Aphelidiomycota Microsporidia Opisthosporidia Rozellomycota Fungi Blastocladiomycota Chytridiomycota Chytridiomyceta Monoblepharidomycota Neocallimastigomycota Zoopagomycota Kickxellomycotina Entomophthoromycotina Zoopagomycotina Glomeromycotina Mucoromycota Mucoromycotina Mortierellomycotina Entorrhizomycota Taphrinomycotina Saccharomycotina Ascomycota Dikarya Pezizomycotina Agaricomycotina+ Wallemiomycotina Pucciniomycotina Basidiomycota Ustilaginomycotina Supplementary Figure 1. Current consensus of evolutionary relationships of major lineag- es within kingdom Fungi. Phyla not sampled in this study are shown in red font. 1 Full matrix Rogue_taxa_removal (1,672 taxa/290 (1,639 taxa) genes) 12 LB_taxa_removal 2 Subset_Dikarya_taxa (1,649 taxa) (540 taxa) 11 Top100_low Top100_DVMC Top100_long_length Top100 _low_LB Top_100 _low_RCFV Top100_slow evolving Top100_complete Top100_high_ABS saturation 3 4 5 6 7 8 9 10 Supplementary Fig. 2. Relationships between the 12 data matrices analyzed in this study. Data matrices with taxon-based ltering are in - purple boxes and those with gene-based ltering are in green boxes. The number for each data matrix corresponds to its number in the Methods - section. See Methods for further information on each data matrix and ltering strategy used to generate it. d u s e us nsis icola us n lis s rouxii s e ubayanus s i nsis alensis nii bzhanskii o ii mrak a r astoris retoriensis rtiniae la hilus s bailii s e romyc a ens l ispora blattae ispora phaffii nia turice romyces e romyces mikatae liftii ens nia solico is r singula a aspor i a populi mentans a n atae ueomyces sinensis nii ns anderwaltozyma polyspora orulaspora delbrueckii orulaspora p lipsoid icroel m spora a orul orulaspora franciscae spora maleeae a orul etrapisispora iriomotensis etrapis etrapis etrapisispora namnaonensis etrapisispora fleetii olischiana na florenti ra ulaspo Zygotor ulaspo Zygotor Y T T T T s u bispor s e romyc a Zygosacch T T T ensis a kombuch s e romyc a Zygosacch V romyc a Zygosacch T Zygosacch a fantastica nom n nom fantastica a e Lachanc T s i dasiens a e Lachanc T otensis r lanza a e Lachanc sii r meye a e Lachanc Candida castellii Nakaseomyces bacillispor a montana a d nsis e quebec a e Lachanc a nothofagi a e Lachanc Candida bracarensis Candida glabrata Nakaseomyces delphensis a waltii a e Lachanc s n tolera o therm a e Lachanc ntina a mir a e Lachanc Candida nivariensis Saccharomyces uvarum Saccha anishii a cidri a e Lachanc Saccharomyces arbor tati n ferme a e Lachanc anderk a kluyveri a e Lachanc Saccharomyces kudriavzevii ri e ac shbya A gossypii m otheciu m re E Saccha Saccharomyces paradoxus riae a cymbal m otheciu m Ere um d sinecau m otheciu m Ere ozyma xylosa Saccharomyces cerevisiae inofer coryli m otheciu m Ere Naumovozyma dairene Naumovozyma castellii ctis a l omyces r luyve K Kazachstania viticola omyces d omyces r luyve K Kazachstania africana arxia m omyces r luyve K stuarii e a omyces r luyve K a xylosilytica a r Kazachstania spencerorum alophila Kazachstania rosi ri uvarum a aspor i Hansen ntiae o clerm a aspor i Hansen Kazachstania kunashirensis Kazachsta ii d mon r illie u pseudog a aspor i Hansen myces siamensis aiens m misu a r indne l Kazachstania ma nsis e hatyai ra e Kloeck agataella pseudop Hansen Kazachstania intestina m u quercu a li u pop ettozyma n Kazachstania bromeliacearum agataell rkliftii valbyensis a aspor i Hansen Kazachstania naganishii myces hawaiiensis vineae a aspor i Hansen Kazachstania taianensis la i osmoph a aspor i Hansen Kazachstania yakushimaensis a orba a d Candi Kazachstania transva ozyma erans l thermoto s e Phaffomyc rmenta Kazachstania siamensis s opuntiae s e Phaffomyc Kazachstania unispora s i antillens s e Phaffomyc ricii s bovis s e momyc a ickerh Candi Kazachstania aerKazachstaobia 3 4 -22 B Y NRRL sp. s e momyc a ickerh tensis a pr ettozyma n Bar ria a salic ettozyma n ar B Pachysolen tannop s canadensis s e momyc a ickerh onensis Peter aishia og s alni s e momyc a ickerh mae iiensis a haw ettozyma n Bar Peterozyma toletana Bar Nakazawaea holstii aishia m Nakazawaea peltata rosiae nica r califo ettozyma n Bar ntoma W Kom W Kom lactativora a rmi e W Komagataella phaffii W Citero da arab Cyber Citeromyces matritensis rae u macl a r indne l Cyber Citero malus rae a vartiova a d Candi Kur ii n jadi a r indne l Cyber Kur s u saturn a r indne l Cyber Kuraishia capsulata a suaveo a r indne l Cyber Candida boidi kii a mr a r indne l Cyber Ogataea methylivora icana r ame a r indne l Cyber uxellensis Ogataea ramenticola ma pseudov ncae i i mycetang a d Candi ensis r hampshi s e momyc a ickerh cqiae r Candida succiphila nii o peters a r indne l Cyber Ogataea nag ma vande s u anomal s e momyc a ickerh i i fabian a r indne l Cyber s ciferrii s e momyc a ickerh Ogataea pilisensis indne l Cyber Ogataea nitratoaversa ma oreg a freyschussii a d Candi Candi W Ogataea treh W Ogataea methanolica W ma phile Ogataea trehaloabstin ethioni m a era m tar S Ogataea populialbae licola a stellim a d Candi Ogataea zsoltii rcuum e qu era m tar S opachyd r Ogataea gluc abiesophila osae r ponde a d Candi Ogataea hen ns e rubesc a e Ascoid Ogataea pini a asiatica a e Ascoid Ogataea nonfe a ga n mala sis p omyco r Saccha Ogataea minuta is r capsula sis p omyco r accha S rosiozy Ogataea koda rmi e opachyd r Spo Ogataea philodend rosiozyma monospora po S rosiozy Ogataea parapolymorpha a silvae losa ecoeti l hy scoidea a Allo Ogataea polymorpha rosiozyma amb ensis i peor trys o Blastob Ambrosiozyma maleeae icana r ame trys o Blastob Ambrosiozyma kashinagacola cola i bomb a l s n menta r raffinosife trys o lastob B Ambrosiozy s n ivora n adeni trys o Blastob Amb a hagleri . elongata . tis n serpe trys o Blastob Amb trys nivea trys o Blastob . fulvescens . Amb evii ferans i prol trys o Blastob Amb gervanrija delftensisniozym ranifaciens aii n mokoe trys o lastob B Ambrosiozy gervanrija fluxuum a l muscico trys o Blastob Brettanomyces custersianus idus aea p euro a l tinsiel r rma e Spenc Brettanomyces ano scens e sifluor e ca siella n Didde Brettanomyces br um abitans h ligno a l mael a Sugiy Kre aensis n Zygoascus ofu Zygoascus Kre eyerae m Zygoascus ngensis u Marti nispora serradocipensis ticensis n salma a m aldozy w Groene a dome a l miel a ickerh Saturnispora mendo a apicola a l erel m tar S da sorboxy a versatilis a l miel a ickerh Saturnispor erel m Star a infanticola a l miel a ickerh Saturnispora saitoi W hidar a cacticola a l miel a ickerh Saturnispora zaruensis W Saturnispora dispora a occidentalis W Saturnispor a kudriavz W us m sper a tetr siomyces u Satur a norvegensis niensis ta a clav ochaete r unis m incom a d Candi Pichia terricola ensis n india a m Deakozy Candi asii s u albid scus a Dipod Pichia memb atus l genicu scus a Dipod Pichi m u candid m Geotrichu Pichi Sap Pichi da schatavii Magn lytica o lip wia o arr Pichia exigua is myces tepae myces o lhoven e Midd wia keel wia o arr Pichia heedii manieldala fragicleridarum Y mans r defo wia o arr Pichia nakasei Y gata l divu wia o arr Babjeviella inositovora aramus Y Cephaloascus alb da gorg la u bub wia o arr Y Cephaloascus fragrans da tamma nsenii Y Candi ensis i hispan a d Candi Kurtz r va fulvescens a i Nadson Candi lytica o casein a r ortispo 99 rosopid r va fulvescens a i Nadson Candida ascalap a acaciae i r gante a r ortispo T ri e starm a r ortispo Candi T Candiamadazyma scolyti T Y amadazyma tenuis ria a vin nopsis o rig a l todophi a nem a m Botryozy amadazyma philogaea s i iabil r va nopsis o rig Y T Y amadazyma nakazawaerozyma caribbica plophilus T Y rescens brius m mese yces m Lipo Candida athensensis ryomyces m yces arxii yces m Lipo Meyerozyma guillieerozymrmondii ryomyces nepalensis yces starkeyi yces m Lipo Candida carpophila ryomyces ha koae n konone yces m Lipo um Meye ryomyces fabryi i i njong e door yces m Lipo Mill ryomyces p nsis e suomi yces m Lipo Deba ryomyces subglobosus haga p oligo yces m Lipo Deba yces lipofer yces m Lipo Deba cus i japon yces m Lipo Deba eomyces carsonii us r octospo yces m ccharo a Schizos Deba ilus h cryop yces m ccharo a Schizos Deba e b pom yces m ccharo a chizos S eomyces castillae Pric icus n japo yces m ccharo a chizos S myces kruisii ebilis d ces lactucae ces Priceomyces medius bra u flavor na i ii n cari ocystis m neu P myces cretensis Priceomycesickerh haamia fluo etipori ina r mu ocystis m neu P Pric vecii o jir ocystis m Pneu ri e wiesn na i aphr meri W eunomyces gatunensis T ans m defor na i aphr T euno orus aphr T T euno T ina l popu na i aphr T T Suhomyces pyralidae omyces stipitis y m Proto Suhomyces tanzawameaeansisda la restingae laris u reg r Neolecta i Neolecta Suhomyces emberor rioi icata l comp la l aitoe S Suhomyces canberraensis longisp nulata n ugosoa r aria h Strop Aciculoconidium aculeatum teritium a subl ma o Hyphol Koda spora o micr ota i Phol Candi um r rospo d cylin ma o Hebel Kodamaea oh s i dilep us l Gymnopi is Scheffers inata g mar a n Galeri 83 Scheffersomyces lignosus niensisns e cyanescens e b Psilocy Spathaspora hagerdaliae acea r cylind cybe o Agr da corydali Spathaspora gorwiae ns e cyanesc olus e ana P romyces e Spathaspora passalidarum rioens rea e cin nopsis i Copr Spathaspora arborariae milentoma ayeri m stross nopsis i Copr Spathaspora gi lis i rcescib a m nopsis i Copr Candi da dubli nsis e dar r abe lla e sathyr P Lodde da albica icaceus m nellus i Copr Candida parapsilosis i mii us r bispo a amethystina a i Laccar o Candida orthopsilosis t r.