1. Combined analysis Bayesian consensus 0.1 Neurospora crassa Chaetomium globosum 100 Saccharomyces cerevisiae 100 Pneumocystis carinii Schizosaccharomyces pombe 100 Coprinopsis cinerea Phanerochaete chrysosporium 100 Cryptococcus neoformans Ustilago maydis 100 Glomus mosseae Glomus intraradices 100 Scutellospora heterogama 100 Paraglomus occultum Geosiphon pyriforme 100 Rhizopus stolonifer Cokeromyces recurvatus 100 Phycomyces blakesleeanus 100 Umbelopsis ramanniana 100 Endogone pisiformis Endogone lactiflua 100 Mortierella verticillata Mortierella sp. 100 Smittium culisetae Furculomyces boomerangus 100 Coemansia reversa Orphella haysii 100 97 Spiromyces aspiralis 100 Dimargaris bacillispora 100 Kuzuhaea moniliformis Piptocephalis corymbifera 100 Rhopalomyces elegans 100 Entomophthora muscae Conidiobolus coronatus Basidiobolus ranarum Olpidium brassicae Allomyces arbusculus Catenophlyctis sp. 100 Coelomomyces stegomyiae 100 Physoderma maydis 100 Rhizophydium brooksianum Rhizophlyctis harderi 100 Rhizophydium macroporosum 100 Rhizophydium sphaerotheca 100 Batrachochytrium dendrobatidis Entophlyctis helioformis 100 Spizellomyces punctatus Powellomyces sp. 100 Gaertneriomyces semiglobiferus 100 Rhizophlyctis rosea Catenomyces sp. Polychytrium aggregatum Karlingiomyces sp. 100 99 Rhizoclosmatium sp. chytrid 187 100 Rhizophydium sp. 354 Phlyctochytrium planicorne 100 Synchytrium decipiens Synchytrium macrosporum 100 Cladochytrium replicatum Nowakowskiella sp. 100 Chytriomyces angularis 98 100 Monoblepharella sp. Oedigoniomyces sp. 100 Hyaloraphidium curvatum 100 99 Neocallimastix sp. 99 Encephalitozoon cuniculi Antonospora locustae 100 Rozella sp. 100 Rozella allomycis 100 Caenorhabditis elegans Drosophila melanogaster 100 Ciona intestinalis 100 Monosiga brevicollis 100 Phytophthora sojae Thalassiosira pseudonana 100 Dictyostelium discoideum Arabidopsis thaliana Oryza sativa 100 Dikaryofungi 100% Glomeromycota 100% fungi is Microsporidia 96 100 98 100 99 100 fungi is Blastocladiales Chytridiales Spizellomycetales Chytridiales Monoblepharidiales Neocallimastigales Entomophthorales Zoopagales Dimargaritales Harpellales + Kickxellales (and presumably Asellariales) Mortierellales Endogonales Mucorales

2. Basidiomycota Ascomycota Glomeromycota Mucorales+Endogonales Zoopagales Kickxellales+Harpellales+ Dimargaritales Entomophthorales Neurospora crassa Chaetomium globosum 100 Saccharomyces cerevisiae 100 Pneumocystis carinii Schizosaccharomyces pombe 100 Coprinopsis cinerea Phanerochaete chrysosporium 100 Cryptococcus neoformans Ustilago maydis 100 Glomus mosseae Glomus intraradices 100 Scutellospora heterogama 100 Paraglomus occultum Geosiphon pyriforme 100 Rhizopus stolonifer Cokeromyces recurvatus 100 Phycomyces blakesleeanus 100 Umbelopsis ramanniana 100 Endogone pisiformis Endogone lactiflua 100 Mortierella verticillata Mortierella sp. 100 Smittium culisetae Furculomyces boomerangus 100 Coemansia reversa Orphella haysii 100 97 Spiromyces aspiralis 100 Dimargaris bacillispora Kuzuhaea moniliformis Piptocephalis corymbifera 100 Rhopalomyces elegans 100 Entomophthora muscae Conidiobolus coronatus Basidiobolus ranarum Olpidium brassicae 96 100 98 100

3. Blastocladiales Chytridiales Spizellomycetales Monoblepharidales Microsporidia Allomyces arbusculus Catenophlyctis sp. 100 Coelomomyces stegomyiae 100 Physoderma maydis 100 Rhizophydium brooksianum Rhizophlyctis harderi 100 Rhizophydium macroporosum 100 Rhizophydium sphaerotheca 100 Batrachochytrium dendrobatidis Entophlyctis helioformis 100 Spizellomyces punctatus Powellomyces sp. 100 Gaertneriomyces semiglobiferus 100 Rhizophlyctis rosea Catenomyces sp. Polychytrium aggregatum Karlingiomyces sp. 100 99 Rhizoclosmatium sp. chytrid 187 100 Rhizophydium sp. 354 Phlyctochytrium planicorne 100 Synchytrium decipiens Synchytrium macrosporum 100 Cladochytrium replicatum Nowakowskiella sp. 100 Chytriomyces angularis 98 100 Monoblepharella sp. Oedigoniomyces sp. 100 Hyaloraphidium curvatum 100 99 Neocallimastix sp. 99 Encephalitozoon cuniculi Antonospora locustae 100 Rozella sp. 100 Rozella allomycis 100 Caenorhabditis elegans Drosophila melanogaster 100 Ciona intestinalis 100 Monosiga brevicollis 100 Chytridiales 100 99