automated phylogenetic taxonomy in fungi. ds. hibbett
TRANSCRIPT
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
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
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”
“Chytridiomycota”
“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
M
MSS
SS
SY
S
S
II
AY
ASP
AAS
PA
SS
SS
SA
P
SS
SS
?A
AY
O
H
AA
P
OO
OO
O
AP
PS
SA
S
S
SS
AAA
AS
P
SS
SS
S
SS
SS
SS
SSS
LL
LP
S
LS
P
SS
P
LL
LL
LLLLLLL
S
S
S
S
A
A
SAA
S AS
S
LL
LL
LL
LLLL
LLL
LL
LL
LS
SSS
SP
PP
PS
SS
SS
SY
S
SS
PP
PP
PSS
SS
H
H
H
H
H
M
M
S
P
I
SS
M
*
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
I. Progress in phylogenetic reconstruction in Fungi/AgaricomycetesII. Progress in classification in AgaricomycetesIII. Automated Phylogenetic Taxonomy in AgaricomycetesIV. Conclusions and future directions
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)
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
I. Progress in phylogenetic reconstruction in Fungi/AgaricomycetesII. Progress in classification in AgaricomycetesIII. Automated Phylogenetic Taxonomy in AgaricomycetesIV. Conclusions and future directions
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:
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
I. Progress in phylogenetic reconstruction in Fungi/AgaricomycetesII. Progress in classification in AgaricomycetesIII. Automated Phylogenetic Taxonomy in AgaricomycetesIV. Conclusions and future directions
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