Automated phylogenetic taxonomy in Fungi. DS. Hibbett

Automated Phylogenetic Taxonomy in FungiDavid Hibbett, Henrik Nilsson, Moran Shonfeld, Mario Fonseca, Marc Snyder, Pete Stein, Ryan Twomey,

Janine Costanzo, Brandon Gaytan, J. P. Burke, and Daniel Menard, Clark University, and Thomas Heider, College of the Holy Cross,

Worcester, Massachusetts USA

Uses of comprehensive trees:IdentificationCuration of public sequence databasesIdentification of environmental samplesDiscovery of new speciesBiogeographyDescriptive biogeography—estimation of rangesHistorical biogeographyEpidemiology, plant pathologyConservation—phylogenetic diversity analysesCharacter evolutionAncestral state reconstructionAnalyses of directionalityTests of key innovation hypotheses

Uses of classifications:CommunicationResearchTeachingLegislationRepresentation of the history of life

I. Progress in phylogenetic reconstruction in Fungi/AgaricomycetesII. Progress in classification in AgaricomycetesIII. Automated Phylogenetic Taxonomy in AgaricomycetesIV. Conclusions and future directions


Fungal diversity:Total species of Fungi Described species of Fungi Described species of Agaricomycetes

Fungal sequence data in GenBank: Fungi

Core nucleotide seqsNo. unique names including uncultured, unspecified

No. spp. excluding uncultured, unspecified

AgaricomycetesCore nucleotide seqsNo. unique names including uncultured, unspecified No. spp. excluding uncultured, unspecified

Nuc-lsu rDNA sequences > 800 bp ITS rDNA sequences

93 94 95 96 97 98 99 00 01 02 03 04 05 06 07

ID to speciesAll names

No. new names Deposited

(Fungi)

1,500,000 (Hawksworth, 1995)

70,000-100,000 (Rossman, 1995)

20,000 (Kirk et al. 2001)

631,46432,76617,131 (17-24% of described spp.; 1% of extant spp.)

38,5898,0614,842 (24% of described spp.)

3,94013,905

http://aftol.orghttp://ocid.nacse.org/research/deephyphae/

LABS/PEOPLE5 labs (Hibbett/Clark University; Lutzoni & Vilgalys/DukeUniversity; McLaughlin/Univ. of Minnesota;Spatafora/Oregon State Univ.8 post-docs12 Ph.D. students26 visiting students and scholars17 undergraduates

DATA5191 sequences, 7 genes, 2087 species41 subcellular characters, 30 species

PUBLICATIONS49 articles in print, 14 in press/in review

INFORMATICSWASABI: http://www.lutzonilab.net/aftol/mor: http://mor.clarku.edu/Structural and Biochemical Database: http://aftol.umn.edu/

OUTREACHWorkshops for teachersTeaching the Fungal Tree of Life websitehttp://www.clarku.edu/faculty/dhibbett/TFTOL/index.html

http://aftol.org/

T. James et 69 al.T. James et 69 al.

199 Fungi199 Fungi15 non-fungi15 non-fungi

6436 6436 bpbp: : rpb1,rpb1,rpb2, tef1-rpb2, tef1-αα, , nuc-nuc-lsu rDNAlsu rDNA, , nuc-ssunuc-ssurDNArDNA, , nuc nuc 5.8s5.8srDNArDNA

Ascomycota:Taphrinomycotina

Ascomycota:Saccharomycotina

Ascomycota: Orbi liomycetes

Ascomycota :Pezizomycetes

Ascomycota:Arthoniomycetes

Ascomycota:Dothideomycetes

Ascomycota:Lichinomycetes

Ascomycota:Dothideomycetes

Ascomycota :Lecanor omycetes

Ascomycota :Leotiomycetes

Viridiplantae

Rhodophyta

Stramenopiles

ApicomplexaMycetozoaChoanoflagellida

Metazoa

“Chytridiomycota”



“Zygomycota”

Microspor idia

Glomeromycota

Basidiomycota:Urediniomycotina

Basidiomycota:Ustilaginomycotina

Basidiomycota:Agaricomycotina

“Zygomycota”

1087Copr inopsis cinerea480 Lycoperdon pyriforme626Copr inus comatus

563Clavar ia zollingeri673Amanita brunnescens625 Pluteus romellii285 Cortinarius iodes564 Pleurotus ostreatus449 Armillar ia mellea558 Flammulina velutipes556 Marasmius alliaceus542 Ampulloclitocybe clavipes557Collybia tuberosa468 Henningsomyces candidus729 Hygrocybe aff. conica439 Calostoma cinnabar inum

713 Boletellus projectellus714 Hygrophoropsis aurantiaca717 Suillus pictus576 Fibulorhizoctonia sp.455 Echinodontium tinctorium682 Lactarius deceptivus

452 Bondarzewia montana492 Stereum hirsutum

447Coltricia perennis688 Fomitipor ia mediterranea

484 Phlebia radiata767 Climacodon septentr ionalis776 Phanerochaete chrysosporium562 Grifola sordulenta701 Grifola frondosa770 Fomitopsis pinicola518 Hyphoderma praetermissum700 Cotylidia sp.466 Gautier ia otthii724 Ramaria rubella471 Hydnum albomagnum438Calocera cornea454 Dacryopinax spathularia

1088 Cryptococcus neoformans505 Ustilago maydis867 Cintractia sorghi vulgaris

870 Tilletiopsis sp.865 Tilletiar ia anomala

675 Agaricostilbum hyphaenes

674 Rhodotorula hordea456 Endocronartium harknessii1459 Puccinia graminis

710 Platygloea disciformis138Scutellospora heterogama139Glomus mosseae845 Glomus intraradices574 Geosiphon pyriformis844 Paraglomus occultum141 Mortierella verticillata144Umbelopsis ramanniana

184 Phycomyces blakesleeanus1241 Rhizopus oryzae

539 Endogone pisiformis136 Dimargaris bacillispora

140 Coemansia reversa1062 Orphella aff. haysii

29 Smittium culisetae185 Spiromyces aspiralis

142 Rhopalomyces elegans145 Piptocephalis corymbifera

301 Basidiobolus ranarum633 Olpidium brassicae

28 Entomophthora muscae137 Conidiobolus coronatus

19 Physodermamaydis18 Coelomomyces stegomyiae

300Allomyces arbusculus20 Rhizoclosmatium sp.

24 Polychytr ium aggregatum27 Cladochytrium replicatum

21Batrachochytr ium dendrobatidis689 Rhizophydium macroporosum

43 Rhizophlyctis rosea182 Spizellomyces punctatus

635 Synchytr ium macrosporum25 Monoblepharella sp.26Hyaloraphidium curvatum

638Neocallimastix sp.1068 Encephalitozoon cuniculi

1089 Antonospora locustae297 Rozella allomycis

Caenorhabditis elegansCiona intestinalis

Homo sapiensDrosophila melanogaster

Monosiga brevicollisDictyostelium discoideum

Cryptospor idium parvumToxoplasma gondii

Phytophthora sojaeThalassiosira pseudonana

Cyanidioschyzon merolaeArabidopsis thalianaPopulus trichocarpaOryza sativa

Chlamydomonas reinhardtii

0.05 substitutions/site

to Ascomycota

709 Colacogloea peniophorae

1078 Neurospora crassa216Sordaria fimicola1085 Podospora anser ina217 Chaetomium globosum

1081 Magnaporthe grisea935 Diapor the eres952 Gnomonia gnomon51 Xylaria hypoxylon63 Xylaria acuta1082 Fusarium graminearum

161 Fusarium aff. solani186 Hydropisphaera erubescens

52Hypocrea citr ina914 Microascus tr igonosporus413 Lindra thalassiae

424 Lulworthia grandispora1 Leotia lubrica147 Coccomyces dentatus

744 Potebniamyces pyri151 Chlorociboria aeruginosa76Mollisia cinerea279 Monilinia fructicola59Botryotinia fuckeliana

941 Dermea acerina166 Cudoniella clavus

49 Lachnum virgineum56 Geoglossum nigritum64 Trichoglossum hirsutum1004 Pleopsidium chlorophanum1005 Acarospora schleicheri1007 Acarospora laqueata

106 Echinoplaca str igulacea958 Diploschistes ocellatus

78 Acarosporina microspora398 Stictis radiata

296 Orceolina kerguelensis962 Trapelia placodioides224 Pertusaria dactylina358 Dibaeis baeomyces

645 Umbilicar ia mammulata687 Hypocenomyce scalaris

134 Peltigera degenii196 Mycoblastus sanguinarius639 Lecanora hybocarpa6 Canoparmelia caroliniana3 Cladonia caroliniana642 Bacidia schweinitzii84Physcia aipolia1079 Aspergillus fumigatus1080 Aspergillus nidulans

426 Monascus purpureus1083 Histoplasma capsulatum

1084 Coccidioides immitis430Spiromastix warcupii

657 Capronia pilosella668 Exophiala dermatitidis659 Ramichlor idium anceps669 Exophiala pisciphila684 Agonimia sp.91 Dermatocarpon miniatum661 Endocarpon pallidulum697 Staurothele frustulenta342 Pyrgillus javanicus387 Pyrenula pseudobufonia

891 Peltula umbilicata892 Peltula auriculata896 Lichinella iodopulchra

101 Anisomeridium polypor i1036 Trematosphaeria heterospora1037 Westerdykella cylindrica283 Pyrenophora phaeocomes54 Cochliobolus heterostrophus940 Pleospora herbarum110 Trypethelium sp.

274 Dothidea sambuci921 Dothidea insculpta939 Capnodium coffeae

355 Dendrographa minor126 Roccella fuciformis80Simonyella variegata

148 Cheilymenia stercorea62 Scutellinia scutellata65 Aleur ia aurantia949 Pyronema domesticum50Sarcoscypha coccinea

152 Caloscypha fulgens176 Gyromitra californica179 Disciotis sp.60 Morchella aff. esculenta66 Helvella compressa181 Ascobolus crenulatus507 Peziza vesiculosa71Peziza proteana905 Orbilia vinosa906 Orbilia auricolor1069 Saccharomyces cerevisiae1070 Saccharomyces castellii1073 Candida glabrata1071 Kluyveromyces waltii1072 Ashbya gossypii1075 Kluyveromyces lactis

1074 Candida albicans1269Candida tropicalis1270 Candida guilliermondii1077 Debaryomyces hansenii1268 Candida lusitaniae1076 Yarrow ia lipolytica

1199 Schizosaccharomyces pombe265 Taphr ina wiesneri266 Protomyces inouyei

1192 Pneumocystis carinii

to basallineages

100/100

100/81

100/94

100/93

100/98

100/94

100/100

100/92

100/73

100/80

100/71

--/85

phototrophO

phagotrophH

plant pathogenP

animal pathogenA

insect commensualI

mycoparasi teY

lichenizedL

saprobeS

mycorrhizalM

uncertain?

genome sequenced

motilecell stage present

phagotrophphototrophmutualistpathogensaprobeuncertain

SS

S?M

SM

SS P

?

SS

SS

SM

MS

M

S

SM

S

?

S PS

SS

S PS P

S PS

MM

MS

SA

PP

PP

SY

S PP

PY

MM

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MSS

SS

SY

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II

AY

ASP

AAS

PA

SS

SS

SA

P

SS

SS

?A

AY

O

H

AA

P

OO

OO

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AP

PS

SA

S

S

SS

AAA

AS

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SS

SS

S

SS

SS

SS

SSS

LL

LP

S

LS

P

SS

P

LL

LL

LLLLLLL

S

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A

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LL

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*

T. James et 69 al.T. James et 69 al.

199 Fungi199 Fungi15 non-fungi15 non-fungi

6436 6436 bpbp: : rpb1,rpb1,rpb2, tef1-rpb2, tef1-αα, , nuc-nuc-lsu rDNAlsu rDNA, , nuc-ssunuc-ssurDNArDNA, , nuc nuc 5.8s5.8srDNArDNA

Mycologia 98(6) 2006:

1. James et al. “Chytridiomycota”2. White et al. “Zygomycota”3. Redecker & Rabb Glomeromycota4. Aime et al. Pucciniomycotina5. Begerow et al. Ustilaginomycotina6. Hibbett Agaricomycotina7. Larsson et al. Hymenochaetales8. Moncalvo et al. Cantharellales9. Hosaka et al. Phallomycetidae10. Miller et al. Russulales11. Binder & Hibbett Boletales12. Matheny et al. Agaricales13. Sugiyama et al. Ascomycota14. Suh et al. Saccharomycetales15. Spatafora et al. Pezizomycotina16. Hansen & Pfister Pezizomycetes17. Schoch et al. Dothideomycetes18. Geiser et al. Eurotiomycetes19. Wang et al. Leotiomycetes20. Zhang et al. Sordariomycetes21. Miadlikowska et al. Lecanoromycetes

Papers citing AFTOL

P. Matheny et al. MPE 2007.

Data: 146 OTUs, five genes:nuc-lsu rDNAnuc-ssu rDNAnuc 5.8S rDNAtef1, rpb2Total: 8671 bp

Analyses/Support:Bayesian analysisof all-nucleotide dataset B = post. prob. = 1.0

Parsimony bootstrap ofrDNA nucleotide/proteinamino acid dataset: P = 70-89% P > 90%

Ustilaginomycotina

Uredinomycotina

ASCOMYCOTA

AgaricalesAgaricales

BoletalesBoletales

AthelialesAtheliales

RussulalesRussulales

Corticiales

Polyporales

Trechisporales

Hymenochaetales

ThelephoralesThelephorales

Cantharellales

Phallomycetidae

Auriculariales

Sebacinales

Tremellomycetes

Dacrymycetes

BP

BP

NABP

BP

BP

B

BP

BPBP

B

BP

B

BP

B

BP

B

BP

B

B

B

BP

BP

BP

BP

NA

BP

BP

BP

BP

BP

Agaricomycetes

P. Matheny et al. MPE 2007.

Data: 146 OTUs, five genes:nuc-lsu rDNAnuc-ssu rDNAnuc 5.8S rDNAtef1, rpb2Total: 8671 bp

107 recent studies (1999-2007) on individual clades of Agaricomycetes

Weiss et al. (2004), Selosse et al. (2002)Sebacinales

Kõljalg et al. (2000, 2001, 2002)Thelephorales

DePriest et al. (2005), Diederich et al. (2003), Matsuura et al. (2000), Sikaroodi et al. (2001)Corticiales

Eberhardt et al. (1999), Kernaghan et al. (2002), Lilleskov et al. (2002)Atheliales

Dahlman et al. (2000), Dunham et al. (2003),Gonzalez et al. (2001), Kottke et al. (2003), Moncalvo et al. (2007)Cantharellales

Dai et al. (2006), De Koker et al. (2003), Desjardin et al. (2004), Hong et al. (2002), Hong and Jung (2004), Kimet al. (2005), Ko et al. (2001), Krüger (2004), Nilsson et al. (2003), Wang et al. (2004)

Polyporales

Decock et al. (2005), Fischer and Binder (2004), Geslebin et al. (2004), Paulus et al. (2002), Redberg et al.(2003), Wagner and Fischer (2001, 2002a, 2002b), Larsson et al. (2007)

Hymenochaetales

Henkel et al. (2000), E. Larsson et al. (2003), E. Larsson and Hallenberg (2001), Lickey et al. (2002), Miller etal. (2001, 2002), Nuytinck et al. (2004), Wu et al. (1999), Lebel et al. (2004), Miller et al. (2007)

Russulales

Bakker et al. (2004), Binder and Bresinsky (2002), Bresinksky et al. (1999), Den Bakker et al. (2004), Grubishaet al. (2001, 2002), Jarosch and Besl (2001), Jarosch (2001), Kretzer and Bruns (1999), Kretzer et al. (2003),Miller (2002, 2003), Peintner et al. (2003), Reddy et al. (2005), Taylor et al. (2006), Binder and Hibbett (2007)

Boletales

K.-H. Larsson (2001)Trechisporales

Geml et al. (2005), Humpert et al. (1999), Hosaka et al. (2007)Phallomycetidae

Aanen et al. (2000), de Arruda et al. (2003), Binder et al. (2001), Boyle et al. (2006), Callac et al. (2005),Challen et al. (2003), Chapela and Garbelotto (2004), Coetzee et al. (2000, 2001, 2002, 2003, 2005), Dentingeret al. (2007), Drehmel et al. (1999), Frøslev et al. (2004, 2004), Garnica et al. (2003), Gulden et al. (2005),Hofstetter et al. (2002), Høiland and Holst-Jensen (2000), Hopple and Vilgalys (1999), Hughes et al. (2001),Hwang and Kim (2000), Kerrigan et al. (2005), Kirchmair et al. (2004), Krüger et al. (2001), Martin andRaccabruna (1999), Mata et al. (2001), Matheny et al. (2002), Mitchell and Bresinsky (1999), Moncalvo et al.(2000a, 2000b, 2002), Mwenje et al. (2003), Oda et al. (2004), Peintner et al. (2001, 2002, 2003, 2004),Redhead et al. (2002), Seidl (2000), Thorn et al. (2000), Vellinga (2003, 2004), Wilson et al. (2005), Yang et al.(2005)

Agaricales

Most inclusive phylogenetic analyses of Agaricomycetes

J. M. Moncalvo et al. 2002. One hundred and seventeenclades of euagarics (Agaricales)Data: nuc-lsu rDNANo. seqs. sampled 877No. species sampled 877Nuc-lsu rRNA > 800 bp in GenBank 2309Species in GenBank 2429

M. Binder et al. 2005. The phylogenetic distribution ofresupinate forms across the major clades ofhomobasidiomycetes (Agaricomycetes)Data: mt/nuc lsu/ssu rDNANo. seqs. sampled 656No. species sampled 640Nuc-lsu rRNA > 800 bp in GenBank 3940Species in GenBank 4842

M. Binder and D. S. Hibbett. 2006. Molecular systematicsand biological diversification of Boletales.Data: nuc lsu rDNANo. seqs. sampled 435No. species sampled 301Nuc-lsu rRNA > 800 bp in GenBank 469Species in GenBank 442


Tulostomatales Tulasnellales Thelephorales Stereales Sclerodermatales Schizophyllales Russulales Poriales Phallales Nidulariales Melanogastrales

*not Homobasidiomycetes Lycoperdales*non-monophyletic Lachnocladiales

Hymenogastrales Thelephorales Hymenochaetales Russulales* Hericiales Polyporales* Gomphales Phallales Gautieriales Hymenochaetales Ganodermatales Dacrymycetales* Fistulinales Ceratobasidiales Dacrymycetales Cantharellales Cortinariales Boletales* Ceratobasidiales Auriculariales Cantharellales Agaricales* BondarzewialesAgaricomycetidae* Boletales Tulasnellales AgaricalesTremellomycetidae p.p.*HolobasidiomycetidaeKirk et al. (2001)Hawksworth et al. (1995)

"The NCBI taxonomy database is not a primarysource for taxonomic or phylogenetic information.Furthermore, the database does not follow a singletaxonomic treatise but rather attempts to incorporatephylogenetic and taxonomic knowledge from avariety of sources, including the published literature,web-based databases, and the advice of sequencesubmitters and outside taxonomy experts.Consequently, the NCBI taxonomy database is not aphylogenetic or taxonomic authority and should notbe cited as such."http://www.ncbi.nlm.nih.gov:80/Taxonomy/taxonomyhome.html

Tulostomatales Tulasnellales Thelephorales Stereales Phallales Nidulariales

Thelephorales Melanogastrales Russulales* Lycoperdales Polyporales* Hymenogastrales Phallales Hymenochaetales Hymenochaetales Hericiales Dacrymycetales* Geastrales Ceratobasidiales Gautieriales Cantharellales Echinodontiaceae Boletales* Ceratobasidiales Auriculariales Cantharellales Agaricales* BoletalesAgaricomycetidae* Aphyllophorales Tulasnellales AgaricalesTremellomycetidae p.p.*HomobasidiomycetesKirk et al. (2001)GenBank (2006)

Tulostomatales Tulasnellales Thelephorales Stereales Phallales

Trechisporales Nidulariales Thelephorales Melanogastrales Sebacinales Lycoperdales Russulales Hymenogastrales Polyporales Hymenochaetales Phallomycetidae Hericiales Hymenochaetales Geastrales Gloeophyllales Gautieriales Corticiales Echinodontiaceae Cantharellales Ceratobasidiales Boletales Cantharellales Auriculariales Boletales Atheliales Aphyllophorales Agaricales AgaricalesAgaricomycetesHomobasidiomycetesGenBank (2007)GenBank (2006)

Tulostomatales Tulasnellales Thelephorales Stereales Phallales

Trechisporales Nidulariales Thelephorales Melanogastrales Sebacinales Lycoperdales Russulales Hymenogastrales Polyporales Hymenochaetales Phallomycetidae Hericiales Hymenochaetales Geastrales Gloeophyllales Gautieriales Corticiales Echinodontiaceae Cantharellales Ceratobasidiales Boletales Cantharellales Auriculariales Boletales Atheliales Aphyllophorales Agaricales AgaricalesAgaricomycetesHomobasidiomycetesGenBank (2007)GenBank (2006)

http://www.abc.net.au/science/scribblygum/

http://www.mykoweb.com/CAF/index.html

Genera resolved as non-monophyletic in Binder et al. (2005):

Acanthophysium, Albatrellus, Aleurodiscus, Antrodia, Antrodiella, Athelia,Ceraceomyces, Ceriporia, Dendrothele, Fuscoporia, Gloeocystidiellum,Hericium, Hydnochaete, Hymenochaete, Hyphoderma, Hyphodontia,Hypochnicium, Kavinia, Leucogyrophana, Marchandiomyces, Oligoporus,Peniophora, Phanerochaete, Phellinus, Phlebia, Phlebiella, Physalacria,Polyporus, Polyporus, Pseudotomentella, Schizopora, Scytinostroma,Sistotrema, Stereum, Xylobolus (34)

Genera resolved as non-monophyletic in Moncalvo et al. (2002):

Agaricus, Agrocybe, Amanita, Boletus, Clitocybe, Collybia, Coprinus, Cortinarius,Cystoderma, Cystolepiota, Entoloma, Galerina, Gerronema, Gloiocephala,Gymnopilus, Gymnopus, Hemimycena, Hohenbuehelia, Hydropus, Hypholoma,Lepiota, Lepista, Leptonia, Leucoagaricus, Leucocoprinus, Limacella,Lyophyllum, Macrolepiota, Marasmiellus, Marasmius, Montagnea, Mycena,Naucoria, Omphalina, Omphalotus, Pholiota, Poromycena, Psathyrella,Psilocybe, Resinomycena, Resupinatus, Rhodocybe, Russula, Stropharia (44)

Summary: current status of homobasidiomycete systematics

Largely incomplete documentation of extant species Ca. 20% of described species represented in GenBank Steady accumulation of “taxonomic” sequences, accelerating accumulation of

“environmental” sequences Higher-level analyses resolve broad outlines of Agaricomycete phylogeny A plethora of analyses at lower taxonomic levels Lack of integration of existing data Unacceptably slow translation of phylogenies into classifications A disconnect between phylogenetic reconstruction and classification, creating a

(widening?) gap between taxonomy and understanding of phylogeny

What is needed to achieve a comprehensive, phylogenetically accurateclassification of homobasidiomycetes?

A dramatic increase in the rate of species discovery, including sequence-baseddiscovery and description

Automated integration of emerging data into comprehensive trees Automated translation of trees into classifications


Acquisition andScreening

Alignment andAnalysis

Backbone monophyly constraint220 species, based on multi-locus analyses

Create General Constraint tree(220 species, based on multilocusanalyses).

Load General Constraint as backbonemonophyly constraint.Add new sequences to dataset and tree andperform branch swapping (TBR, 5 hours).Save new tree as Temporary Constraint.

Load Temporary Constraint as backbonemonophyly constraint.Add new sequences to dataset and tree, butperform no swapping.Save new tree as Temporary Constraint(i.e., overwrite file).

Load General Constraint as backbone.Use (new) Temporary Constraint as a startingtree for branch swapping (TBR, 5 hours).Save new tree as Temporary Constraint.Go to 3.

1 2

3 4

Heuristic search strategy:

Classification

A B C D E F G H A B C E D F G H

Parsing a node-based phylogenetic taxon definition:

“Taxon X is the least-inclusive clade that contains D and H”.

D and H are “specifiers”

Tree 1 (A(B(C(D(E(F(G,H))))))) Taxon X = D, E, F, G, H

Tree 2 (A(B(C(E(D(F(G,H))))))) Taxon X = D, F, G, H

1 2


Conclusions

Current taxonomic and phylogenetic practices are failing in two key areas: Integration of available and emerging data Translation of trees into classifications

Core elements of taxonomy--tree building and translation of trees into classifications--canbe automated. Phylogenetic definitions of taxa (ranked or unranked) are essential forthis purpose.

But, expert user input is still required for: Curation of the backbone tree Clade definition

mor does not replace traditional taxonomy, produce monographs or keys

mor is most useful for mega-diverse, poorly-known groups, with large quantities ofemerging data, including Fungi and all groups of “microbes”

Future directions

Enhancements:Improvements to alignment and phylogenetic analysis routines RAxML, Parsimony Ratchet, TNT, DCM…

Incorporation of ITS data, including environmental sequences Will dramatically expand taxonomic content May enable sequence-based species discovery Will require automated supertree analyses Will require protocols to assign correspondence between ITS and nuc-lsu

sequences

Expansion to all groups of Fungi (AFTOL2)Definition of many more clades

Integration with traditional taxonomy Possible because taxonomic hierarchies have an inherent tree structure Will require protocols for determining correspondence between sequences and

names (difficult when type specimen has not been sequenced) Will allow automated construction of trees and classifications that approach the

total knowledge of fungal diversity and phylogeny

R. R. Henrik Henrik NilssonNilsson

Not shown: Moran Shonfeld*, Mario Fonseca*,Thomas Heider*, Daniel Menard*

*undergraduates Marc Snyder*Brandon Gaytán*Janine Costanzo*

Ryan Twomey*, Pete Stein*

J. P. Burke*

Business

Automated phylogenetic taxonomy in Fungi. DS. Hibbett