoids are rheophytes, tolerant of seasonal ooding. is is very much in line with the
idea that vegetative, ower and fruit characters may be equally homoplasious, as found in
other legume groups such as the dalbergioid clade in Papilionoideae (Lavin et al. 2001).
Pre-eminence of certain morphological characters over others in classication of a
group and the prevalence of ‘organogenera’ (sensu Nielsen 1981) united by just a single
character, in situations where morphology is pervasively homoplasious, has been at the
root of many of the disagreements about generic delimitation in mimosoids, as pointed
out by Guinet (1981).
Trans-continental sampling
A second important reason for the extensive generic non-monophyly is the lack of pan-
tropical synthesis and integration that has been the hallmark of much taxonomic work
on Caesalpinioideae up to now and the lack of adequate pantropical sampling of taxa
in previous phylogenies. In this light, it is notable that two of the most productive and
inuential mimosoid taxonomists of the twentieth century, both of whom signicantly
reshaped the generic classication – Rupert Barneby and Ivan Nielsen – worked largely
independently in dierent geographical areas, especially on genera of the former tribe
Ingeae. While both were very much aware of the wider pantropical dimensions and
elements of their groups, Barneby focused primarily on New World mimosoids (e.g.
Phylogenomics of Caesalpinioideae: generic re-delimitation 31
Barneby 1991, 1998; Barneby and Grimes 1996, 1997), while Nielsen concentrated on
Australasian mimosoids (e.g. Nielsen 1981, 1992) and neither was fully familiar with
the details of species of the other (see e.g. Barneby and Grimes 1996), such that no pan-
tropical synthesis across mimosoids was fully achieved and New World – Old World
clades that span the Old World and New World or conversely, amphi-Atlantic genera
that are non-monophyletic, although hypothesised by both authors, were not resolved.
Our new phylogeny with its near-complete generic sampling reveals several in-
stances of Old World – New World connections and disconnects that have important
implications for generic delimitation and which were not fully apparent before. First,
the amphi-Atlantic genus Prosopis is shown to be non-monophyletic (Figs 4 and 5),
conrming earlier evidence of Catalano et al. (2008). Prosopis africana (Guill. & Perr.)
Taub. forms a monospecic lineage unrelated to the rest of Prosopis, while the remain-
ing three Old World species are sister to the Indo-Nepalese Indopiptadenia Brenan and
New World Prosopis has the Namibian-Namaqualand monospecic Xerocladia Harv.
nested within it (Fig. 5). It is, therefore, clear that Burkart’s (1976) broad trans-con-
tinental concept of Prosopis s.l., which followed Bentham’s (1842, 1875) circumscrip-
tion, is not sustainable (see Hughes et al. 2022a). A second example of disconnection
between Old and New World elements of a pantropical genus is Albizia, where species
of New World section Arthrosamanea (Britton & Rose) Barneby & J.W. Grimes form
a clade quite separate from Old World Albizia s.s. (Figs 9 and 10; Koenen et al. 2020b:
see Aviles et al. 2022). Conversely, two previously poorly understood New World – Old
World connections have been revealed. First, it is now clear that the African rainforest
species Albizia obliquifoliolata De Willd. and A. rhombifolia Benth. (previously often
referred to the genus Cathormion) are nested within the New World Balizia / Hydrocho-
rea clade (Fig. 9), which is the focus of generic re-delimitation by Soares et al. (2022).
Similarly, the recently segregated Neotropical Robrichia (formerly Enterolobium section
Robrichia – see de Souza et al. 2022a) is sister to a clade of African mainly rainforest
species (Albizia dinklagei (Harms) Harms / A. altissima Hook. f. / A. eriorhachis Harms
/ A. leptophylla Harms) whose generic placements in Albizia, Cathormion or Samanea
(Benth.) Merr. have long been uncertain and neglected (Fig. 11), also prompting fur-
ther generic re-arrangement in this Special Issue by Koenen (2022a). For the rst time,
the pantropical sampling employed here is more fully documenting these issues.
The mimosoid clade
We recover both Chidlowia and Sympetalandra as rmly nested in the mimosoid clade
(Fig. 4), conrming previous molecular phylogenetic studies (Chidlowia: Manzanilla and
Bruneau 2012; LPWG 2017; Koenen et al. 2020b; Sympetalandra: LPWG 2017). Of
the ten genera previously included in the Dimorphandra group (sensu Polhill and Vidal
1981), Sympetalandra, comprising ve species (van Steenis 1975; Hou 1996) in the for-
ests of Malaya, Borneo, the Philippine Islands and the Lesser Sunda Islands, is unique in
having its stamens shortly joined to the petals and Chidlowia Hoyle (Hoyle 1932) from
West Africa (Sierra Leone to Ghana) stands out by having dorsixed (rather than basi-
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
32
xed) anthers. ese two genera are placed between the Xylia and Entada clades of the
early-diverging lineages of the mimosoid clade (Fig. 4), outside the core mimosoid clade
sensu Koenen et al. (2020b). For Chidlowia, once-pinnate leaves and relatively large
owers with showy red petals which are strongly imbricate in bud are more suggestive
of placement outside the mimosoids. For example, Hoyle (1932) suggested an anity
with the detarioid genus Schotia Jacq., but the regular owers with equally-sized petals,
the showy red stamen laments partly joined at the base (they were described as free in
the genus protologue (Hoyle 1932)) and the small campanulate, gamosepalous calyces,
support placement in the mimosoid clade. e placement of Sympetalandra in the mi-
mosoid clade, based on molecular analyses, is supported by its racemose or paniculate
inorescences of small, essentially regular, owers. Finally, the genus Dinizia, which on
morphological grounds has sometimes been included in mimosoids in the past (Burkart
1943), is here placed in the grade of genera directly subtending the mimosoid clade,
conrming the results of previous molecular phylogenetic studies (Luckow et al. 2005;
Bouchenak-Khelladi et al. 2010; Marazzi and Sanderson 2010; Manzanilla and Bruneau
2012; Cardoso et al. 2013; Kyalangalilwa et al. 2013; LPWG 2017; Zhang et al. 2020).
e mimosoid clade, i.e. the subfamily formerly known as the mimosoideae, was
traditionally diagnosed by petals valvate, as opposed to imbricate, in bud. Valvate petal
aestivation is mostly a reection of whether or not the owers are actinomorphic vs.
zygomorphic, i.e. as the owers become radially symmetrical the petals become valvate
in bud. Across the non-mimosoid grade of Caesalpinioideae subtending the mimosoid
clade, taxa with imbricate and valvate aestivation are phylogenetically intermingled.
Although the vast majority of mimosoids do, indeed, have valvate petal aestivation,
three exceptions: Chidlowia (as indicated above), alongside Mimozyganthus Burkart
and Parkia R.Br., both of which are deeply nested within the mimosoid clade, show
imbricate petal aestivation, providing further evidence of the homoplasy of this char-
acter. Further work to characterise petal aestivation across all relevant genera of Caesal-
pinioideae is needed, but it is clear that valvate aestivation does not provide a unique
diagnostic synapomorphy for the mimosoid clade.
All other aspects of higher-level relationships are discussed in ALS14 Part 2.
Taxonomy in the age of phylogenomics
Once purely the domain of morphological analyses (e.g. Barneby and Grimes 1996,
1997; Barneby 1998), decisions on delimiting and naming taxa have increasingly been
based on genes rather than morphology (Muñoz-Rodríguez et al. 2019). Employing a
large phylogenomic dataset and explicitly considering numbers of genes that support
particular generic congurations contribute to naming taxa that are more likely to be
robust to future sampling of additional species and genomic regions and, hence, to
taxonomic stability (Orthia et al. 2005; Pfeil and Crisp 2005; Humphreys and Linder
2009). However, use of ever larger phylogenomic datasets also raises questions about
how to delimit taxa and especially about how conict amongst gene trees reecting the
widely dierent evolutionary histories of dierent parts of the genome (e.g. Salichos and
Phylogenomics of Caesalpinioideae: generic re-delimitation 33
Rokas 2013; Wang et al. 2019; Jiang et al. 2020; Koenen et al. 2020a, b) should inform
delimitation of taxa. For example, what fraction of genes supporting a clade should be
used as a cut-o for delimiting taxa? To what extent does it matter if there are alterna-
tive topologies that are supported by a substantial fraction of genes, even if that number
is lower than the number of genes that supports the ‘main’ topology and what are the
classicatory implications when only a small fraction of genes is informative for certain
relationships (Shen et al. 2017)? Employing large numbers of genes is also enhancing
our ability to identify putative hard polytomies on nodes where all, or almost all, genes
lack phylogenetic signal (e.g. Koenen et al. 2020b), raising questions about whether it is
justied to delimit multiple segregate genera when the relationships amongst them are
unresolved and potentially form a polytomy. Large phylogenomic datasets also highlight
cases of cytonuclear discordance even more starkly than before, raising questions about
what is the best approach when dierent genomes (i.e. nuclear, plastid and mitochon-
drial) have dierent evolutionary histories, as is often the case (e.g. Bruun-Lund et al.
2017; ielsch et al. 2017; Lee-Yaw et al. 2019; Rose et al. 2021; Debray et al. 2022)?
Finally, we might also ask what, fundamentally, is now the role of morphology in delim-
iting taxa in the phylogenomic era (Muñoz-Rodríguez et al. 2019)?
e phylogeny of Caesalpinioideae presented here (Figs 2–12) poses many of these
questions and provides some possible answers. First, the ubiquity of gene tree conict
found here and more generally in phylogenomics (Salichos and Rokas 2013; Wang et
al. 2019; Jiang et al. 2020; Koenen et al. 2020b; Yang et al. 2020), suggests that the
presence of conicting topologies for a particular node alone is not sucient reason to
avoid naming the clade subtended by that node. If many conicting topologies exist,
but none of these occurs at a high frequency amongst the gene trees, low support values
are indicative of lack of signal rather than true conict (Koenen et al. 2020b) and do
not need to aect classicatory decisions if there is support for the species tree topol-
ogy amongst a sizable fraction of the gene trees. e nodes subtending Macrosamanea
Britton & Rose, Zygia and Inga (Figs 11 and 12) are good examples of an abundance
of conicting topologies none of which is widespread and the monophyly of these
genera is, therefore, not in question (except for a few outlier species of Zygia – see
Appendix 1). However, if low support for a node in the species tree is caused by an
alternative topology that is common across gene trees, the situation is more complex
and the clade in question should probably not be named pending further study with
additional accessions and genomic regions. e crown node of Archidendron (Fig. 8)
provides an example of a node with a relatively abundant alternative topology, raising
doubts about the monophyly of Archidendron (see Appendix 1; Brown et al. 2022).
Second, in cases of cytonuclear discordance (as we see across several key nodes that af-
fect decisions about generic delimitation), the smaller size of the plastid dataset and the
fact that the chloroplast genome can be considered as a single, albeit large, uniparen-
tally-inherited locus, suggest that, in most cases, nuclear phylogenies provide a more
accurate approximation of the true species tree (see Terra et al. 2022).
Finally, despite providing the main (usually sole) source of information for classi-
cation for centuries, morphology was rapidly eclipsed as a source of data for phylogeny
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
34
reconstruction with the advent of molecular data (e.g. Scotland et al. 2003). Neverthe-
less, despite the dominance of phylogenomic data for building accurate and robust
trees, morphology continues to play a central role as a complementary source of evi-
dence for delimiting taxa in the light of monophyly inferred from phylogenomic data
(Humphreys and Linder 2009; Gagnon et al. 2016). For example, placement of Zygia
sabatieri and Z. inundata not in a clade with the remainder of Zygia, but instead as the
sister clade of Inga in the nuclear ASTRAL phylogeny (Fig. 12) or in a grade subtend-
ing Inga in the plastome phylogeny (Suppl. material 3; Ferm et al. 2019), presents
several options for delimiting genera: transfer these two species to the genus Inga, place
both species in a new segregate genus or place each species in separate segregate genera.
All three options are valid from the perspective of monophyly, but not from a mor-
phological standpoint, because Z. sabatieri and Z. inundata have dehiscent pods and
Z. sabatieri has bipinnate leaves, in contrast to the once-pinnate leaves and indehiscent
pods that are diagnostic of the genus Inga. From a morphological perspective, it will be
preferable to assign Z. inundata and Z. sabatieri to a new segregate genus rather than to
transfer them to Inga, thereby retaining the morphological integrity and diagnosability
of the genus Inga (see Appendix 1). is example demonstrates the important role that
morphology continues to play in the era of phylogenomics: not to determine relation-
ships and infer monophyly, but to inform and guide decisions about how to partition
a phylogeny into monophyletic taxa (see also Terra et al. 2022 for another example).
Conclusions and future work
Here, we present a series of phylogenomic analyses including detailed assessment
of gene tree conict and support that suggest that about one quarter of mimosoid
genera are non-monophyletic (Figs 2–12). is new backbone phylogeny, building
on the 122-taxon version of Koenen et al. (2020b), provides robust foundations for
aligning genera with monophyletic groups across a clade where generic delimita-
tion has long been contentious with starkly contrasting generic systems (Lewis et
al. 2005; Brown 2008) and for the higher-level classication presented in Advances
in Legume Systematics 14, Part 2. e limitations of previous work focused either
just on the Old World (e.g. Nielsen 1981, 1992) or just on the New World (e.g.
Barneby and Grimes 1996, 1997; Barneby 1998) have become more starkly appar-
ent now that pantropical sampling has been achieved, revealing the non-monophy-
ly of well-known pantropical genera, such as Albizia (Koenen et al. 2020b; Aviles
et al. 2022) and Prosopis (Hughes et al. 2022a), as well as previously unrecognised
clades with trans-Atlantic distributions (Soares et al. 2022; Koenen 2022a). Our
analyses provide a glimpse of the likely extent of morphological homoplasy (Figs
13–15).
However, despite including 420 taxa in the current analyses, it is clear that addition-
al taxon sampling will be needed to fully resolve all the possible non-monophyly issues
within Caesalpinioideae. Several priorities for future research are apparent. First, denser
taxon sampling across Senegalia and allies is needed to address the unusual dilemmas
Phylogenomics of Caesalpinioideae: generic re-delimitation 35
posed by extreme lack of resolution and cytonuclear discordance surrounding delimita-
tion of the genera across the paraphyletic grade comprising Senegalia, Pseudosenegalia,
Parasenegalia and Mariosousa (Fig. 7) that are explored here by Terra et al. (2022) who
provided a list of priority taxa for future sampling with molecular data. Second, the
likely non-monophyly of Archidendron (see Brown et al. 2022 and Appendix 1) also
remains unresolved with a clear need for additional work, especially as many species are
known from incomplete material. Archidendron and Senegalia are now the largest gen-
era in Caesalpinioideae where doubts remain about their monophyly and delimitation.
ird, a much more comprehensively sampled study is needed to address the longstand-
ing non-monophyly of Dimorphandra Schott (Fig. 3). Fourth, the generic anities
of Calliandra umbrosa (Fig. 7; de Souza et al. 2016) and Calliandra sp. nov., the last
species removed from Calliandra by Barneby (1998) yet to be placed in another genus,
remain to be assessed. Finally, the taxonomic implications of the non-monophyly of
Zygia revealed by Ferm et al. (2019) and conrmed here (Figs 11 and 12) have not yet
been addressed. Like Archidendron, many species of Zygia remain poorly understood.
Furthermore, although there is no evidence that any large clades in Caesalpin-
ioideae are subtended by whole genome duplication (WGD) events (Koenen et al.
2020a), it is clear that polyploidisation events have happened many times more re-
cently, scattered across the phylogeny of Caesalpinioideae, for example in Leucaena
(Govindarajulu et al. 2011; Bailey et al., in prep.), Vachellia and Mimosa (Dahmer
et al. 2011; Simon et al. 2011). Furthermore, high numbers of gene duplications de-
tected on branches subtending, for example, Sympetalandra, Lemurodendron Villiers &
P. Guinet and Schleinitzia Warb. point to possible additional WGDs (Ringelberg et al.,
unpublished data). More work is needed to understand all these possible polyploidisa-
tion events, whether they involved auto- or allopolyploidisation and how such events
aect assessments of character evolution, homoplasy and generic delimitation.
Finally, our preliminary assessments of homoplasy (Figs 13–15) notwithstanding,
there is a clear need for rigorous analysis and comparison of morphological traits across
the subfamily, based on more detailed homology assessment of morphological, develop-
mental and genomic data. Morphological diagnosability of taxa is centrally important,
especially for the acceptance of novel taxonomy by the end-users of scientic names, a
group that is much larger than that of the scientic taxonomic community. We hope that
the new phylogeny presented here can provide the evolutionary framework for future
morphological studies that assess character evolution and homoplasy in greater detail.
Acknowledgements
e authors thank B. Adhikari, D. Lorence, B. Marazzi, É. de Souza, the G, K, JRAU,
L, MEL, NY, FHO, P, RB, WAG and Z Herbaria, the Millennium Seed Bank, Kew, the
South African National Botanical Institute, the Direction de Environment, New Caledonia
and the National Tropical Botanical Garden, Hawaii, U.S.A. for provision of leaf or DNA
samples; P. Ribeiro, É. de Souza, M. Morim, M. Simon and F. Bonadeu in Brazil and sta
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
36
of the Kew Madagascar Conservation Centre and Botanical and Zoological Garden of
Tsimbazaza, Madagascar for eldwork support; the national regulatory authorities of Bra-
zil for access to DNA of Brazilian plants (authorised through SISGEN n° A464716), and
Madagascar (research permit 006/14/MEF/SG/DGF/DCB.SAP/SCB); U. Grossniklaus,
V. Gagliardini, Dept Plant & Microbial Biology, Univ. Zurich for use of their TapeStation;
the S3IT, Univ. Zurich for use of the ScienceCloud computational infrastructure; and the
Club Botanique de Toliara, Madagascar, the Flora Mendocina project, Argentina, B. Ma-
slin, G. Sankowsky, M. Simon, and X. Cornejo for permission to use photos included in
Figs 13–15. is work was supported by the Swiss National Science Foundation through
grants 310003A_156140 and 31003A_182453/1 to CEH and an Early.Postdoc.Mobility
fellowship P2ZHP3_199693 to EJMK, the Claraz Schenkung Foundation, Switzerland
to CEH, the Natural Sciences and Engineering Research Council of Canada, NSERC, to
AB, FAPESB, Brazil (PTX0004 & APP0096 to LPdQ) and CNPq, Brazil (480530/2012-
2 & 311847/2021-8 to JRI and PROTAX 440487 to LPdQ).
References
Aberer AJ, Krompass D, Stamatakis A (2013) Pruning rogue taxa improves phylogenetic ac-
curacy: An ecient algorithm and webservice. Systematic Biology 62(1): 162–166. https://
doi.org/10.1093/sysbio/sys078
Aebli A (2015) Assembly of the Madagascan biota by replicated adaptive radiations: Case stud-
ies in Leguminosae-Mimosoideae. Unpublished MSc thesis, University of Zurich.
Aviles GP, Koenen E, Riina R, Hughes CE, Ringelberg JJ, Fernández-Concha GC, Morillo
IR, Itza LLC, Tamayo-Cen I, Prado JHR, Cornejo X, Mattapha S, de Stefano RD (2022)
Re-establishment of the genus Pseudalbizzia (Leguminosae, Caesalpinioideae: mimosoid
clade): the New World species formerly placed in Albizia. In: Hughes CE, de Queiroz LP,
Lewis GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae
Part 1: New generic delimitations. PhytoKeys 205: 371–400. https://doi.org/10.3897/
phytokeys.205.76821
Babineau M, Bruneau A (2017) Phylogenetic and biogeographical history of the Afro-Mada-
gascan genera Delonix, Colvillea and Lemuropisum (Fabaceae: Caesalpinioideae). Botanical
Journal of the Linnean Society 184(1): 59–78. https://doi.org/10.1093/botlinnean/box009
Banks H, Himanen I, Lewis GP (2010) Evolution of pollen, stigmas and ovule numbers at
the caesalpinioid-mimosoid interface (Fabaceae). Botanical Journal of the Linnean Society
162(4): 594–615. https://doi.org/10.1111/j.1095-8339.2010.01038.x
Barneby RC (1991) Sensitivae Censitae - A description of the genus Mimosa Linnaeus (Mi-
mosaceae) in the New World. Memoirs of the New York Botanical Garden 65: 1–835.
Barneby RC (1998) Silk tree, guanacaste, monkey’s earring. A generic system for the synan-
drous Mimosaceae of the Americas. Part III: Calliandra. Memoirs of the New York Botani-
cal Garden 74: 1–223.
Barneby RC, Grimes JW (1996) Silk tree, guanacaste, monkey’s earring. A generic system for
the synandrous Mimosaceae of the Americas. Part I: Abarema, Albizia, and allies. Memoirs
of the New York Botanical Garden 74: 1–292.
Phylogenomics of Caesalpinioideae: generic re-delimitation 37
Barneby RC, Grimes JW (1997) Silk tree, guanacaste, monkey’s earring. A generic system for
the synandrous Mimosaceae of the Americas. Part II: Pithecellobium, Cojoba, and Zygia.
Memoirs of the New York Botanical Garden 74: 1–149.
Barrett CF, Bacon CD, Antonelli A, Cano Á, Hofmann T (2016) An introduction to plant
phylogenomics with a focus on palms. Botanical Journal of the Linnean Society 182(2):
234–255. https://doi.org/10.1111/boj.12399
Bentham G (1841) Notes on Mimoseae, with a short synopsis of species. Journal of Botany
(Hooker) 4: 323–417.
Bentham G (1842) Notes on Mimoseae, with a synopsis of species. Tribe III. Acacieae (cont.).
e London Journal of Botany 1: 318–392.
Bentham G (1875) Revision of the suborder Mimoseae. Transactions of the Linnean Society of
London 30(3): 335–664. https://doi.org/10.1111/j.1096-3642.1875.tb00005.x
Boatwright JS, Maurin O, van der Bank M (2015) Phylogenetic position of Madagascan species of
Acacia s.l. and new combinations in Senegalia and Vachellia (Fabaceae, Mimosoideae, Acacieae).
Botanical Journal of the Linnean Society 179(2): 288–294. https://doi.org/10.1111/boj.12320
Borges L, Inglis PW, Simon M, Ribeiro P, de Queiroz L (2022) Misleading fruits: e non-
monophyly of Pseudopiptadenia and Pityrocarpa supports generic re-circumscriptions and
a new genus within mimosoid legumes. In: Hughes CE, de Queiroz LP, Lewis GP (Eds)
Advances in Legume Systematics 14. Classication of Caesalpinioideae Part 1: New gener-
ic delimitations. PhytoKeys 205: 239–260. https://doi.org/10.3897/phytokeys.205.82275
Bouchenak-Khelladi Y, Maurin O, Hurter J, van der Bank M (2010) e evolutionary his-
tory and biogeography of Mimosoideae (Leguminosae): An emphasis on African aca-
cias. Molecular Phylogenetics and Evolution 57(2): 495–508. https://doi.org/10.1016/j.
ympev.2010.07.019
Brown GK (2008) Systematics of the tribe Ingeae. Muelleria 26: 27–42.
Brown GK, Murphy DJ, Miller JT, Ladiges PY (2008) Acacia s.s. and its relationship among
tropical legumes, tribe Ingeae (Leguminosae: Mimosoideae). Systematic Botany 33(4):
739–751. https://doi.org/10.1600/036364408786500136
Brown GK, Murphy DJ, Ladiges PY (2011) Relationships of the Australo-Malesian genus Para-
serianthes (Mimosoideae: Leguminosae) identies the sister group of Acacia sensu stricto
and two biogeographical tracks. Cladistics 27(4): 380–390. https://doi.org/10.1111/
j.1096-0031.2011.00349.x
Brown GK, Aju J, Bayly MJ, Murphy DJ, McLay TGB (2022) Phylogeny and classication
of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis
(Leguminosae, subfamily Caesalpinioideae, mimosoid clade). In: Hughes CE, de Queiroz
LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae
Part 1: New generic delimitations. PhytoKeys 205: 299–334. https://doi.org/10.3897/
phytokeys.205.79381
Bruneau A, Mercure M, Lewis GP, Herendeen PS (2008) Phylogenetic patterns and diversica-
tion in the caesalpinioid legumes. Botany 86(7): 697–718. https://doi.org/10.1139/B08-058
Bruun-Lund S, Clement WL, Kjellberg F, Rønsted N (2017) First plastid phylogenomic study
reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Morace-
ae). Molecular Phylogenetics and Evolution 109: 93–104. https://doi.org/10.1016/j.
ympev.2016.12.031
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
38
Burkart A (1943) Las leguminosas argentinas, silvestres y cultivadas. Acme Agency, Buenos
Aires, Argentina.
Burkart A (1976) A monograph of the genus Prosopis (Leguminosae subfam. Mimosoidae).
Journal of the Arnold Arboretum 57(3): 219–525. https://doi.org/10.5962/p.185864
Candolle AP de (1825) Prodromus systematis naturalis regni vegetabilis - pars II.
Capuron R (1970) Contribution à l’étude de la orestière de Madagascar: Notes sur les Albizia
Duraz. Adansonia 2: 357–382.
Cardoso D, Pennington RT, de Queiroz LP, Boatwright JS, Van Wyk BE, Wojciechowski MF,
Lavin M (2013) Reconstructing the deep-branching relationships of the papilionoid legumes.
South African Journal of Botany 89: 58–75. https://doi.org/10.1016/j.sajb.2013.05.001
Catalano SA, Vilardi JC, Tosto D, Saidman BO (2008) Molecular phylogeny and diversi-
cation history of Prosopis (Fabaceae: Mimosoideae). Biological Journal of the Linnean
Society. Linnean Society of London 93(3): 621–640. https://doi.org/10.1111/j.1095-
8312.2007.00907.x
Clark RP, Jiang K-W, Gagnon E (2022) Reinstatement of Ticanto (Leguminosae-Caesalpin-
ioideae) – the nal piece in the Caesalpinia group puzzle. In: Hughes CE, de Queiroz LP,
Lewis GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae
Part 1: New generic delimitations. PhytoKeys 205: 59–98. https://doi.org/10.3897/phy-
tokeys.205.82300
Clarke HD, Downie SR, Seigler DS (2000) Implications of chloroplast DNA restriction site
variation for systematics of Acacia (Fabaceae : Mimosoideae). Systematic Botany 25(4):
618–632. https://doi.org/10.2307/2666724
Contreras Jiménez JL (1986) Desmanthus balsensis (Leguminosae: Mimosoideae), una especie
nueva de la depresión del Río Balsas en Guerrero, Mexico. Phytologia 60: 89–92. https://
doi.org/10.5962/bhl.part.3792
da Silva MF (1986) Dimorphandra (Caesalpiniaceae). Flora Neotropica 44: 1–127.
Dahmer N, Simon MF, Schino-Wittmann MT, Hughes CE, Miotto STS, Giuliani JC (2011)
Chromosome numbers in the genus Mimosa L.: Cytotaxonomic and evolutionary impli-
cations. Plant Systematics and Evolution 291(3–4): 211–220. https://doi.org/10.1007/
s00606-010-0382-2
de Faria SM, Ringelberg JJ, Gross E, Koenen EJM, Cardoso D, Ametsitsi GKD, Akomatey J,
Maluk M, Tak N, Gehlot HS, Wright KM, Teaumroong N, Songwattana P, De Lima HC,
Prin Y, Zartmann C, Sprent JI, Ardley J, Hughes CE, James EK (2022) e innovation of
the symbiosome has enhanced the evolutionary stability of nitrogen xation in legumes.
New Phytologist. https://doi.org/10.1111/nph.18321
de la Estrella M, Forest F, Klitgård B, Lewis GP, Mackinder BA, De Queiroz LP, Wieringa JJ,
Bruneau A (2018) A new phylogeny-based tribal classication of subfamily Detarioideae,
an early branching clade of orally diverse tropical arborescent legumes. Scientic Reports
8(1): 1–14. https://doi.org/10.1038/s41598-018-24687-3
de Souza ÉR, Lewis GP, Forest F, Schnadelbach AS, van den Berg C, de Queiroz LP (2013)
Phylogeny of Calliandra (Leguminosae: Mimosoideae) based on nuclear and plastid mo-
lecular markers. Taxon 62(6): 1200–1219. https://doi.org/10.12705/626.2
Phylogenomics of Caesalpinioideae: generic re-delimitation 39
de Souza ÉR, Krishnaraj MV, de Queiroz LP (2016) Sanjappa, a new genus in the tribe Ingeae
(Leguminosae: Mimosoideae) from India. Rheedea 26: 1–12.
de Souza ÉR, Luz ARM, Rocha L, Lewis GP (2022a) Molecular and morphological analysis
supports the separation of Robrichia as a genus distinct from Enterolobium (Leguminosae:
Caesalpinioideae: Mimosoid Clade). Systematic Botany 47(1): 268–277. https://doi.org/1
0.1600/036364422X16442669847067
de Souza ÉR, de Almeida PGC, Rocha L, Koenen EJM, Burgos MA, Lewis GP, Hughes
CE (2022b) Boliviadendron, a new segregate genus of mimosoid legume (Leguminosae,
Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of
Bolivia. In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics
14. Classication of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205:
439–452. https://doi.org/10.3897/phytokeys.205.82256
Debray K, Le Paslier M-C, Bérard A, ouroude T, Michel G, Marie-Magdelaine J, Bruneau A,
Foucher F, Malécot V (2022) Unveiling the patterns of reticulated evolutionary processes
with phylogenomics: Hybridization and polyploidy in the genus Rosa. Systematic Biology
71(3): 547–569. https://doi.org/10.1093/sysbio/syab064
Demeulenaere E, Schils T, Burleigh JG, Ringelberg JJ, Koenen EJM, Ickert-Bond SM (2022) Phy-
logenomic assessment prompts recognition of the Serianthes clade and conrms the mono-
phyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider in-
goid clade (Leguminosae, Caesalpinioideae). In: Hughes CE, de Queiroz LP, Lewis GP (Eds)
Advances in Legume Systematics 14. Classication of Caesalpinioideae Part 1: New generic
delimitations. PhytoKeys 205: 335–362. https://doi.org/10.3897/phytokeys.205.79144
Dodsworth S, Pokorny L, Johnson MG, Kim JT, Maurin O, Wickett NJ, Forest F, Baker WJ
(2019) Hyb-Seq for owering plant systematics. Trends in Plant Science 24(10): 887–891.
https://doi.org/10.1016/j.tplants.2019.07.011
Du Puy DJ, Labat J-N, Rabevohitra R, Villiers J-F, Bosser J, Moat J (2002) e Leguminosae
of Madagascar. Royal Botanic Gardens, Kew, United Kingdom, 737 pp.
Elias TS (1981) Mimosoideae. In: Polhill RM, Raven PH (Eds) Advances in Legume Systemat-
ics 1. Royal Botanic Gardens, Kew, United Kingdom, 143–152.
Engler HGA, Prantl KAE (1897) Die Natürlichen Panzenfamilien 2–4, Nachträge 1. Wil-
helm Engelmann, Leipzig, Germany.
Ferm J, Korall P, Lewis GP, Ståhl B (2019) Phylogeny of the Neotropical legume genera Zygia
and Marmaroxylon and close relatives. Taxon 68(4): 661–672. https://doi.org/10.1002/
tax.12117
Gagnon E, Bruneau A, Hughes CE, de Queiroz L, Lewis GP (2016) A new generic system
for the pantropical Caesalpinia group (Leguminosae). PhytoKeys 71: 1–160. https://doi.
org/10.3897/phytokeys.71.9203
Gagnon E, Ringelberg JJ, Bruneau A, Lewis GP, Hughes CE (2019) Global Succulent Biome
phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae). New
Phytologist 222(4): 1994–2008. https://doi.org/10.1111/nph.15633
Geesink R (1984) Scala Milletiearum: a survey of the genera of the tribe Millettieae (Leguminos-
ae-Papilionoideae). Leiden Botanical Series 1, EJ Brill & Leiden University Press, Leiden.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
40
Goldblatt P, Davidse G (1977) Chromosome numbers in legumes. Annals of the Missouri
Botanical Garden 64(1): 121–128. https://doi.org/10.2307/2395237
Gómez-Acevedo S, Rico-Arce L, Delgado-Salinas A, Magallón S, Eguiarte LE (2010) Neotropical
mutualism between Acacia and Pseudomyrmex: Phylogeny and divergence times. Molecular
Phylogenetics and Evolution 56(1): 393–408. https://doi.org/10.1016/j.ympev.2010.03.018
Govindarajulu R, Hughes CE, Alexander PJ, Donovan Bailey C (2011) e complex evolution-
ary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae).
American Journal of Botany 98(12): 2064–2076. https://doi.org/10.3732/ajb.1100260
Grimes J (1999) Inorescence morphology, heterochrony, and phylogeny in the Mimosoid
tribes Ingeae and Acacieae (Leguminosae: Mimosoideae). Botanical Review 65(4): 317–
347. https://doi.org/10.1007/BF02857753
Guerra E, Morim MP, Iganci J (2016) A new species of Abarema (Fabaceae) from Brazil. Phy-
totaxa 289(1): 77–82. https://doi.org/10.11646/phytotaxa.289.1.6
Guerra E, Andrade BO, Morim MP, Vieira Iganci JR (2019) Taxonomic delimitation of species
complexes: A challenge for conservation; First steps with the Abarema cochliacarpos complex.
Systematic Botany 44(4): 818–825. https://doi.org/10.1600/036364419X15710776741422
Guinet Ph (1981) Mimosoideae: the characters of their pollen grains. In: Polhill RM, Raven
PH (Eds) Advances in Legume Systematics Part 1, Royal Botanic Gardens, Kew.
Hart ML, Forrest LL, Nicholls JA, Kidner CA (2016) Retrieval of hundreds of nuclear loci
from herbarium specimens. Taxon 65(5): 1081–1092. https://doi.org/10.12705/655.9
Hernández HM (1986) Zapoteca: A new genus of Neotropical Mimosoideae. Annals of the
Missouri Botanical Garden 73(4): 755–763. https://doi.org/10.2307/2399204
Hou D (1996) Sympetalandra. In: Hou D, Larsen K, Larsen SS, Laferriere JE, Duyes BEE
(Eds) Fl. Malesiana Series 1. Rijksherbarium / Hortus Botanicus, Leiden University, Lei-
den, the Netherlands, 709–714.
Hoyle AC (1932) Chidlowia, a new tree genus of Caesalpiniaceae from West Tropical Africa.
Kew Bulletin of Miscellaneous Information: 101–103. https://doi.org/10.2307/4113372
Hu JM, Lavin M, Wojciechowski MF, Sanderson MJ (2000) Phylogenetic systematics of the
tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its impli-
cations for evolutionary patterns in Papilionoideae. American Journal of Botany 87(3):
418–430. https://doi.org/10.2307/2656638
Hughes CE (1997) Variation in anther and pollen morphology in Leucaena Benth. (Legumi-
nosae-Mimosoideae). Botanical Journal of the Linnean Society 123(3): 177–196. https://
doi.org/10.1111/j.1095-8339.1997.tb01412.x
Hughes CE, Bailey CD, Krosnick S, Luckow MA (2003) Relationships among genera of the
informal Dichrostachys and Leucaena groups (Mimosoideae) inferred from nuclear ribo-
somal ITS sequences. In: Klitgaard B, Bruneau A (Eds) Advances in Legume Systematics
Part 10, Royal Botanic Gardens, Kew, United Kingdom, 221–238.
Hughes CE, Ringelberg JJ, Lewis GP, Catalano SA (2022a) Disintegration of the genus Pros-
opis L. (Leguminosae, Caesalpinioideae, mimosoid clade). In: Hughes CE, de Queiroz LP,
Lewis GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae
Part 1: New generic delimitations. PhytoKeys 205: 147–190. https://doi.org/10.3897/
phytokeys.205.75379
Phylogenomics of Caesalpinioideae: generic re-delimitation 41
Hughes CE, Ringelberg JJ, Luckow M, Jiménez JLC (2022b) Mezcala – a new segregate genus
of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic
to the Balsas Depression in Mexico. In: Hughes CE, de Queiroz LP, Lewis GP (Eds)
Advances in Legume Systematics 14. Classication of Caesalpinioideae Part 1: New generic
delimitations. PhytoKeys 205: 191–202. https://doi.org/10.3897/phytokeys.205.78297
Humphreys AM, Linder HP (2009) Concept versus data in delimitation of plant genera. Taxon
58(4): 1054–1074. https://doi.org/10.1002/tax.584002
Iganci J, Soares M, Guerra E, Morim M (2016) A Preliminary molecular phylogeny of the
Abarema alliance (Leguminosae) and implications for taxonomic rearrangement. Interna-
tional Journal of Plant Sciences 177(1): 34–43. https://doi.org/10.1086/684078
Jiang X, Edwards SV, Liu L (2020) e multispecies coalescent model outperforms concatena-
tion across diverse phylogenomic data sets. Systematic Biology 69(4): 795–812. https://
doi.org/10.1093/sysbio/syaa008
Jobson RW, Luckow M (2007) Phylogenetic study of the genus Piptadenia (Mimosoideae: Le-
guminosae) using plastid trnL-F and trnK/matK sequence data. Systematic Botany 32(3):
569–575. https://doi.org/10.1600/036364407782250544
Johnson MG, Gardner EM, Liu Y, Medina R, Gonet B, Shaw AJ, Zerega NJC, Wickett NJ
(2016) HybPiper: Extracting coding sequence and introns for phylogenetics from high-
throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7):
e1600016. https://doi.org/10.3732/apps.1600016
Johnson MG, Pokorny L, Dodsworth S, Botigué LR, Cowan RS, Devault A, Eiserhardt
WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis
DE, Soltis PS, Wong GKS, Baker WJ, Wickett NJ (2019) A universal probe set for
targeted sequencing of 353 nuclear genes from any owering plant designed using
k-medoids clustering. Systematic Biology 68(4): 594–606. https://doi.org/10.1093/
sysbio/syy086
Jumah A (1991) Studies on the morphology of pollen grains of the leguminosae - e mimosoide-
ae. Ghana Journal of Science 31–36: 29–35. https://doi.org/10.4314/gjs.v36i1.47978
Karimi N, Grover CE, Gallagher JP, Wendel JF, Ané C, Baum DA (2019) Reticulate evolution
helps explain apparent homoplasy in oral biology and pollination in Baobabs (Adansonia;
Bombacoideae; Malvaceae). Systematic Biology 69(3): 462–478. https://doi.org/10.1093/
sysbio/syz073
Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Dictionary of the Fungi (10th edn.).
CABI, Wallingford, United Kingdom, 551 pp.
Koenen EJM (2022a) Osodendron gen. nov. (Leguminosae, Caesalpinioideae), a new genus of
mimosoid legumes of tropical Africa. In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Ad-
vances in Legume Systematics 14. Classication of Caesalpinioideae Part 1: New generic
delimitations. PhytoKeys 205: 453–470. https://doi.org/10.3897/phytokeys.205.82821
Koenen EJM (2022b) On the taxonomic anity of Albizia carbonaria Britton (Leguminos-
ae, Caesalpinioideae-mimosoid clade). In: Hughes CE, de Queiroz LP, Lewis GP (Eds)
Advances in Legume Systematics 14. Classication of Caesalpinioideae Part 1: New gener-
ic delimitations. PhytoKeys 205: 363–370. https://doi.org/10.3897/phytokeys.205.82288
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
42
Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy
OJ, Pennington RT, Bruneau A, Hughes CE (2020a) Largescale genomic sequence data
resolve the deepest divergences in the legume phylogeny and support a nearsimultaneous
evolutionary origin of all six subfamilies. New Phytologist 225(3): 1355–1369. https://doi.
org/10.1111/nph.16290
Koenen EJM, Kidner CA, de Souza ÉR, Simon MF, Iganci JRV, Nicholls JA, Brown GK, de
Queiroz LP, Luckow MA, Lewis GP, Pennington RT, Hughes CE (2020b) Hybrid capture
of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and re-
veals the polytomous origins of a large pantropical radiation. American Journal of Botany
107(12): 1710–1735. https://doi.org/10.1002/ajb2.1568
Kyalangalilwa B, Boatwright JS, Daru BH, Maurin O, van der Bank M (2013) Phylogenetic
position and revised classication of Acacia s.l. (Fabaceae: Mimosoideae) in Africa, includ-
ing new combinations in Vachellia and Senegalia. Botanical Journal of the Linnean Society
172(4): 500–523. https://doi.org/10.1111/boj.12047
Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic reconstruc-
tion with innite mixtures of proles in a parallel environment. Systematic Biology 62(4):
11–615. https://doi.org/10.1093/sysbio/syt022
Lavin M, Pennington RT, Klitgaard BB, Sprent JI, de Lima HC, Gasson PE (2001) e dal-
bergioid legumes (Fabaceae): Delimitation of a pantropical monophyletic clade. American
Journal of Botany 88(3): 503–533. https://doi.org/10.2307/2657116
Lavin M, Schrire BP, Lewis GP, Pennington RT, Delgado-Salinas A, ulin M, Hughes CE,
Matos AB, Wojciechowski MF (2004) Metacommunity process rather than continen-
tal tectonic history better explains geographically structured phylogenies in legumes.
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
359(1450): 1509–1522. https://doi.org/10.1098/rstb.2004.1536
Lee-Yaw JA, Grassa CJ, Joly S, Andrew RL, Rieseberg LH (2019) An evaluation of alternative
explanations for widespread cytonuclear discordance in annual sunowers (Helianthus).
New Phytologist 221(1): 515–526. https://doi.org/10.1111/nph.15386
Lewis GP (1998) Caesalpinia: a revision of the Poincianella-Erythrostemon group. Royal Bo-
tanic Gardens, Kew, United Kingdom, 233 pp.
Lewis GP, Guinet P (1986) Notes on Gagnebina (Leguminosae: Mimosoideae) in
Madagascar and neighbouring islands. Kew Bulletin 41(2): 463–470. https://doi.
org/10.2307/4102962
Lewis GP, Schrire BD (2003) ailentadopsis Kostermans (Leguminosae: Mimosoideae: Ingeae)
resurrected. Kew Bulletin 58(2): 491–494. https://doi.org/10.2307/4120634
Lewis GP, Schrire B, Mackinder B, Lock M (2005) Legumes of the World. Royal Botanic Gar-
dens, Kew, United Kingdom, 592 pp.
Lima A, de Paula-Souza J, Ringelberg JJ, Simon MF, de Queiroz L, Borges L, Mansano V,
Souza V, Scalon V (2022) New Segregates from the Neotropical genus Stryphnodendron
(Leguminosae, Caesalpinioideae, mimosoid clade). In: Hughes CE, de Queiroz LP, Lewis
GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae Part 1:
New generic delimitations. PhytoKeys 205: 203–238. https://doi.org/10.3897/phytok-
eys.205.82220
Phylogenomics of Caesalpinioideae: generic re-delimitation 43
Linnaeus C von (1753) Species Plantarum 1.
LPWG (2013) Legume phylogeny and classication in the 21st century: Progress, prospects and
lessons for other species-rich clades. Taxon 62(2): 217–248. https://doi.org/10.12705/622.8
LPWG (2017) A new subfamily classication of the Leguminosae based on a taxonomically
comprehensive phylogeny – e Legume Phylogeny Working Group (LPWG). Taxon
66(1): 44–77. https://doi.org/10.12705/661.3
Luckow MA (1993) Monograph of Desmanthus (Leguminosae-Mimosoideae). Systematic Bot-
any Monographs 38: 1–166. https://doi.org/10.2307/25027822
Luckow MA, Grimes J (1997) A survey of anther glands in the mimosoid legume tribes
Parkieae and Mimoseae. American Journal of Botany 84(3): 285–297. https://doi.
org/10.2307/2446002
Luckow MA, White PJ, Bruneau A (2000) Relationships among basal genera of mimosoid leg-
umes. In: Herendeen PS, Bruneau A (Eds) Advances in Legume Systematics, part 9. Royal
Botanic Gardens, Kew, United Kingdom, 165–180.
Luckow MA, Miller JT, Murphy DJ, Livshultz T (2003) A phylogenetic analysis of the Mi-
mosoideae (Leguminosae) based on chloroplast DNA sequence data. In: Klitgaard BB,
Bruneau A (Eds) Advances in Legume Systematics, part 10, Higher Level Systematics.
Royal Botanic Gardens, Kew, United Kingdom, 197–220.
Luckow MA, Fortunato RH, Sede S, Livshultz T (2005) e phylogenetic anities of two mys-
terious monotypic mimosoids from southern South America. Systematic Botany 30(3):
585–602. https://doi.org/10.1600/0363644054782206
Manzanilla V, Bruneau A (2012) Phylogeny reconstruction in the Caesalpinieae grade (Legumi-
nosae) based on duplicated copies of the sucrose synthase gene and plastid markers. Molecular
Phylogenetics and Evolution 65(1): 149–162. https://doi.org/10.1016/j.ympev.2012.05.035
Marazzi B, Sanderson MJ (2010) Large-scale patterns of diversication in the widespread
legume genus Senna and the evolutionary role of extraoral nectaries. Evolution 64(12):
3570–3592. https://doi.org/10.1111/j.1558-5646.2010.01086.x
Marazzi B, Gonzalez AM, Delgado-Salinas A, Luckow MA, Ringelberg JJ, Hughes CE (2019)
Extraoral nectaries in Leguminosae: Phylogenetic distribution, morphological diversity and
evolution. Australian Systematic Botany 32: 409–458. https://doi.org/10.1071/SB19012
Miller JT, Bayer RJ (2000) Molecular systematics of the tribe Acaciae (Leguminosae: Mi-
mosoideae). In: Herendeen PS, Bruneau A (Eds) Advances in Legume Systematics 9. Royal
Botanic Gardens, Kew, United Kingdom, 181–200.
Miller JT, Bayer RJ (2001) Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based
on the chloroplast matK coding sequence and anking trnK intron spacer regions. Austral-
ian Journal of Botany 88(4): 697–705. https://doi.org/10.2307/2657071
Miller JT, Bayer RJ (2003) Molecular phylogenetics of Acacia subgenera Acacia and Aculeif-
erum (Fabaceae: Mimosoideae), based on the chloroplast matK coding sequence and ank-
ing trnK intron spacer regions. Australian Systematic Botany 16(1): 27–33. https://doi.
org/10.1071/SB01035
Miller JT, Seigler D (2012) Evolutionary and taxonomic relationships of Acacia s.l. (Legu-
minosae: Mimosoideae). Australian Systematic Botany 25(3): 217–224. https://doi.
org/10.1071/SB11042
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
44
Miller JT, Andrew R, Bayer RJ (2003) Molecular phylogenetics of the Australian acacias of
subg. Phyllodineae (Fabaceae: Mimosoideae) based on the trnK intron. Australian Journal
of Botany 51(2): 167–177. https://doi.org/10.1071/BT01099
Miller JT, Murphy DJ, Ho SYW, Cantrill DJ, Seigler D (2013) Comparative dating of Acacia:
Combining fossils and multiple phylogenies to infer ages of clades with poor fossil records.
Australian Journal of Botany 61(6): 436–445. https://doi.org/10.1071/BT13149
Miller JT, Terra V, Riggins C, Ebinger JE, Seigler DS (2017) Molecular phylogenetics of Para-
senegalia and Pseudosenegalia (Fabaceae: Mimosoideae). Systematic Botany 42(3): 465–
469. https://doi.org/10.1600/036364417X696140
Mishler BD, Knerr N, González-Orozco CE, ornhill AD, Laan SW, Miller JT (2014)
Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia.
Nature Communications 5(1): e4473. https://doi.org/10.1038/ncomms5473
Moore AJ, De Vos JM, Hancock LP, Goolsby E, Edwards EJ (2018) Targeted enrichment
of large gene families for phylogenetic inference: Phylogeny and molecular evolution of
photosynthesis genes in the Portullugo clade (Caryophyllales). Systematic Biology 67(3):
367–383. https://doi.org/10.1093/sysbio/syx078
Muñoz-Rodríguez P, Carruthers T, Wood JRI, Williams BRM, Weitemier K, Kronmiller B,
Goodwin Z, Sumadijaya A, Anglin NL, Filer D, Harris D, Rausher MD, Kelly S, Liston A,
Scotland RW (2019) A taxonomic monograph of Ipomoea integrated across phylogenetic
scales. Nature Plants 5(11): 1136–1144. https://doi.org/10.1038/s41477-019-0535-4
Murphy DJ, Miller JT, Bayer RJ, Ladiges PY (2003) Molecular phylogeny of Acacia subge-
nus Phyllodineae (Mimosoideae: Leguminosae) based on DNA sequences of the inter-
nal transcribed spacer region. Australian Systematic Botany 16(1): 19–26. https://doi.
org/10.1071/SB01042
Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG,
Stone GN, Kidner CA (2015) Using targeted enrichment of nuclear genes to increase phy-
logenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).
Frontiers in Plant Science 6. https://doi.org/10.3389/fpls.2015.00710
Nielsen I (1981) Tribe 5. Ingeae. In: Polhill RM, Raven PH (Eds) Advances in Legume System-
atics Part 1. Royal Botanic Gardens, Kew, United Kingdom, 173–190.
Nielsen I (1992) Flora Malesiana - series I: Spermatophyta. Volume 11, part 1: Mimosaceae
(Leguminosae - Mimosoideae). Rijksherbarium / Hortus Botanicus, Leiden University,
Leiden, the Netherlands.
O’Donnell S, Ringelberg JJ, Lewis GP (2022) Re-circumscription of the mimosoid genus En-
tada including new combinations for all species of the phylogenetically nested Elephantor-
rhiza (Leguminosae, Caesalpinioideae, mimosoid clade). In: Hughes CE, de Queiroz LP,
Lewis GP (Eds) Advances in Legume Systematics 14. Classication of Caesalpinioideae
Part 1: New generic delimitations. PhytoKeys 205: 99–146. https://doi.org/10.3897/phy-
tokeys.205.76790
Orthia LA, Cook LG, Crisp MD (2005) Generic delimitation and phylogenetic uncertainty:
An example from a group that has undergone an explosive radiation. Australian Systematic
Botany 18(1): 41–47. https://doi.org/10.1071/SB04016
Paul SR (1979) e genus Calliandra (Mimosaceae) in the Indian subcontinent. Feddes Reper-
torium 90(3): 155–164. https://doi.org/10.1002/fedr.19790900303
Phylogenomics of Caesalpinioideae: generic re-delimitation 45
Pease JB, Brown JW, Walker JF, Hinchli CE, Smith SA (2018) Quartet sampling distinguishes
lack of support from conicting support in the green plant tree of life. American Journal of
Botany 105(3): 385–403. https://doi.org/10.1002/ajb2.1016
Pfeil BE, Crisp MD (2005) What to do with Hibiscus? A proposed nomenclatural resolution
for a large and well known genus of Malvaceae and comments on paraphyly. Australian
Systematic Botany 18(1): 49–60. https://doi.org/10.1071/SB04024
Phillipson PB, Lewis GP, Andriambololonera S, Rakotonirina N, ulin M, Wilding N (2022)
Leguminosae (Fabaceae). In: Goodman SM (Ed.) e New Natural History of Madagas-
car. Princeton University Press, Princeton, New Jersey, United States of America.
Polhill RM (1994) Classication of the Leguminosae and complete synopsis of legume genera.
In: Bisby FA, Buckingham J, Harborne JB (Eds) Phytochemical Dictionary of the Legumi-
nosae. Chapman and Hall, Cambridge, United Kingdom, xxxv–lvii.
Polhill RM, Vidal JE (1981) Caesalpinieae. In: Polhill RM, Raven PH (Eds) Advances in Leg-
ume Systematics Part 1. Royal Botanic Gardens, Kew, United Kingdom, 81–95.
R Core Team (2022) R: A language and environment for statistical computing. R Foundation
for Statistical Computing, Vienna. https://www.R-project.org/
Revell LJ (2012) phytools: An R package for phylogenetic comparative biology (and other
things). Methods in Ecology and Evolution 3(2): 217–223. https://doi.org/10.1111/
j.2041-210X.2011.00169.x
Ribeiro PG, Luckow M, Lewis GP, Simon MF, Cardoso D, de Souza ÉR, Silva APC, Jesus
MC, dos Santos FAR, Azevedo V, de Queiroz LP (2018) Lachesiodendron, a new mono-
specic genus segregated from Piptadenia (Leguminosae: Caesalpinioideae: Mimosoid
clade): Evidence from morphology and molecules. Taxon 67(1): 37–54. https://doi.
org/10.12705/671.3
Ringelberg JJ, Zimmermann NE, Weeks A, Lavin M, Hughes CE (2020) Biomes as evolu-
tionary arenas: Convergence and conservatism in the trans-continental succulent biome.
Global Ecology and Biogeography 29(7): 1100–1113. https://doi.org/10.1111/geb.13089
Ringelberg JJ, Koenen EJM, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP,
Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF,
Jordão LSB, Morales M, Bailey CD, Nageswara-Rao M, Loiseau O, Pennington RT,
Dexter KG, Zimmermann NE, Hughes CE (2022) Precipitation is the main axis of
tropical phylogenetic turnover across space and time. https://www.biorxiv.org/con-
tent/10.1101/2022.05.27.493777
Robinson J, Harris SA (2000) A plastid DNA phylogeny of the genus Acacia Miller (Acacieae,
Leguminoseae). Botanical Journal of the Linnean Society 132(3): 195–222. https://doi.
org/10.1111/j.1095-8339.2000.tb01527.x
Rokas A, Carroll SB (2006) Bushes in the tree of life. PLoS Biology 4(11): 1899–1904. https://
doi.org/10.1371/journal.pbio.0040352
Rose JP, Toledo CAP, Lemmon EM, Lemmon AR, Sytsma KJ (2021) Out of sight, out of mind:
widespread nuclear and plastid-nuclear discordance in the owering plant genus Polemoni-
um (Polemoniaceae) suggests widespread historical gene ow despite limited nuclear signal.
Systematic Biology 70(1): 162–180. https://doi.org/10.1093/sysbio/syaa049
Salichos L, Rokas A (2013) Inferring ancient divergences requires genes with strong phyloge-
netic signals. Nature 497(7449): 327–331. https://doi.org/10.1038/nature12130
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
46
Sandwith NY (1932) Contributions to the ora of tropical America. XIV. Bulletin of Miscellaneous
Information (Royal Botanic Gardens, Kew) 8: 395–406. https://doi.org/10.2307/4113483
Sauter B (2019) Evolutionary diversication of Mimosa and the Piptadenia Group – An exam-
ple of phylogenetic biome conservatism. Unpublished MSc thesis, University of Zürich.
Sayyari E, Mirarab S (2018) Testing for polytomies in phylogenetic species trees using quartet
frequencies. Genes 9(3): e132. https://doi.org/10.3390/genes9030132
Scalon VR (2007) Revisão Taxonômica do gênero Stryphnodendron Mart. (Leguminosae-Mi-
mosoideae). PhD thesis, University of São Paulo.
Schrire BD, Lavin M, Lewis GP (2005) Global distribution patterns of the Leguminosae: In-
sights from recent phylogenies. Biologiske Skrifter 55: 375–422.
Scotland RW, Olmstead RG, Bennett JR (2003) Phylogeny reconstruction: e role of mor-
phology. Systematic Biology 52(4): 539–548. https://doi.org/10.1080/10635150309309
Seigler DS, Ebinger JE, Miller JT (2006a) Mariosousa, a new segregate genus from Acacia s.l. (Fa-
baceae, Mimosoideae) from Central and North America. Novon 16: 413–420. https://doi.
org/10.3417/1055-3177(2006)16[413:mansgf]2.0.co;2
Seigler DS, Ebinger JE, Miller JT (2006b) e genus Senegalia (Fabaceae: Mimosoideae) from
the New World. Phytologia 88: 38–93. https://doi.org/10.5962/bhl.part.17845
Seigler DS, Ebinger JE, Riggins CW, Terra V, Miller JT (2017) Parasenegalia and Pseudosen-
egalia (Fabaceae): New genera of the Mimosoideae. Novon 25: 180–205. https://doi.
org/10.3417/2015050
Shen X-X, Hittinger CT, Rokas A (2017) Contentious relationships in phylogenomic studies
can be driven by a handful of genes. Nature Ecology & Evolution 1: e0126. https://doi.
org/10.1038/s41559-017-0126
Simon MF, Grether R, de Queiroz LP, Särkinen TE, Dutra VF, Hughes CE (2011) e evo-
lutionary history of Mimosa (Leguminosae): Toward a phylogeny of the sensitive plants.
American Journal of Botany 98(7): 1201–1221. https://doi.org/10.3732/ajb.1000520
Simon MF, Pastore JFB, Souza AF, Borges LM, Scalon VR, Ribeiro PG, Santos-Silva J, Souza
VC, Queiroz LP (2016) Molecular phylogeny of Stryphnodendron (Mimosoideae, Legumi-
nosae) and generic delimitations in the Piptadenia group. International Journal of Plant
Sciences 177(1): 44–59. https://doi.org/10.1086/684077
Sinou C, Cardinal-McTeague W, Bruneau A (2020) Testing generic limits in Cercidoideae
(Leguminosae): Insights from plastid and duplicated nuclear gene sequences. Taxon 69(1):
67–86. https://doi.org/10.1002/tax.12207
Smith SA, Moore MJ, Brown JW, Yang Y (2015) Analysis of phylogenomic datasets reveals
conict, concordance, and gene duplications with examples from animals and plants.
BMC Evolutionary Biology 15(1): e150. https://doi.org/10.1186/s12862-015-0423-0
Soares MVB, Guerra E, Morim MP, Iganci JRV (2021) Reinstatement and recircumscription
of Jupunba and Punjuba (Fabaceae) based on phylogenetic evidence. Botanical Journal
of the Linnean Society 196(4): 456–479. https://doi.org/10.1093/botlinnean/boab007
Soares M, Koenen E, Iganci J, Morim M (2022) A new generic circumscription of Hydrochorea
(Leguminosae, Caesalpinioideae, mimosoid clade) with an amphi-Atlantic distribution. In:
Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Clas-
sication of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 401–438.
https://doi.org/10.3897/phytokeys.205.82775
Phylogenomics of Caesalpinioideae: generic re-delimitation 47
Sprent JI, Ardley J, James EK (2017) Biogeography of nodulated legumes and their nitrogen-
xing symbionts. New Phytologist 215(1): 40–56. https://doi.org/10.1111/nph.14474
Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis
of large phylogenies. Bioinformatics (Oxford, England) 30(9): 1312–1313. https://doi.
org/10.1093/bioinformatics/btu033
Tamayo-Cen I, Torke BM, López Contreras JE, Carnevali Fernández-Concha G, Ramírez Mo-
rillo I, Can Itza LL, Duno de Stefano R (2022) Revisiting the phylogeny and taxonomy of
the Pithecellobium clade (Leguminosae, Caesalpinioideae) with new generic circumscrip-
tions. In: Hughes CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics
14. Classication of Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205:
279–298. https://doi.org/10.3897/phytokeys.205.82728
Terra V, Garcia FCP, Queiroz LP de (2017) Phylogenetic relationships in Senegalia (Legumi-
nosae-Mimosoideae) emphasizing the South American lineages. Systematic Botany 42(3):
458–464. https://doi.org/10.1600/036364417X696122
Terra V, Ringelberg JJ, Maslin B, Koenen EJM, Ebinger J, Seigler D, Hughes CE (2022) Di-
lemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade):
how to reconcile phylogenomic evidence with morphology and taxonomy? In: Hughes
CE, de Queiroz LP, Lewis GP (Eds) Advances in Legume Systematics 14. Classication of
Caesalpinioideae Part 1: New generic delimitations. PhytoKeys 205: 261–278. https://doi.
org/10.3897/phytokeys.205.79378
ielsch A, Knell A, Mohammadyari A, Petrusek A, Schwenk K (2017) Divergent clades or
cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evolution-
ary Biology 17(1): 1–9. https://doi.org/10.1186/s12862-017-1070-4
Tulasne ML-R (1844) Legumineuses arborescentes de L’Amerique du Sud - Dimorphandra.
Archives du Muséum d’Histoire Naturelle Paris 4: 182–198.
Turland NJ, Wiersema JH, Barrie FR, Greuter W, Hawksworth DL, Herendeen PS, Knapp S,
Kusber W-H, Li D-Z, Marhold K, May TW, McNeill J, Monro AM, Price MJ, Smith GF
[Eds] (2018) International Code of Nomenclature for algae, fungi, and plants (Shenzhen
Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July
2017. Regnum Vegetabile 159. Koeltz Botanical Books, Glashütten, Germany.
van Steenis CGGJ (1975) A review of the genus Sympetalandra Stapf and its position in Caesal-
pinioideae. Blumea 22: 159–167.
Villiers J-F (1984) Le genre Calpocalyx (Legiminosae, Mimosoideae) en Afrique. Adansonia 3:
297–311. https://doi.org/10.1017/CBO9781107415324.004
Villiers J-F (1994) Alantsilodendron Villiers, genre nouveau de Leguminosae-Mimosoideae de
Madagascar. Bulletin du Muséum National d’Histoire Naturelle Paris, 4e sér., Section B.
Adansonia 16: 65–70.
Wang N, Yang Y, Moore MJ, Brockington SF, Walker JF, Brown JW, Liang B, Feng T, Edwards
C, Mikenas J, Olivieri J, Hutchison V, Timoneda A, Stoughton T, Puente R, Majure LC,
Eggli U, Smith SA (2019) Evolution of Portulacineae marked by gene tree conict and
gene family expansion associated with adaptation to harsh environments. Molecular Biol-
ogy and Evolution 36(1): 112–126. https://doi.org/10.1093/molbev/msy200
Wight R, Walker-Arnott GA (1834) Prodromus Florae Peninsulae Indiae Orientalis, volume 1.
Parbury, Allen, & Co, London, United Kingdom.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
48
Willdenow CL (1805) Species Plantarum. Editio quarta. Tomus 4, pars 1. G.C. Nauk, Bero-
lini, 629 pp.
Yang Y, Smith SA (2014) Orthology inference in nonmodel organisms using transcriptomes and
low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Mo-
lecular Biology and Evolution 31(11): 3081–3092. https://doi.org/10.1093/molbev/msu245
Yang L, Su D, Chang X, Foster CSP, Sun L, Huang C-H, Zhou X, Zeng L, Ma H, Zhong B (2020)
Phylogenomic insights into deep phylogeny of Angiosperms based on broad nuclear gene sam-
pling. Plant Communications 1(2): e100027. https://doi.org/10.1016/j.xplc.2020.100027
Zhang C, Rabiee M, Sayyari E, Mirarab S (2018) ASTRAL-III: Polynomial time species tree
reconstruction from partially resolved gene trees. BMC Bioinformatics 19(S6): 15–30.
https://doi.org/10.1186/s12859-018-2129-y
Zhang R, Wang YH, Jin JJ, Stull GW, Bruneau A, Cardoso D, De Queiroz LP, Moore MJ,
Zhang SD, Chen SY, Wang J, Li DZ, Yi TS (2020) Exploration of plastid phylogenomic
conict yields new insights into the deep relationships of Leguminosae. Systematic Biology
69(4): 613–622. https://doi.org/10.1093/sysbio/syaa013
Zhao Y, Zhang R, Jiang K, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi T-S, Huang C-H,
Ma H (2021) Nuclear phylotranscriptomics/phylogenomics support numerous polyploidi-
zation events and hypotheses for the evolution of rhizobial nitrogen-xing symbiosis in
Fabaceae. Molecular Plant 14(5): 748–773. https://doi.org/10.1016/j.molp.2021.02.006
Zhou X, Lutteropp S, Czech L, Stamatakis A, Von Looz M, Rokas A (2020) Quartet-based
computations of internode certainty provide robust measures of phylogenetic incongru-
ence. Systematic Biology 69(2): 308–324. https://doi.org/10.1093/sysbio/syz058
Appendix 1
Generic non-monophyly in Caesalpinioideae – towards a new generic system for
the subfamily
Caesalpinia
Divergent circumscriptions of the genus Caesalpinia L. were largely resolved by Gagnon
et al. (2016) who reduced Caesalpinia to ca. nine species and established a new generic
system for the Caesalpinia Group as a whole, with 26 genera plus their ‘Ticanto clade’
(Caesalpinia crista L. and allies) as a putative 27th genus. is 27th genus accounts for the
non-monophyly of Caesalpinia in our analysis (Fig. 2) with Caesalpinia crista representing
the Ticanto clade that is re-instated as a genus in this Special Issue by Clark et al. (2022).
Dimorphandra
In line with previous studies (Luckow et al. 2005; LPWG 2017), Dimorphandra Schott
is non-monophyletic in the nuclear phylogeny (Fig. 3), but robustly supported (99%
bootstrap support (BS)) as monophyletic in the plastid tree (Suppl. material 3), in-
dicating cytonuclear discordance. is implies either splitting Dimorphandra into
two genera or sinking Mora Schomb. ex Benth., Stachyothyrsus Harms and Burkea
Phylogenomics of Caesalpinioideae: generic re-delimitation 49
Benth. into Dimorphandra (which predates these other three genera). Evidence sug-
gests splitting Dimorphandra as the preferred option. First, the three Dimorphandra
species sampled here represent the three morphologically delimited subgenera (da Silva
1986) with representatives of these subgenera intermingled with other genera render-
ing Dimorphandra polyphyletic in the legume-wide matK phylogeny (LPWG 2017)
and Burkea and Mora are not closely related to Dimorphandra in the plastid phylogeny
(Suppl. material 3; Stachyothyrsus is not included in the plastid analysis). Second, while
Mora has been included in Dimorphandra based on morphological similarities (Sand-
with 1932; van Steenis 1975), the two genera dier in oral, seed and pod morphol-
ogy and have generally been treated as distinct (Sandwith 1932; van Steenis 1975; da
Silva 1986). African Stachyothyrsus and Burkea are morphologically (van Steenis 1975)
and geographically distinct from South American Dimorphandra and Mora. All of this
suggests that Dimorphandra will need to be split into two genera or potentially three,
although the robustly supported sister group relationship between D. davisii and D.
macrostachya (internode certainty 0.77, subtended by a long branch) would perhaps fa-
vour two genera, rather than three. Additional taxon sampling, to test the monophyly
of the three subgenera, is required before taxonomic re-arrangements can be made. If
the genus is to be split, the name Dimorphandra would remain attached to subgenus
Dimorphandra, here represented by D. gardneriana Tul. Dimorphandra exaltata Schott
is the type species of the genus. e names of the other two subgenera, Phaneropsia Tu -
lasne and Pocillum Tulasne, would be available for the remaining species. Both names
originate from the same publication (Tulasne 1844), but since Pocillum also refers to a
genus of fungi (Kirk et al. 2008), Phaneropsia would be the more suitable generic name
for the species not in Dimorphandra s.s. However, as taxon names have no priority at
dierent rank (Turland et al. 2018), a new generic name may also be proposed.
Xylia and Calpocalyx
e non-monophyly of Xylia with Calpocalyx nested within it was documented using
matK sequences (LPWG 2017) and is conrmed here (Fig. 4). is does not come as
a great surprise, as these genera have always been considered closely related (Villiers
1984; Lewis et al. 2005). ey have overlapping geographical and ecological distribu-
tions mainly in the tropical rainforests of central and western Africa (although Xylia
has a wider distribution in Africa, Madagascar and Asia). e two genera also share a
suite of morphological characteristics (Villiers 1984; Luckow et al. 2003), including
robust woody sickle-shaped explosively dehiscent fruits (Fig. 13), a chromosome count
of 2n = 12 (Goldblatt and Davidse 1977) and pollen grains in small-sized polyads
(Jumah 1991). Since the name Xylia (Bentham 1841) predates Calpocalyx (Engler and
Prantl 1897) and given the morphological and ecological similarities of the two genera,
the most straightforward solution to the non-monophyly presented here would be the
transfer of the species of Calpocalyx to Xylia. However, this apparently straightforward
incorporation of Calpocalyx into Xylia is complicated by the name Esclerona Raf., an
apparently valid name predating Xylia, raising the possibility of proposing conserva-
tion of the name Xylia prior to merging these two genera.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
50
Entada and Elephantorrhiza
A close relationship between Entada Adans. and Elephantorrhiza Benth. has long been
suggested in all molecular phylogenies that sampled these genera (e.g. Luckow et al.
2003; Koenen et al. 2020b). With denser sampling of species, it has become clear that
Elephantorrhiza is nested within Entada (LPWG 2017), a result that is conrmed here
(Fig. 4) and which provides the basis for re-circumscription of Entada to include El-
ephantorrhiza by O’Donnell et al. (2022) in this Special Issue.
Prosopis
One of the most striking and robustly supported examples of generic non-monophyly
in our analyses is Prosopis s.l. whose species are placed in four separate lineages (Figs
4 and 5). e nodes supporting this non-monophyly are some of the most robustly
supported across the Caesalpinioideae phylogeny as a whole (Fig. 5). is shows that
P. africana is not closely related to the rest of Prosopis s.l., but is placed in a grade with
other monospecic or species-poor genera subtending the core mimosoid clade (Fig.
4), conrming results from earlier studies (Catalano et al. 2008; LPWG 2017; Koenen
et al. 2020b). e rest of Old World Prosopis (three species) is sister to the Indo-Nepa-
lese genus Indopiptadenia and New World Prosopis has the Namibian – S. African Xero-
cladia nested within it (Fig. 5). A new generic classication of Prosopis s.l., accounting
for this non-monophyly, is presented in this Special Issue by Hughes et al. (2022a).
Desmanthus
e non-monophyly of Desmanthus with the monospecic Hawaiian endemic Kanaloa
Lorence & K.R. Wood nested within it (Fig. 5) mirrors earlier phylogenies (Hughes et
al. 2003; Luckow et al. 2003, 2005) and is in line with the morphological distinctiveness
of Desmanthus balsensis J.L. Contreras from the remaining species of Desmanthus (Con-
treras Jiménez 1986; Luckow 1993). A new monospecic segregate genus to account for
this non-monophyly is proposed in this Special Issue by Hughes et al. (2022b).
Dichrostachys, Gagnebina and Alantsilodendron
Dichrostachys (DC.) Wight & Arn. and Alantsilodendron Villiers are both recovered as
non-monophyletic in our sparsely sampled analysis (Fig. 5), raising questions about the
monophyly of Gagnebina Neck. ex DC., here represented by just a single species. e
Malagasy members of these three genera (all species in our phylogeny, except D. cinerea
R. Vig.) cluster together in a clade characterised by very short branches and extensive
gene tree conict (Fig. 5) suggestive of an early burst model of diversication typical of
a rapid radiation on Madagascar (Aebli 2015). Previous molecular phylogenetic studies
have also found at least some of these genera to be non-monophyletic (Hughes et al.
2003; Luckow et al. 2003, 2005; Aebli 2015) and some species have been transferred
between genera based on morphology (Lewis and Guinet 1986). Each of these genera
contains several other species from Madagascar not sampled here. While a parsimoni-
ous solution could be to merge the three genera into Gagnebina (de Candolle 1825) (a
name predating Dichrostachys (Wight and Walker-Arnott 1834) and Alantsilodendron
Phylogenomics of Caesalpinioideae: generic re-delimitation 51
(Villiers 1994)), such a move would result in a highly variable genus, with no consistent
morphological character to distinguish it. A forthcoming monograph (Luckow, unpub-
lished data) will resolve the non-monophyly of these genera by transferring two species
of Dichrostachys to Alantsilodendron and seven to a new genus (Phillipson et al. 2022).
Additional sampling of non-Malagasy species of Dichrostachys would also be important,
especially Australian D. spicata, as it has been placed as sister to the combined Dichros-
tachys / Gagnebina / Alantsilodendron + Calliandropsis nervosa (Britton & Rose) H.M.
Hern. & Guinet clade in several studies (Hughes et al. 2003; Luckow et al. 2003, 2005;
Aebli 2015). e African species D. dehiscens Balf. f. and D. kirkii Benth. also need to be
sampled as they share a dehiscent fruit type with members of the new Madagascan genus.
Stryphnodendron and Pseudopiptadenia
Our analyses support the monophyly of the Stryphnodendron clade sensu Koenen et al.
(2020b) comprising the genera Parapiptadenia Brenan, Pityrocarpa (Benth. & Hook.f.)
Britton & Rose, Pseudopiptadenia Rauschert and Stryphnodendron Mart. (Fig. 6) and
presumably Microlobius C. Presl., which, although not sampled here, has been shown
to be nested within or sister to Stryphnodendron (Ribeiro et al. 2018; Simon et al. 2016;
see also Lima et al. 2022). Of these genera, only Parapiptadenia is monophyletic in
our analyses, although Pityrocarpa is here only represented by a single taxon (Fig. 6).
Stryphnodendron is non-monophyletic as S. duckeanum Occhioni does not group with
the rest of the genus (Fig. 6), in line with ower, fruit and branching characteristics that
suggested transfer of S. duckeanum to another genus (Scalon 2007) and with previous
molecular phylogenies showing S. duckeanum separated from the rest of Stryphnoden-
dron (Jobson and Luckow 2007; Simon et al. 2016; Ribeiro et al. 2018; Sauter 2019).
Similarly, Pseudopiptadenia is also non-monophyletic with P. schumanniana placed as
sister to the single sampled species of Pityrocarpa, rather than forming a clade with
Pseudopiptadenia contorta (DC.) G.P. Lewis & M.P. Lima and P. psilostachya (DC.) G.P.
Lewis & M.P. Lima (Fig. 6). Several previous molecular phylogenies also found Pseu-
dopiptadenia to be non-monophyletic – however, those studies did not include P. schu-
manniana and found P. brenanii G.P. Lewis & M.P. Lima (not sampled here) to be the
outlier instead (Simon et al. 2016; Ribeiro et al. 2018). e sparsely sampled backbone
phylogeny of the Stryphnodendron clade presented here provides the foundations for
more densely sampled analyses and re-delimitation of both Stryphnodendron (Lima et
al. 2022) and Pseudopiptadenia / Pityrocarpa (Borges et al. 2022) in this Special Issue.
e remaining genera in the Stryphnodendron and Mimosa clades are all monophyletic (Fig.
6), conrming previous phylogenetic studies and taxonomic rearrangements, including seg-
regation of Lachesiodendron P.G. Ribeiro, L.P. Queiroz & Luckow from Piptadenia (Ribeiro
et al. 2018), as well as placement of amphi-Atlantic Adenopodia C. Presl as sister to Mimosa
and the sister group relationships amongst the main clades of Mimosa (Simon et al. 2011).
Senegalia and allied genera
e striking cytonuclear discordance whereby Senegalia Raf. appears as non-mono-
phyletic in the analyses of nuclear gene sequences, but as monophyletic in the analyses
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
52
of plastomes, was rst revealed by Koenen et al. (2020b), a result conrmed here by
sampling more species of Senegalia, plus the closely related Mariosousa, Parasenegalia
and Pseudosenegalia (Fig. 7). In the nuclear gene analyses, the two clades of Senegalia
plus these three other genera and the incompletely known Albizia leonardii Britton &
Rose ex Barneby & J.W. Grimes form a paraphyletic grade with very short and poorly
supported or unsupported internal branches (Fig. 7). e complex and intriguing is-
sues these features raise for delimitation of Senegalia are explored by Terra et al. (2022),
who conclude that sequencing of more species is required.
Calliandra
Following reduction of Bentham’s (1875) broad trans-continental circumscription of
Calliandra Benth. to just the New World species by Barneby (1998), ve genera have
been segregated to account for the majority of the Old World species. Now just a
handful of Old World species remain to be resolved, including the Asian Calliandra sp.
nov. (Poilane 9150), that, as expected, does not group together with the New World
Calliandra s.s., but is instead sister to the Indian monospecic genus Sanjappa É.R.
Souza & M.V. Krishnaraj in the Zapoteca clade (Fig. 7). Bentham (1875) included
four Asian species in Calliandra (de Souza et al. 2013), which share the apically dehis-
cent pods of Calliandra (Fig. 13a–f), but in other respects present anomalies, especially
in the conguration of their polyads. e identities of these Asian Calliandra species
have long been considered ambiguous (Barneby 1998). Two of these Asian species have
been assigned to dierent genera (C. cynometroides Bedd. to Sanjappa (de Souza et al.
2016) and C. geminata (Wight & Arn.) Benth. to ailentadopsis Kosterm. (Lewis
and Schrire 2003)), while the generic placement of the remaining species, C. umbrosa
(Wall.) Benth., remains unknown. e fourth species, C. grithii Baker ex Benth.,
is now considered a subspecies of C. umbrosa (Paul 1979). Calliandra umbrosa has
never been included in a molecular phylogenetic analysis (de Souza et al. 2013, 2016)
and, unfortunately, sequencing of C. umbrosa was unsuccessful in this study. However,
polyad, leaf, corolla and pod morphology, plus the presence of facultatively spinescent
stipules, distinguish C. umbrosa from other genera, suggesting that it should poten-
tially be assigned to a new genus (de Souza et al. 2013, 2016). Until DNA sequences
of C. umbrosa can be obtained to ascertain its relationship to Calliandra sp. nov., this
residual non-monophyly of the genus Calliandra cannot be resolved.
Pithecellobium and allies
While the Pithecellobium alliance is the only one of the informal alliances of Barneby
and Grimes (1996) whose monophyly has withstood the test of phylogenomic analysis
(Koenen et al. 2020b), other than Pithecellobium Mart. itself, our sparsely sampled
phylogeny of this clade suggests that the monophyly of the four other genera placed
in the Pithecellobium clade (Painteria Britton & Rose, Havardia Small, Ebenopsis
Britton & Rose and Sphinga Barneby & J.W. Grimes) is doubtful and needs to be
further tested with more complete taxon sampling (Fig. 7). Even with our limited
taxon sampling, Painteria and Havardia are clearly non-monophyletic (Fig. 7), raising
Phylogenomics of Caesalpinioideae: generic re-delimitation 53
signicant doubts about the taxonomic status of Ebenopsis and Sphinga, which are
both represented by only one species in our trees. Painteria is especially poorly distin-
guished from Havardia; Sphinga was originally described in Havardia and previous
studies (Nielsen 1981; Polhill 1994) placed all four genera in a more broadly dened
Havardia (Brown 2008). Such a solution might, therefore, seem sensible, but together
they form a paraphyletic grade in our phylogenies (Fig. 7), suggesting that unless all
four genera were to be sunk back into Pithecellobium (from which they were segregated
(Barneby and Grimes 1996)), these four genera require at least three names, as they
are divided over three (poorly-supported) lineages: one comprising Spinga acatlensis
(Benth.) Barneby & J.W. Grimes and Havardia campylacantha (L. Rico & M. Sousa)
Barneby & J.W. Grimes, one Painteria leptophylla (DC.) Britton & Rose, Pa. elachis-
tophylla (A. Gray ex S. Watson) Britton & Rose and Ebenopsis connis (Standl.) Brit-
ton & Rose and one H. pallens (Benth.) Britton & Rose, which is the type species of
Havardia and sister to Pithecellobium. Clearly, taxon sampling in our phylogeny is too
limited to draw rm taxonomic conclusions. A new phylogeny of the Pithecellobium
clade, presented here in this Special Issue, is used as the basis for erecting two new
genera to account for these generic non-monophyly issues (Tamayo-Cen et al. 2022).
is new phylogeny, based on a small set of DNA sequence loci, but with denser taxon
sampling than that encompassed here, is not fully congruent with the phylogenomic
backbone presented in Fig. 7.
e Archidendron clade
e genera and lineages of the large Archidendron clade comprising Acacia Mill., Archi-
dendron F. Muell. and six smaller genera (Fig. 8; Koenen et al. 2020b), together make
up over one third of all mimosoid species and are restricted to Australasia. Relation-
ships across the backbone of this clade are complex and generally poorly resolved with
very short branches and high levels of gene tree conict and lack of phylogenetic signal
across a signicant fraction of genes (Fig. 8), such that the topologies across dierent
analytical approaches can dier. is suggests that some nodes across this backbone
should better be viewed as putative polytomies. ree genera in this clade, Wallaceoden-
dron Koord., Pararchidendron I.C. Nielsen and Paraserianthes I.C. Nielsen, are mono-
specic. Falcataria (I.C. Nielsen) Barneby & J.W. Grimes comprises three species but
is represented by only one taxon in our phylogeny, so no conclusion can, therefore, be
made about its monophyly, although our results support the segregation of this genus
from Paraserianthes (Barneby and Grimes 1996; Brown et al. 2011). ree of the four
remaining genera are monophyletic: Acacia, Archidendron and Serianthes Benth. (con-
rming the results of Demeulenaere et al. (2022) in this Special Issue). However, the
monophyly of Archidendron remains doubtful as it is supported by few gene trees and
opposed by many (Fig. 8) and the genus is not monophyletic in the plastid tree (Suppl.
material 3). is is very much in line with previous ndings of a non-monophyletic Ar-
chidendron (Brown et al. 2008, 2011; Iganci et al. 2016; LPWG 2017). e likely non-
monophyly of Archidendron is explored in more detail in this Special Issue by Brown
et al. (2022). It is notable that the two well-supported Archidendron subclades found
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
54
here are replicated by Brown et al. (2022), where their morphological and geographical
identities are discussed in detail. Finally, the non-monophyly of Archidendropsis I.C.
Nielsen, documented and addressed in this Special Issue by Brown et al. (2022), is
conrmed by the much larger phylogenomic dataset analysed here (Fig. 8).
Our results weakly support Paraserianthes lophantha as sister to Acacia (Fig. 8), in
line with earlier ndings (Brown et al. 2008, 2011; Koenen et al. 2020b) and shared
morphological similarities including hard seeds that are stimulated to germinate by
re (Brown et al. 2011), minute anthers and numerous stamens (Barneby and Grimes
1996). As P. lophantha contains two geographically disjunct subspecies, P. lophantha
subsp. montana (Jungh.) I.C. Nielsen in Indonesia and P. lophantha subsp. lophantha
(the subspecies sequenced here) in southern Australia (Brown et al. 2011), sequencing
the missing subspecies would be worthwhile to check that the two cluster together
as sister to Acacia. However, it is important to note that this relationship is sensitive
to the type of dataset and phylogenetic method: the ASTRAL trees (Fig. 8) recover
P. lophantha as the sister of Acacia, whereas the nuclear RAxML phylogenies (Ringel-
berg et al. 2022) nd a sister relationship between Acacia and Archidendron plus Archi-
dendropsis xanthoxylon (C.T. White & W.D. Francis) I.C. Nielsen, the PhyloBayes gene
jack-kning phylogeny (Ringelberg et al. 2022) resolves the whole Archidendron clade
as one large polytomy lacking a clear sister lineage to Acacia and the plastid tree (Suppl.
material 3) recovers Archidendropsis xanthoxylon as sole sister of Acacia. Furthermore,
P. lophantha and several species of Archidendron are also identied as species often
changing positions across trees by RogueNarok (Aberer et al. 2013). e high levels of
intergenic conict, very short branches, extremely low bootstrap support values espe-
cially in the nucleotide RAxML phylogenies, lack of concordance and signal amongst
the gene trees and failure to reject a polytomy by ASTRAL (Fig. 8), all suggest that the
backbone of the Archidendron clade should perhaps best be viewed as one large poly-
tomy, as depicted in the PhyloBayes consensus tree (Ringelberg et al. 2022). However,
the number (eight in the PhyloBayes phylogeny) and precise identity of lineages aris-
ing from this tangle remain unclear and relationships amongst the genera of this clade
remain highly uncertain pending additional taxon sampling and detailed investigation
of the causes of gene tree conict and possible evidence for introgression.
Albizia
At the start of this study, the genus Albizia was dubbed the last pantropical so-called
‘dustbin’ genus pending resolution (Koenen et al. 2020b). Here, we show that Albizia
s.l. is rampantly non-monophyletic, most notably because the bulk of the Old and New
World species are placed in separate clades (Figs 9 and 10). is Old World – New World
split is remedied in this Special Issue by Aviles et al. (2022) who resurrect the genus Pseu-
dalbizzia Britton & Rose for the majority of the New World species placed in Barneby’s
Albizia section Arthrosamanea, with Albizia s.s. now restricted to just the Old World
species, which still includes ca. 90 spp. (Koenen et al., unpubl. data). Furthermore, the
disparate placements of several other species of Albizia across the phylogeny, viz: Albizia
carbonaria Britton (Fig. 8), the long-neglected African Albizia species previously often
Phylogenomics of Caesalpinioideae: generic re-delimitation 55
placed in Cathormion or Samanea (Benth.) Merr. (Figs 9 and 11) and Albizia leonardii
(Fig. 7), are all accounted for with new generic placements and nomenclatural combina-
tions (Koenen 2022b; Soares et al. 2022), one synonymisation (Terra et al. 2022) and a
new segregate genus (Koenen 2022a), all of them being published in this Special Issue.
Abarema, Hydrochorea and Balizia
e recent re-circumscription of Abarema Pittier to include just two species and transfer of
the remaining species to the re-instated Punjuba Britton & Rose and Jupunba Britton &
Rose (Guerra et al. 2016, 2019; Iganci et al. 2016; Soares et al. 2021), is broadly supported
here (Figs 9 and 11), except for the anomalous placement of Jupunba macradenia (Pittier)
M.V.B. Soares, M.P. Morim & Iganci which is sister to the Hydrochorea + Balizia clade (Fig.
9). is placement is unexpected and somewhat suspect considering J. macradenia is rmly
placed in Jupunba in Soares et al. (2021). As found by Iganci et al. (2016), Koenen et al.
(2020b) and Soares et al. (2021), Balizia is non-monophyletic with the genus Hydrochorea
plus two African species of Albizia nested within it (Fig. 9). Hydrochorea is re-circumscribed
to accommodate all these elements by Soares et al. (2022) in this Special Issue.
Leucochloron
Koenen et al. (2020b) showed that Leucochloron is polyphyletic and that result is conrmed
here, split between the Albizia and Inga clades (Figs 10 and 11). A new segregate genus to
account for this non-monophyly is proposed in this Special Issue by de Souza et al. (2022b).
Zygia, Macrosamanea and Inga
Alongside Archidendron, the large Neotropical, mainly rainforest genus Zygia remains
one of the least well-documented genera of mimosoids, with many species known from
incomplete material (Barneby and Grimes 1997). Previous work by Ferm et al. (2019)
showed that, while the bulk of genus Zygia is monophyletic, a handful of outlier species
have anities to other genera: Zygia ocumarensis (Pittier) Barneby & J.W. Grimes is sister
to Macrosamanea Britton & Rose ex Britton & Killip, Marmaroxylon magdalenae Kil-
lip ex. L. Rico (treated as a synonym of Z. ocumarensis by Barneby and Grimes (1997))
is nested in Jupunba and Z. inundata and Z. sabatieri are together sister to Inga. With
the exception of M. magdalenae, which is not included in this study, these placements
are conrmed here with phylogenomic data (Figs 11 and 12) and reect the morpho-
logical distinctiveness of these species from the rest of the genus (Barneby and Grimes
1997; Ferm et al. 2019) which prompted placements in their own separate monospe-
cic sections of Zygia (Barneby and Grimes 1997). New nomenclatural combinations to
deal with these outlier Zygia species are still pending. We suggest that Zygia ocumarensis
should best be transferred to Macrosamanea, as it shares bipinnate leaves with multiple
pairs of pinnae and an absence of cauli-/ramiory (which is almost universal in Zygia)
with several species of Macrosamanea (Barneby and Grimes 1996; Ferm et al. 2019).
e identity of Marmaroxylon magdalenae needs to be re-evaluated, but the evidence of
Ferm et al. (2019), who sampled the type material, suggests it should be transferred to
Jupunba. e generic placements of Z. inundata and Z. sabatieri are more contentious.
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
56
Arguments can be made to transfer Z. inundata to Inga (Ferm et al. 2019): it was origi-
nally described in Inga and it shares once-pinnate leaves and absence of cauli-/ramiory
with Inga (Barneby and Grimes 1997; Ferm et al. 2019). However, Z. inundata was
placed as the sole sister of Inga in the plastid tree (Suppl. material 3) and by Ferm et al.
(2019), whereas the nuclear gene data suggest that Z. inundata is sister to Z. sabatieri and
together these two species form the sister clade of Inga (Fig. 12). Zygia sabatieri has bi-
pinnate leaves and both Z. sabatieri and Z. inundata have dehiscent pods, characteristics
that distinguish these species from Inga with its uniformly once-pinnate leaves and inde-
hiscent pods. In order to maintain a morphologically coherent and homogeneous Inga
with respect to these diagnostic characters, segregating Z. inundata and Z. sabatieri as a
new genus would appear to be advantageous. Ingopsis Barneby & J.W. Grimes and Pseu-
docojoba Barneby & J.W. Grimes, the names for the monospecic sections containing
Z. inundata and Z. sabatieri, respectively (Barneby and Grimes 1997), are two available
names, of which Ingopsis would be preferable given the morphological and phylogenetic
proximity of this clade to Inga and the lack of a close relationship to Cojoba Britton &
Rose. However, since these sectional names have no priority at generic rank (Turland et
al. 2018), alternatively, a new name could equally be proposed. Finally, while Zygia s.s.
was reasonably well sampled by Ferm et al. (2019) and also in the current study (Fig.
12), alongside further herbarium taxonomic work and eld studies to clarify species,
denser phylogenetic taxon sampling is desirable, in particular to include Z. eperuetorum
(Sandwith) Barneby & J.W. Grimes. is species is known only from the Essequibo
Valley in Guyana, was placed in its own section by Barneby and Grimes (1997), has an
unusual combination of morphological characters not found elsewhere in Zygia and the
fruit remains unknown. Zygia eperuetorum may well, therefore, represent an additional
separate lineage that could potentially merit recognition as a distinct genus.
Supplementary material 1
Table S1
Authors: Jens J. Ringelberg, Erik J.M. Koenen, João R. Iganci, Luciano P. de Quei-
roz, Daniel J. Murphy, Myriam Gaudeul, Anne Bruneau, Melissa Luckow, Gwilym P.
Lewis, Colin E. Hughes
Data type: excel le.
Explanation note: Samples included in this study.
Copyright notice: is dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). e Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.
Link: https://doi.org/10.3897/phytokeys.205.85866.suppl1
Phylogenomics of Caesalpinioideae: generic re-delimitation 57
Supplementary material 2
Table S2
Authors: Jens J. Ringelberg, Erik J.M. Koenen, João R. Iganci, Luciano P. de Quei-
roz, Daniel J. Murphy, Myriam Gaudeul, Anne Bruneau, Melissa Luckow, Gwilym P.
Lewis, Colin E. Hughes
Data type: excel le.
Explanation note: Trait data used for character evolution analyses.
Copyright notice: is dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). e Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.
Link: https://doi.org/10.3897/phytokeys.205.85866.suppl2
Supplementary material 3
Figure S1
Authors: Jens J. Ringelberg, Erik J.M. Koenen, João R. Iganci, Luciano P. de Quei-
roz, Daniel J. Murphy, Myriam Gaudeul, Anne Bruneau, Melissa Luckow, Gwilym P.
Lewis, Colin E. Hughes
Data type: Pdf le.
Explanation note: Chloroplast phylogeny of Caesalpinioideae. Only bootstrap support
values lower than 100% are shown.
Copyright notice: is dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). e Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.
Link: https://doi.org/10.3897/phytokeys.205.85866.suppl3
Jens J. Ringelberg et al. / PhytoKeys 205: 3–58 (2022)
58
Supplementary material 4
Supplementary tree le
Authors: Jens J. Ringelberg, Erik J.M. Koenen, João R. Iganci, Luciano P. de Quei-
roz, Daniel J. Murphy, Myriam Gaudeul, Anne Bruneau, Melissa Luckow, Gwilym P.
Lewis, Colin E. Hughes
Data type: Tree le (Newick format).
Explanation note: Tree le of the ASTRAL phylogeny based on the single-copy genes
(depicted in Figs 2–12), in which taxon labels have been updated to reect taxo-
nomic changes made in all the entries in Advances in Legume Systematics 14 Part 1.
Copyright notice: is dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). e Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.
Link: https://doi.org/10.3897/phytokeys.205.85866.suppl4
Content uploaded by Jens Ringelberg
Author content
All content in this area was uploaded by Jens Ringelberg on Aug 23, 2022
Content may be subject to copyright.
