Automated phylogenetic taxonomy in Fungi. DS. Hibbett

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Automated phylogenetic taxonomy in Fungi. DS. Hibbett

  1. 1. Automated Phylogenetic Taxonomy in Fungi David 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
  2. 2. Uses of comprehensive trees: Identification Curation of public sequence databases Identification of environmental samples Discovery of new species Biogeography Descriptive biogeography—estimation of ranges Historical biogeography Epidemiology, plant pathology Conservation—phylogenetic diversity analyses Character evolution Ancestral state reconstruction Analyses of directionality Tests of key innovation hypotheses Uses of classifications: Communication Research Teaching Legislation Representation of the history of life
  3. 3. I. Progress in phylogenetic reconstruction in Fungi/Agaricomycetes II. Progress in classification in Agaricomycetes III. Automated Phylogenetic Taxonomy in Agaricomycetes IV. Conclusions and future directions
  4. 4. I. Progress in phylogenetic reconstruction in Fungi/Agaricomycetes II. Progress in classification in Agaricomycetes III. Automated Phylogenetic Taxonomy in Agaricomycetes IV. Conclusions and future directions
  5. 5. Fungal diversity: Total species of Fungi 1,500,000 (Hawksworth, 1995) Described species of Fungi 70,000-100,000 (Rossman, 1995) Described species of Agaricomycetes 20,000 (Kirk et al. 2001) Fungal sequence data in GenBank: Fungi Core nucleotide seqs 631,464 No. unique names including uncultured, unspecified 32,766 No. spp. excluding uncultured, unspecified 17,131 (17-24% of described spp.; 1% of extant spp.) Agaricomycetes Core nucleotide seqs 38,589 No. unique names including uncultured, unspecified 8,061 No. spp. excluding uncultured, unspecified 4,842 (24% of described spp.) Nuc-lsu rDNA sequences > 800 bp 3,940 ITS rDNA sequences 13,905 ID to species No. new names All names Deposited (Fungi) 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07
  6. 6. http://aftol.org http://ocid.nacse.org/research/deephyphae/
  7. 7. LABS/PEOPLE 5 labs (Hibbett/Clark University; Lutzoni & Vilgalys/Duke University; McLaughlin/Univ. of Minnesota; Spatafora/Oregon State Univ. 8 post-docs 12 Ph.D. students 26 visiting students and scholars 17 undergraduates DATA 5191 sequences, 7 genes, 2087 species 41 subcellular characters, 30 species http://aftol.org/ PUBLICATIONS 49 articles in print, 14 in press/in review INFORMATICS WASABI: http://www.lutzonilab.net/aftol/ mor: http://mor.clarku.edu/ Structural and Biochemical Database: http://aftol.umn.edu/ OUTREACH Workshops for teachers Teaching the Fungal Tree of Life website http://www.clarku.edu/faculty/dhibbett/TFTOL/index.html
  8. 8. T. James et 69 al. 199 Fungi 15 non-fungi 6436 bp: rpb1, bp: rpb2, tef1-α, nuc- tef1-α lsu rDNA, nuc-ssu rDNA, rDNA, nuc 5.8s rDNA, rDNA
  9. 9. 1078 Neur ospora crassa S 216 Sordaria fimicola S 1085 Podospora anser ina S phagotroph to Ascomycota 217 Chaetomium globosum S H T. James et 69 al. 1081 Magnaporthe grisea P phototroph O 1087 Copr inopsis cinerea S 935 Diapor the er es P lichenized L 480 Lycoper don pyrifor me S 952 Gnomonia gnomon P mycorrhizal M 626 C opr inus comatus S 51 Xylaria hypoxylon S plant pathogen 563 C lavar ia zollingeri ? P 63 Xylaria acuta S 100/100 animal pathogen 673 Amanita brunnescens M A 1082 F usarium gr aminearum P 625 Pluteus romellii S mycoparasi te 161 Fusarium aff. solani P Y 285 Cortinarius iodes M insect commensual 186 Hydropisphaer a erubescens S 199 Fungi I 564 Pleurotus ostreatus S 52 Hypocrea citr ina Y saprobe S 449 Armillar ia mellea S P M 914 Microascus tr igonospor us S uncertain ? 558 Flammulina velutipes S 413 Lindra thalassiae S 556 Marasmius alliaceus S 15 non-fungi 424 Lulworthia gr andispora S genome sequenced 542 Ampulloclitocybe clavipes ? 1 Leotia lubrica S 557 Collybia tuberosa S motile cell stage present 147 Coccomyces dentatus S 468 Henningsomyces candidus S 744 Potebniamyces pyri P 729 Hygrocybe aff. conica S phagotroph 151 Chlorociboria aer uginosa S phototroph 439 Calostoma cinnabar inum M 76 Mollisia cinerea P 100/71 713 Boletellus projectellus M mutualist 279 Monilinia fr ucticola P Ascomycota : pathogen 714 Hygrophor opsis aurantiaca S 59 Botryotinia fuckeliana P Leotiomycetes 6436 bp: rpb1, saprobe bp: 717 Suillus pictus M 941 Dermea acerina S uncertain 576 Fibulorhizoctonia sp. I 166 Cudoniella clavus S 455 Echinodontium tinctorium S 49 Lachnum virgineum S 682 Lactarius deceptivus M 56 Geoglossum nigritum S rpb2, tef1-α, nuc- tef1-α 452 Bondarzewia montana S 64 Trichoglossum hirsutum S Basidiomycota: 492 Stereum hirsutum S 1004 Pleopsidium chlor ophanum L Agaricomycotina 447 C oltricia perennis M 1005 Acarospora schleicheri L 688 Fomitipor ia mediterranea S P 1007 Acarospora laqueata L lsu rDNA, nuc-ssu rDNA, 484 Phlebia radiata S 106 Echinoplaca str igulacea L 767 Climacodon septentr ionalis S 958 Diploschistes ocellatus L 776 Phanerochaete chrysosporium S 78 Acarosporina microspora S 562 Grifola sordulenta S P 398 Stictis radiata S rDNA, nuc 5.8s rDNA, 100/100 701 Grifola fr ondosa S P 296 Orceolina ker guelensis L 770 Fomitopsis pinicola S P 962 Trapelia placodioides L 518 Hyphoderma praetermissum S 224 Pertusaria dactylina L 100/92 Asco mycota : 700 Cotylidia sp. ? 358 Dibaeis baeomyces L rDNA Lecanor omycetes 466 Gautieria otthii M 645 Umbilicar ia mammulata L 100/73 724 Ramaria rubella M 687 Hypocenomyce scalaris L 471 Hydnum albomagnum M 134 Peltigera degenii L 438 Calocera cornea S 196 Mycoblastus sanguinarius L 454 Dacryopinax spathularia S 639 Lecanora hybocar pa L 1088 Cryptococcus neoformans A 6 Canoparmelia caroliniana L 505 Ustilago maydis P 3 Cladonia car oliniana L Basidiomycota: 867 Cintractia sorghi vulgaris P 642 Bacidia schweinitzii L Ustilaginomycotina 870 Tilletiopsis sp. P 84 Physcia aipolia L 865 Tilletiar ia anomala P 1079 Aspergillus fumigatus S A 100/80 675 Agaricostilbum hyphaenes S 1080 Aspergillus nidulans S 709 Colacogloea peniophorae Y 426 Monascus purpureus S Basidiomycota: 674 Rhodotorula hor dea S P 1083 Histoplasma capsulatum A Urediniomycotina 456 Endocronartium harknessii P 1084 Coccidioides immitis A 1459 Puccinia graminis P 430 Spiromastix warcupii S 710 Platygloea disciformis Y 657 Capronia pilosella S 138 Scutellospora heter ogama M 668 Exophiala dermatitidis S A 100/81 139 Glomus mosseae M 659 Ramichlor idium anceps S Glomeromycota 845 Glomus intraradices M 669 Exophiala pisciphila S A 574 Geosiphon pyriformis M 684 Agonimia sp. L L 844 Paraglomus occultum M 91 Dermatocar pon miniatum L * 141 Mortierella verticillata S 661 Endocarpon pallidulum L 144 Umbelopsis ramanniana S 697 Staurothele fr ustulenta L 184 Phycomyces blakesleeanus S 342 Pyrgillus javanicus L 1241 Rhizopus or yzae S 387 Pyrenula pseudobufonia L 539 Endogone pisiformis S 891 Peltula umbilicata L Ascomycota : “Z ygomycota” 136 Dimargaris bacillispora Y 892 Peltula auriculata L Lichinomycetes 140 Coemansia reversa S 896 Lichinella iodopulchra L 1062 Orphella aff. haysii I 101 Anisomeridium polypor i L 29 Smittium culisetae I 1036 Trematosphaeria heter ospora S 185 Spiromyces aspiralis S 1037 Westerdykella cylindrica S Ascomycota: 142 Rhopalomyces elegans A 283 Pyrenophora phaeocomes P Dothi deom ycet es 145 Piptocephalis corymbifera Y --/85 54 Cochliobolus heterostr ophus P 301 Basidiobolus ranarum S A 940 Pleospora herbarum S “Chytri diomycota” 633 Olpidium brassicae P 110 Trypethelium sp. L 28 Entomophthora muscae A 274 Dothidea sambuci P “Z ygomycota” Ascomycota : 137 Conidiobolus cor onatus S A 921 Dothidea insculpta S Dothideomycetes 19 Physoderma maydis P 939 Capnodium coffeae P 18 Coelomomyces stegomyiae A 355 Dendr ographa minor L A scomycota: 300 Allomyces arbusculus S 126 Roccella fuciformis L 80 Simonyella variegata L A rthoniomycetes 20 Rhizoclosmatium sp. S 24 Polychytrium aggregatum S 148 Cheilymenia stercor ea S 27 Cladochytrium replicatum S 62 Scutellinia scutellata S 21 Batrachochytr ium dendr obatidis A 100/94 “Chytridiomycota” 65 Aleur ia aurantia S 689 Rhizophydium macroporosum S 949 Pyronema domesticum S 43 Rhizophlyctis rosea S 50 Sarcoscypha coccinea S 182 Spizellomyces punctatus S 152 Caloscypha fulgens S Ascomycota : 635 Synchytr ium macrosporum P 176 Gyromitr a californica S Pezizomycetes 25 Monoblepharella sp. S 179 Disciotis sp. S 26 H yalor aphidium curvatum S 60 Morchella aff. esculenta S 638 Neocallimastix sp. ? 66 Helvella compr essa S 1068 Encephalitozoon cuniculi A 181 Ascobolus crenulatus S Microspor idia 1089 Antonospora locustae A 507 Peziza vesiculosa S 297 Rozella allomycis Y “Chytri diomycota” 100/93 71 Peziza pr oteana S Caenorhabditis elegans H 905 Orbilia vinosa S Ascom ycota: Orbiliomycetes Ciona intestinalis H 906 Orbilia auricolor S Metazoa Homo sapiens H 1069 Saccharomyces cer evisiae S Drosophila melanogaster H 1070 Saccharomyces castellii S Choanoflagellida Monosiga brevicollis H 1073 Candida glabrata A Mycetozoa Dictyostelium discoideum H 1071 Kluyveromyces waltii S C ryptospor idium parvum A Apicomplexa 1072 Ashbya gossypii P 100/94 Ascomycota: Toxoplasma gondii A 1075 Kluyveromyces lactis S Phytophthora sojae P Saccharomycotina 1074 Candida albicans A Stramenopiles Thalassiosira pseudonana O to basal 1269 C andida tropicalis A Rhodophyta Cyanidioschyzon merolae O 1270 Candida guilliermondii A lineages Arabidopsis thaliana O 1077 Debaryomyces hansenii S Viridiplantae Populus trichocarpa O 1268 Candida lusitaniae A Oryza sativa O 1076 Yarrow ia lipolytica S Chlamydomonas reinhar dtii O 1199 Schizosaccharomyces pombe S Ascomycota: 265 Taphr ina wiesneri P 266 Protomyces inouyei P Taphrinomycotina 100/98 0.05 substitutions/site 1192 Pneumocystis carinii A
  10. 10. Mycologia 98(6) 2006: 1. James et al. “Chytridiomycota” 2. White et al. “Zygomycota” 3. Redecker & Rabb Glomeromycota 4. Aime et al. Pucciniomycotina 5. Begerow et al. Ustilaginomycotina 6. Hibbett Agaricomycotina 7. Larsson et al. Hymenochaetales 8. Moncalvo et al. Cantharellales 9. Hosaka et al. Phallomycetidae 10. Miller et al. Russulales 11. Binder & Hibbett Boletales 12. Matheny et al. Agaricales 13. Sugiyama et al. Ascomycota 14. Suh et al. Saccharomycetales 15. Spatafora et al. Pezizomycotina 16. Hansen & Pfister Pezizomycetes 17. Schoch et al. Dothideomycetes 18. Geiser et al. Eurotiomycetes 19. Wang et al. Leotiomycetes 20. Zhang et al. Sordariomycetes 21. Miadlikowska et al. Lecanoromycetes Papers citing AFTOL
  11. 11. P. Matheny et al. MPE 2007. Data: 146 OTUs, five genes: nuc-lsu rDNA nuc-ssu rDNA nuc 5.8S rDNA tef1, rpb2 Total: 8671 bp
  12. 12. Agaricales P. Matheny et al. MPE 2007. BP Boletales BP Data: 146 OTUs, five genes: BP BP nuc-lsu rDNA Atheliales B NA nuc-ssu rDNA BP nuc 5.8S rDNA tef1, rpb2 Russulales Total: 8671 bp B BP Thelephorales B BP Analyses/Support: B Bayesian analysis Agaricomycetes BP Polyporales B of all-nucleotide dataset B B = post. prob. = 1.0 B Hymenochaetales BP Parsimony bootstrap of BP rDNA nucleotide/protein BP Corticiales BP amino acid dataset: P = 70-89% BP BP P > 90% Trechisporales BP BP Phallomycetidae U BP st BP Auriculariales ila gi no U BP B re Cantharellales di my c n AS om otin Sebacinales BP y a C O cot i M YC na BP Dacrymycetes O TA NA Tremellomycetes
  13. 13. 107 recent studies (1999-2007) on individual clades of Agaricomycetes Aanen et al. (2000), de Arruda et al. (2003), Binder et al. (2001), Boyle et al. (2006), Callac et al. (2005), Agaricales Challen et al. (2003), Chapela and Garbelotto (2004), Coetzee et al. (2000, 2001, 2002, 2003, 2005), Dentinger et 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 and Raccabruna (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) Bakker et al. (2004), Binder and Bresinsky (2002), Bresinksky et al. (1999), Den Bakker et al. (2004), Grubisha Boletales et 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) Henkel et al. (2000), E. Larsson et al. (2003), E. Larsson and Hallenberg (2001), Lickey et al. (2002), Miller et Russulales al. (2001, 2002), Nuytinck et al. (2004), Wu et al. (1999), Lebel et al. (2004), Miller et al. (2007) Decock et al. (2005), Fischer and Binder (2004), Geslebin et al. (2004), Paulus et al. (2002), Redberg et al. Hymenochaetales (2003), Wagner and Fischer (2001, 2002a, 2002b), Larsson et al. (2007) Dai et al. (2006), De Koker et al. (2003), Desjardin et al. (2004), Hong et al. (2002), Hong and Jung (2004), Kim Polyporales et al. (2005), Ko et al. (2001), Krüger (2004), Nilsson et al. (2003), Wang et al. (2004) Dahlman et al. (2000), Dunham et al. (2003),Gonzalez et al. (2001), Kottke et al. (2003), Moncalvo et al. (2007) Cantharellales Eberhardt et al. (1999), Kernaghan et al. (2002), Lilleskov et al. (2002) Atheliales DePriest et al. (2005), Diederich et al. (2003), Matsuura et al. (2000), Sikaroodi et al. (2001) Corticiales Kõljalg et al. (2000, 2001, 2002) Thelephorales Geml et al. (2005), Humpert et al. (1999), Hosaka et al. (2007) Phallomycetidae Weiss et al. (2004), Selosse et al. (2002) Sebacinales K.-H. Larsson (2001) Trechisporales
  14. 14. Most inclusive phylogenetic analyses of Agaricomycetes J. M. Moncalvo et al. 2002. One hundred and seventeen clades of euagarics (Agaricales) Data: nuc-lsu rDNA No. seqs. sampled 877 No. species sampled 877 Nuc-lsu rRNA > 800 bp in GenBank 2309 Species in GenBank 2429 M. Binder et al. 2005. The phylogenetic distribution of resupinate forms across the major clades of homobasidiomycetes (Agaricomycetes) Data: mt/nuc lsu/ssu rDNA No. seqs. sampled 656 No. species sampled 640 Nuc-lsu rRNA > 800 bp in GenBank 3940 Species in GenBank 4842 M. Binder and D. S. Hibbett. 2006. Molecular systematics and biological diversification of Boletales. Data: nuc lsu rDNA No. seqs. sampled 435 No. species sampled 301 Nuc-lsu rRNA > 800 bp in GenBank 469 Species in GenBank 442
  15. 15. I. Progress in phylogenetic reconstruction in Fungi/Agaricomycetes II. Progress in classification in Agaricomycetes III. Automated Phylogenetic Taxonomy in Agaricomycetes IV. Conclusions and future directions
  16. 16. Hawksworth et al. (1995) Kirk et al. (2001) Holobasidiomycetidae Tremellomycetidae p.p.* Agaricales Tulasnellales Boletales Agaricomycetidae* Bondarzewiales Agaricales* Cantharellales Auriculariales Ceratobasidiales Boletales* Cortinariales Cantharellales Dacrymycetales Ceratobasidiales Fistulinales Dacrymycetales* Ganodermatales Hymenochaetales Gautieriales Phallales Gomphales Polyporales* Hericiales Russulales* Hymenochaetales Thelephorales Hymenogastrales Lachnocladiales *non-monophyletic Lycoperdales *not Homobasidiomycetes Melanogastrales Nidulariales Phallales Poriales Russulales Schizophyllales Sclerodermatales Stereales Thelephorales Tulasnellales Tulostomatales
  17. 17. quot;The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.quot; http://www.ncbi.nlm.nih.gov:80/Taxonomy/taxonomyhome.html
  18. 18. GenBank (2006) Kirk et al. (2001) Homobasidiomycetes Tremellomycetidae p.p.* Agaricales Tulasnellales Aphyllophorales Agaricomycetidae* Boletales Agaricales* Cantharellales Auriculariales Ceratobasidiales Boletales* Echinodontiaceae Cantharellales Gautieriales Ceratobasidiales Geastrales Dacrymycetales* Hericiales Hymenochaetales Hymenochaetales Phallales Hymenogastrales Polyporales* Lycoperdales Russulales* Melanogastrales Thelephorales Nidulariales Phallales Stereales Thelephorales Tulasnellales Tulostomatales
  19. 19. GenBank (2006) GenBank (2007) Homobasidiomycetes Agaricomycetes Agaricales Agaricales Aphyllophorales Atheliales Boletales Auriculariales Cantharellales Boletales Ceratobasidiales Cantharellales Echinodontiaceae Corticiales Gautieriales Gloeophyllales Geastrales Hymenochaetales Hericiales Phallomycetidae Hymenochaetales Polyporales Hymenogastrales Russulales Lycoperdales Sebacinales Melanogastrales Thelephorales Nidulariales Trechisporales Phallales Stereales Thelephorales Tulasnellales Tulostomatales
  20. 20. GenBank (2006) GenBank (2007) Homobasidiomycetes Agaricomycetes Agaricales Agaricales Aphyllophorales Atheliales Boletales Auriculariales Cantharellales Boletales Ceratobasidiales Cantharellales Echinodontiaceae Corticiales Gautieriales Gloeophyllales Geastrales Hymenochaetales Hericiales Phallomycetidae Hymenochaetales Polyporales Hymenogastrales Russulales Lycoperdales Sebacinales Melanogastrales Thelephorales Nidulariales Trechisporales Phallales Stereales Thelephorales Tulasnellales Tulostomatales
  21. 21. http://www.abc.net.au/science/scribblygum/
  22. 22. http://www.mykoweb.com/CAF/index.html
  23. 23. 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)
  24. 24. 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 accurate classification of homobasidiomycetes? A dramatic increase in the rate of species discovery, including sequence-based  discovery and description Automated integration of emerging data into comprehensive trees  Automated translation of trees into classifications 
  25. 25. I. Progress in phylogenetic reconstruction in Fungi/Agaricomycetes II. Progress in classification in Agaricomycetes III. Automated Phylogenetic Taxonomy in Agaricomycetes IV. Conclusions and future directions
  26. 26. Acquisition and Screening
  27. 27. Alignment and Analysis
  28. 28. Backbone monophyly constraint 220 species, based on multi-locus analyses
  29. 29. Heuristic search strategy: 1 2 Load General Constraint as backbone Create General Constraint tree monophyly constraint. (220 species, based on multilocus Add new sequences to dataset and tree and analyses). perform branch swapping (TBR, 5 hours). Save new tree as Temporary Constraint. 3 4 Load Temporary Constraint as backbone Load General Constraint as backbone. monophyly constraint. Use (new) Temporary Constraint as a starting Add new sequences to dataset and tree, but tree for branch swapping (TBR, 5 hours). perform no swapping. Save new tree as Temporary Constraint. Save new tree as Temporary Constraint Go to 3. (i.e., overwrite file).
  30. 30. Classification
  31. 31. Parsing a node-based phylogenetic taxon definition: “Taxon X is the least-inclusive clade that contains D and H”. D and H are “specifiers” A B C E D F G H A B C D E F G H 1 2 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
  32. 32. I. Progress in phylogenetic reconstruction in Fungi/Agaricomycetes II. Progress in classification in Agaricomycetes III. Automated Phylogenetic Taxonomy in Agaricomycetes IV. Conclusions and future directions
  33. 33. 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--can be automated. Phylogenetic definitions of taxa (ranked or unranked) are essential for this 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 of emerging data, including Fungi and all groups of “microbes”
  34. 34. 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
  35. 35. Ryan Twomey*, Pete Stein* R. Henrik Nilsson J. P. Burke* Not shown: Moran Shonfeld*, Mario Fonseca*, Thomas Heider*, Daniel Menard* Brandon Gaytán* Marc Snyder* *undergraduates Janine Costanzo*

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