Mushrooms I have known (v2)
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Talk about my experiences as a mushroom hunter. Concentrates on an old favourite, fly agaric, and a strange new visitor to the Netherlands: the Jack-O'-Lantern mushroom. Connections to Data Science, Machine Learning, Big Data and AI. Also environmental issues.
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Mushrooms I have known (v2)
- 1. Mushrooms I have known Richard D. Gill Mathematical Institute, Leiden University http://www.math.leidenuniv.nl/~gill This version: March 21, 2019 Dedicated to Rosa and Rianne
- 2. Warnings • All mushrooms are edible – but some, only once • There are old mushroom hunters, and bold mushroom hunters … but there are no old bold mushroom hunters
- 3. Fungi • Closer to animals than plants • The thing you see above ground (that you call a “mushroom”) is just a temporary reproductive organ • See Wikipedia (next few slides) De grote stinkzwam (Phallus impudicus) is een paddenstoel uit de familie Phallaceae Phallus impudicus, known colloquially as the common stinkhorn, is a widespread fungus recognizable for its foul odor and its phallic shape when mature, the latter feature giving rise to several names in 17th-century England.
- 5. Wikipedia: “fungus” A fungus (plural: fungi[3] or funguses[4]) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and moulds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, fungi, which is separate from the other eukaryotic life kingdoms of plants and animals. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Similar to animals, fungi are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesise. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (form a monophyletic group), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime moulds) and oomycetes (water moulds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek μύκης mykes, mushroom). In the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants.
- 6. Your source for the latest research news Date: Source: Summary: Discovery About Evolution Of Fungi Has Implications For Humans October 23, 2006 University of Minnesota A University of Minnesota researcher says as early fungi made the evolutionary journey from water to land and branched off from animals, they shed tail-like flagella that propelled them through their aquatic environment and evolved a variety of new mechanisms, including explosive volleys and fra‐ grances, to disperse their spores and reproduce in a terrestrial setting. FULL STORY As early fungi made the evolutionary journey from water to land and branched off from animals, they shed tail-like flagella that propelled them through their aquatic environment and evolved a variety of new mechanisms (including explosive volleys and fragrances) to disperse their spores and reproduce in a terrestrial setting. "What's particularly interesting is that species retained their flagella for different lengths of time and developed different mechanisms of spore dispersal," said David McLaughlin, professor of plant biology at the University of Minnesota in the College of Biological Sciences and co-author of a paper published in the Oct. 19 issue of Nature describing how fungi adapted to life on land. The discovery is the latest installment in an international effort to learn the origins of species. McLaughlin is one of five principal investigators leading a team of 70 researchers at 35 institutions. The group analyzed information from six key genetic regions in almost 200 contemporary species to reconstruct the earliest days of fungi and their various relations. McLaughlin is directing the assembly of a shared database of fungal structures obtained through electron micro‐ scopy, which produces detailed images that provide clues to the diversity of these organisms. The work is funded by a $2.65 million "Assembling the Tree of Life" grant from the National Science Foundation that was awarded to Duke University, the University of Minnesota, Oregon State University and Clark University in January 2003. The discovery provides a new glimpse into evolution of life on Earth. It will also help scientists better understand this unusual group of organisms and learn how to develop uses for their unique properties in medicine, agricul‐ ture, conservation and industry. McLaughlin believes fungi are a valuable untapped natural resource. They play a variety of roles in nature, such as supplying plants with nutrients through mutualistic relationships and recycling dead organisms. He estimates that there are about 1.5 million species on the Earth, but only about 10 percent of those are known. And civilization has only identified uses for a few of those, such as using yeast to make bread, beer, wine, cheese and a few antibiotics. https://www.sciencedaily.com/releases/2006/10/061021115712.htm Fungi are also intriguing because their cells are surprisingly similar to human cells, McLaughlin said. In 1998 scientists discovered that fungi split from animals about 1.538 billion years ago, whereas plants split from animals about 1.547 billion years ago. This means fungi split from animals 9 million years after plants did, in which case fungi are actually more closely related to animals than to plants. The fact that fungi had motile cells propelled by flagella that are more like those in animals than those in plants, supports that. https://doi.org/10.1038/nature05110
- 7. Plants, animals, fungi split up 00 Landfall 0 Mushrooms
- 8. Some famous fungi • In penicillin, blue cheese, yoghurt, … • Yeast (beer, bread, wine, …) • Zwemmers eczeem – Athlete’s foot • The largest living organism on the planet? • Alleged cause of death of: Buddha, Emperor Claudius, Hapsburg emperor Charles VI, Julius Schäffer, … • Digests and recycles animal and plant remains; lives in symbiotic relation with plants and trees, animals, … Armillaria ostoyae
- 9. Poisonous mushrooms: 7 most dangerous in UK https://www.woodlandtrust.org.uk/blog/2018/11/poisonous-mushrooms/ Fraaie gifgordijnzwam Groene knolamaniet Kleverige knolamaniet Bundelmosklokje Weidetrechterzwam Panteramaniet ????????
- 10. My two favourites • Amanita muscaria - fly agaric [vliegenzwam] • Omphalotus olearius [?] - jack-o’-lantern mushroom [lantaarnzwam] Photos: below: Wikipedia; above: mine
- 11. Amanita muscaria Musca from the name of the common house fly, musca domesticaAmanita from Ancient Greek ἀµανίτης (amanítēs), mushrooms.
- 12. I have a great deal to say about Amanita muscaria – result of many years research, observation. This creature is not bright red with white spots for nothing!
- 13. Omphalotus olearius [?] Omphalotus from the Byzantine Greek ὀμϕαλοειδής, meaning "navel" Olearius from oleum (“olive oil”) + -ārius
- 14. I think I found Omphalotus olearius in my garden, a year ago; and this winter it returned (same time, same place). I fear it is poisonous.
- 15. Wikipedia
- 16. My photos
- 17. Gallery • 10 years of mushroom hunting (6 slides, 35 pictures per slide)
- 18. (1 of 6)
- 19. (2 of 6)
- 20. (3 of 6)
- 21. (4 of 6)
- 22. (5 of 6)
- 23. (6 of 6)
- 24. Want to learn more about the joys of mushroom hunting? • Go out in the fields or forests with someone with a great deal of experience. • Never pick a mushroom if you don’t have to. • A photograph is not enough to identify a mushroom. Learn about the *important* distinguishing characteristics. • Never eat a mushroom if you are not *absolutely* certain you have identified it correctly. Be patient. They’ll come again next year, same time, same place. • Coffee-table books full of large glossy photographs are not much use. • Internet is wonderful but not everything you read there is true. • Mushrooms *and* people are natural living beings. Variation is “built in”, and it’s enormous.
- 25. Thank you! • Any questions? • http://www.math.leidenuniv.nl/~gill • Slideshare: gill1109
- 26. Extras • Various topics for discussion and further research
- 27. ‘Chytridiomycota’: euchytrids ‘Zygomycota’ microsporidia 1087 Coprinopsis cinerea 480 Lycoperdon pyriforme 626 Coprinus comatus 563 Clavaria zollingeri 673 Amanita brunnescens 625 Pluteus romellii 285 Cortinarius iodes 564 Pleurotus ostreatus 449 Armillaria mellea 558 Flammulina velutipes 556 Marasmius alliaceus 542 Ampulloclitocybe clavipes 557 Collybia tuberosa 468 Henningsomyces candidus 729 Hygrocybe aff. conica 439 Calostoma cinnabarinum 713 Boletellus projectellus 714 Hygrophoropsis aurantiaca 717 Suillus pictus 576 Fibulorhizoctonia sp. 455 Echinodontium tinctorium 682 Lactarius deceptivus 452 Bondarzewia montana 492 Stereum hirsutum 447 Coltricia perennis 688 Fomitiporia mediterranea 484 Phlebia radiata 767 Climacodon septentrionalis 776 Phanerochaete chrysosporium 562 Grifola sordulenta 701 Grifola frondosa 770 Fomitopsis pinicola 518 Hyphoderma praetermissum 700 Cotylidia sp. 466 Gautieria otthii 724 Ramaria rubella 471 Hydnum albomagnum 438 Calocera cornea 454 Dacryopinax spathularia 867 Cintractia sorghi vulgaris 870 Tilletiopsis sp. 865 Tilletiaria anomala 675 Agaricostilbum hyphaenes 674 Rhodotorula hordea 456 Endocronartium harknessii 1459 Puccinia graminis 138 Scutellospora heterogama 139 Glomus mosseae 845 Glomus intraradices 574 Geosiphon pyriformis 141 Mortierella verticillata 144 Umbelopsis ramanniana 184 Phycomyces blakesleeanus 1241 Rhizopus oryzae 136 Dimargaris bacillispora 140 Coemansia reversa 1062 Orphella aff. haysii 29 Smittium culisetae 185 Spiromyces aspiralis 142 Rhopalomyces elegans 145 Piptocephalis corymbifera 28 Entomophthora muscae 19 Physoderma maydis 18 Coelomomyces stegomyiae 24 Polychytrium aggregatum 27 Cladochytrium replicatum 21 Batrachochytrium dendrobatidis 689 Rhizophydium macroporosum 43 Rhizophlyctis rosea 182 Spizellomyces punctatus 635 Synchytrium macrosporum 25 Monoblepharella sp. 26 Hyaloraphidium curvatum 1068 Encephalitozoon cuniculi 1089 Antonospora locustae Ciona intestinalis Homo sapiens Populus trichocarpa Oryza sativa Chlamydomonas reinhardtii 0.05 substitutions per site to Ascomycota 709 Colacogloea peniophorae ‘Zygomycota’: Mucormycotina Dikarya Fungi Y Y Y Y Y Cyanidioschyzon merolae Arabidopsis thaliana Phytophthora sojae Thalassiosira pseudonana Monosiga brevicollis Cryptosporidium parvum Toxoplasma gondii Dictyostelium discoideum Drosophila melanogaster Caenorhabditis elegans 297 Rozella allomycis Y 300 Allomyces arbusculus 20 Rhizoclosmatium sp. 638 Neocallimastix sp. 137 Conidiobolus coronatus ‘Zygomycota’: Entomophthorales 301 Basidiobolus ranarum 633 Olpidium brassicae 844 Paraglomus occultum 539 Endogone pisiformis 710 Platygloea disciformis 1088 Cryptococcus neoformans 505 Ustilago maydis 1078 Neurospora crassa 216 Sordaria fimicola 1085 Podospora anserina 217 Chaetomium globosum 1081 Magnaporthe grisea 935 Diaporthe eres 952 Gnomonia gnomon 51 Xylaria hypoxylon 63 Xylaria acuta 1082 Fusarium graminearum 161 Fusarium aff. solani 186 Hydropisphaera erubescens 52 Hypocrea citrina 914 Microascus trigonosporus 413 Lindra thalassiae 424 Lulworthia grandispora 1 Leotia lubrica 147 Coccomyces dentatus 744 Potebniamyces pyri 151 Chlorociboria aeruginosa 76 Mollisia cinerea 279 Monilinia fructicola 59 Botryotinia fuckeliana 941 Dermea acerina 166 Cudoniella clavus 49 Lachnum virgineum 56 Geoglossum nigritum 64 Trichoglossum hirsutum 1004 Pleopsidium chlorophanum 1005 Acarospora schleicheri 1007 Acarospora laqueata 106 Echinoplaca strigulacea 958 Diploschistes ocellatus 78 Acarosporina microspora 398 Stictis radiata 296 Orceolina kerguelensis 962 Trapelia placodioides 224 Pertusaria dactylina 358 Dibaeis baeomyces 645 Umbilicaria mammulata 687 Hypocenomyce scalaris 134 Peltigera degenii 196 Mycoblastus sanguinarius 639 Lecanora hybocarpa 6 Canoparmelia caroliniana 3 Cladonia caroliniana 642 Bacidia schweinitzii 84 Physcia aipolia 1079 Aspergillus fumigatus 1080 Aspergillus nidulans 426 Monascus purpureus 1083 Histoplasma capsulatum 1084 Coccidioides immitis 430 Spiromastix warcupii 657 Capronia pilosella 668 Exophiala dermatitidis 659 Ramichloridium anceps 669 Exophiala pisciphila 684 Agonimia sp. 91 Dermatocarpon miniatum 661 Endocarpon pallidulum 697 Staurothele frustulenta 342 Pyrgillus javanicus 387 Pyrenula pseudobufonia 891 Peltula umbilicata 892 Peltula auriculata 896 Lichinella iodopulchra 101 Anisomeridium polypori 1036 Trematosphaeria heterospora 1037 Westerdykella cylindrica 283 Pyrenophora phaeocomes 54 Cochliobolus heterostrophus 940 Pleospora herbarum 110 Trypethelium sp. 274 Dothidea sambuci 921 Dothidea insculpta 939 Capnodium coffeae 355 Dendrographa minor 126 Roccella fuciformis 80 Simonyella variegata 148 Cheilymenia stercorea 62 Scutellinia scutellata 65 Aleuria aurantia 949 Pyronema domesticum 50 Sarcoscypha coccinea 152 Caloscypha fulgens 176 Gyromitra californica 179 Disciotis sp. 60 Morchella aff. esculenta 66 Helvella compressa 181 Ascobolus crenulatus 507 Peziza vesiculosa 71 Peziza proteana 905 Orbilia vinosa 906 Orbilia auricolor 1069 Saccharomyces cerevisiae 1070 Saccharomyces castellii 1073 Candida glabrata 1071 Kluyveromyces waltii 1072 Ashbya gossypii 1075 Kluyveromyces lactis 1074 Candida albicans 1269 Candida tropicalis 1270 Candida guilliermondii 1077 Debaryomyces hansenii 1268 Candida lusitaniae 1076 Yarrowia lipolytica 1199 Schizosaccharomyces pombe 265 Taphrina wiesneri 266 Protomyces inouyei 1192 Pneumocystis carinii Pezizomycotina Y Phagotroph Phototroph Lichenized Mycorrhizal Plant pathogen Animal pathogen Mycoparasite Insect commensal Saprobe Uncertain Genome sequenced Motile cell stage present Saprobe Uncertain Pathogen Mutualist Phototroph Phagotroph Viridiplantae Metazoa Glomeromycota Basidiomycota: Pucciniomycotina Basidiomycota: Ustilaginomycotina Basidiomycota: Agaricomycotina 100/100 100/92 100/73 100/71 --/85 ‘Chytridiomycota’: Blastocladiales ... ... Rhodophyta Stramenopiles Apicomplexa Mycetozoa Choanoflagellida ‘Chytridiomycota’ ‘Chytridiomycota’ 100/80 100/100 100/81 100/94 100/93 100/98 100/94 Ascomycota: Lichinomycetes Ascomycota: Eurotiomycetes Ascomycota: Lecanoromycetes Ascomycota: Leotiomycetes Ascomycota:Sordariomycetes H O L M P A I S ? S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S O O O O M M M M M M M M M M M M M M M P P P P P P P P P P P P A A A A A A I I I H H ? ? ? O O P A H A H H S S S S A P S A S M P P A S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S S P P P P P P P P P P P P P P P P A A A A A A A A A A A L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L S S S H Ascomycota: Taphrinomycotina Ascomycota: Saccharomycotina Ascomycota: Orbiliomycetes Ascomycota: Pezizomycetes Ascomycota: Arthoniomycetes Ascomycota: Dothideomycetes Figure 1 | Phylogeny of the kingdom Fungi using bayesian analysis of the combined, six-gene data set. Each fungal species begins with a unique ‘Assembling the Fungal Tree of Life’ identifier, followed by genus and species. Indicated for each terminal taxon are: nutritional mode, whether they produce flagellated cells and if there is a genome sequence for the taxon completed or underway. Thickened branches indicate those that are supported both by heterogeneous bayesian analysis (BPP $95%) and by MLBS ($70%). Almost every branch was supported by BPP and thus values are not shown. Where indicated, support values (percentage of trees in agreement out of 58,611 trees) indicate BPP followed by MLBS. Branches are shaded according to reconstruction of nutritional mode. Microsporidia branches have been shortened three times (double black break) to increase readability. Red vertical ticks on branches indicate alternative placements of microsporidia that might be significantly rejected (P , 0.05) and green ticks indicate placements that cannot be rejected. Quotation marks indicate non- monophyly of the taxon. The name ‘Mucormycotina’ will be validated in a manuscript that is in preparation. Nature: https://doi.org/10.1038/nature05110 Fungi and … Data science Big data Machine learning AI Bayesian statistics
- 33. 2) Tell us where in the World you are? Location can be VERY important. 3) Take pictures of: - top of the cap - underside of the cap - stipe (preferably the whole stipe with the base) - if possible, a longitudinal section to see the context (flesh of the mushroom) and the attachment of the hymenium (gills, tubes, spines, etc) to the stipe' - overview/side view - as many different ages, from small buttons to worn out mushrooms - spore print 3) Make sure that these pictures are: - made preferably in situ (on location), but if that is not possible, then use a neutral background - in the right white balance (colours of the picture should resemble the real colours in daylight) - not too dark or over-exposed (preferably in daylight) - sharp - free of distracting elements like leafs, twigs, dirt etc. The specimen and characteristics have to be clearly visible 4) Always include the following in the description: 4a) if you already have an idea of what species it may be, add: - the name (both scientific and common) - a description of the characteristics you base your ID on - the sources you used for identification (books/websites) 4b) If you don't know what it is: - scent - taste (it is not harmful to nibble a bit off of a mushroom and chew on it for 10 sec. BUT ALWAYS SPIT IT OUT! Even if it tastes nice! Amanita phalloides has quite a slight sweet flavour, but you don't want to swallow a piece of that) - the true colours (if the colours in the picture does not resemble the true colours by daylight) - possible discolouration of the cap/stipe/hymenium/context (this may take a while with some species) - the substrate (mulch/wood/living tree/bare ground/dead animals etc) - habitat (nearest tree species, woods, calcareous grassland, fen, dry/moist soil, high/low elevation etc) - location (if in US: state/region; if abroad: country + region)
- 34. Medically treated severe mushroom poisonings in Germany 2008– 2013 Americans have grizzly bears, Australians have sharks, Japanese have the poisonous globe fish, Germans have poisonous mushrooms. Almost no- one is killed by any of these things.
- 35. Erotische zwammen Dankzij het warme en vochtige weer beleeft de natuur een tweede bloei, dit keer niet van bloemen maar van paddestoelen. Onstuitbaar dringen al die ogenschijnlijk zwakke hoeden in bos en berm door de humuslaag heen. Samen met het afvallende loof geven ze kleur aan het herfstbos. Maar hoe kom je achter de namen van al die bizarre vertegenwoordigers van het zwammenrijk? Volgens een voorzichtige schatting kent de gemiddelde Nederlander niet meer dan drie of vier namen – de vliegenzwam natuurlijk, het eekhoorntjesbrood, de cantharel en vooruit, het elfenbankje. Wie zijn kennis wil vergroten of bijspijkeren, kan het beste met een excursie meegaan. • Gerrit Jan Zwier 11 oktober 2001 De laatste tijd liep ik verschillende keren mee. Nu eens met een boswachter, dan weer met een echte deskundige. Er zijn twee soorten deelnemers op wie deze gidsen het niet zo begrepen hebben – gretige plukkers en verzamelaars van paddo's. De eersten gaat het vooral om de cantharel, die weer in opkomst is. De liefhebbers van paddo's zijn gespitst op kaalkopjes die met name op mesthopen in het open veld te vinden zijn. `Hallucinogeen' luidt de toevoeging in de boeken bij twee bescheiden zwammetjes, het puntig kaalkopje en het franjekaalkopje. Sommigen brouwen er soep van, echte heksensoep dus. De gids moet echt goed thuis zijn in de materie, want alle deelnemers hebben de gewoonte hun vinger naar elke paddestoel uit te steken en naar de naam te vragen. Dat betekent dat je vele honderden soorten (in totaal gaat het in Nederland om een kleine vierduizend), die vaak sterk op elkaar lijken, moet kennen. Echte mycologen (zwammenexperts) beschikken over allerlei foefjes om de ene familie en de ene soort van de andere te onderscheiden. Maar een amateur komt soms voor vele verrassingen te staan.
- 36. Zo was ik laatst met een alleraardigste boswachter op stap die zich kennelijk eerst niet op de hoogte had gesteld van de vele nieuwkomers in het door ons te doorkruisen bos. `Wat een leuk zwammetje!' luidde meestal zijn openingszin, als hij bij een aangewezen exemplaar neerknielde. Daarna hield hij een spiegeltje onder de hoed, opdat iedereen de mooi gevormde lamellen kon zien. `Ik denk een melkzwammetje', zei hij dan. Om dat zeker te weten, moest hij het vlees echter kneuzen, en dat ging hem aan het hart. Lag de paddestoel ondersteboven, en begon hij na een kneep in de lamellen niet te `melken', dan hield hij het meestal op een `ridderzwammetje'. In zijn baard hoorde ik hem mompelen over `ridders en schijnridders'. Op zeker moment begon hij zijn tred te versnellen en allerlei vreemde zwammen te negeren. Hij wilde eigenlijk alleen iets vertellen over goede bekenden, zoals het rodekoolzwammetje en de boschampignon. De gids, die ons laatst in de buurt van Ravenswoud rondleidde, was meer het type van de dorpsonderwijzer. Aan het begin van de wandeling strooide hij wat broodkruimels uit een zakje, om de `bosgeesten mild te stemmen'. Dat deden ze vroeger ook, lichtte hij toe, in de hoop een rijke zwammenflora in het bos aan te treffen. En werkelijk, onze oogst was rijk; laat ik hier slechts de grote oranje bekerzwam, de groene glibberzwam (die uit gelatine gemaakt lijkt te zijn), de radijsvaalhoed en de parelamaniet noemen. De laatste is niet giftig, in tegenstelling tot de panteramaniet, die er sterk op lijkt. Toen de Larousse Encyclopedie het omgekeerde beweerde, moest de hele oplage van 400.000 exemplaren vernietigd worden. Bij vele soorten had onze leidsman een verhaal bij de hand. Moederkoren, een schimmel op graan, zorgde vroeger voor voedselvergiftigingen. Bekend ook is het apocriefe verhaal over de zuster van Darwin, die het uiterlijk van de Phallus impudicus (grote stinkzwam) zo aanstootgevend vond dat zij die elke herfst uit haar tuin liet verwijderen. De wereld van de mycologie heeft toch al een duidelijk erotische ondertoon. Zo ruiken vezelkoppen naar sperma en herinneren woorden als `schede', `volva' (`beurs') en `hymenium' (kiemvlies; hymen = maagdenvlies) aan een seksuologisch handboek. `Heeft u wel eens een pruikzwam gezien?' vroeg ik laatst aan een expert. Deze zwam hangt soms als een wit bevroren watervalletje uit de oksel van een oude beuk. `Jazeker', zei hij, `daar kreeg ik bijna een mycologisch orgasme van.'
- 37. ARTICLES https://doi.org/10.1038/s41559-019-0834-1 Megaphylogeny resolves global patterns of mushroom evolution Torda Varga1 , Krisztina Krizsán1 , Csenge Földi 1 , Bálint Dima 2 , Marisol Sánchez-García3 , Santiago Sánchez-Ramírez 4 , Gergely J. Szöllősi5 , János G. Szarkándi 6 , Viktor Papp 7 , László Albert8 , William Andreopoulos9 , Claudio Angelini10,11 , Vladimír Antonín12 , Kerrie W. Barry9 , Neale L. Bougher13 , Peter Buchanan14 , Bart Buyck15 , Viktória Bense1 , Pam Catcheside 16 , Mansi Chovatia9 , Jerry Cooper 17 , Wolfgang Dämon18 , Dennis Desjardin19 , Péter Finy20 , József Geml21 , Sajeet Haridas 9 , Karen Hughes22 , Alfredo Justo3 , Dariusz Karasiński23 , Ivona Kautmanova24 , Brigitta Kiss1 , Sándor Kocsubé6 , Heikki Kotiranta25 , Kurt M. LaButti9 , Bernardo E. Lechner26 , Kare Liimatainen27 , Anna Lipzen9 , Zoltán Lukács28 , Sirma Mihaltcheva9 , Louis N. Morgado21,41 , Tuula Niskanen27 , Machiel E. Noordeloos21 , Robin A. Ohm29 , Beatriz Ortiz-Santana30 , Clark Ovrebo31 , Nikolett Rácz6 , Robert Riley9 , Anton Savchenko32,42 , Anton Shiryaev33 , Karl Soop34 , Viacheslav Spirin 32 , Csilla Szebenyi6,43 , Michal Tomšovský 35 , Rodham E. Tulloss36,37 , Jessie Uehling38 , Igor V. Grigoriev 9,39 , Csaba Vágvölgyi6 , Tamás Papp6,43 , Francis M. Martin40 , Otto Miettinen 32 , David S. Hibbett3 and László G. Nagy 1 * Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary his- tory are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphol- ogy). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding. 19 March, 2019
- 39. One of the 245 analysed maximum-likelihood trees was randomly chosen and visualized. Trees were inferred from nrLSU, rpb2, ef1-a sequences with a phylogenomic backbone constraint of deep nodes. Branches are coloured by net diversification (speciation minus extinction) rate inferred in Bayesian Analysis of Macroevolutionary Mixtures (BAMM). Warmer colours denote a higher rate of diversification. Significant shifts in diversification rate are shown by triangles at nodes. Only shifts present on >50% of ten trees, with a Bayesian posterior probability >0.5 and a posterior odds ratio >5 are shown. See Supplementary Data 6 for detailed discussion of shifts. Reconstructed probabilities of ancestral plant hosts for order-level clades are shown as pie charts partitioned by the inferred ancestral probability for gymnosperm (green) and angiosperm host (black). Pie charts are given for the most recent common ancestors of each order plus backbone nodes within the Agaricales—for small orders see Supplementary Data 3. Inner and outer bars around the tree denote extant substrate preference (black, angiosperm; green, gymnosperm; grey, generalist) and the placement of species used for inferring the 650-gene phylogenomic backbone phylogeny. Geological time scale is indicated with grey/white concentric rings.