#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on April 19, 2024; 5:30 GMT TreeBASE (cc) 1994-2008 Study reference: Chaverri P., & Samuels G.J. 2013. Evolution of host affiliation and substrate preference in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology. Evolution, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13888] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=144; TAXLABELS Hypocrea_aeruginea Hypocrea_alcalifuscescens Hypocrea_alni Hypocrea_alutacea Hypocrea_americana Hypocrea_andinensis Hypocrea_avellanea Hypocrea_chionea Hypocrea_crystalligena Hypocrea_dacrymycella Hypocrea_danica Hypocrea_decipiens Hypocrea_delicatula Hypocrea_epimyces Hypocrea_eucorticioides Hypocrea_flaviconidia Hypocrea_fomiticola Hypocrea_leucopus Hypocrea_lutea Hypocrea_megalocitrina Hypocrea_microcitrina Hypocrea_moravica Hypocrea_neorufa Hypocrea_nigrovirens Hypocrea_nybergiana Hypocrea_parepimyces Hypocrea_parmastoi Hypocrea_patella Hypocrea_phyllostachydis Hypocrea_pillulifera Hypocrea_placentula Hypocrea_protopulvinata Hypocrea_pseudostraminea Hypocrea_psychrophila Hypocrea_pulvinata Hypocrea_rodmanii Hypocrea_semiorbis Hypocrea_seppoi Hypocrea_spinulosa Hypocrea_straminella Hypocrea_subalpina Hypocrea_sulawesensis Hypocrea_sulfurea Hypocrea_tawa Hypocrea_voglmayrii Hypomyces Sphaerostilbella Trichoderma_aggressivum Trichoderma_amazonicum Trichoderma_arundinaceum Trichoderma_asperelloides Trichoderma_asperellum Trichoderma_atrogelatinosum Trichoderma_atroviride Trichoderma_aureoviride Trichoderma_austrokoningii Trichoderma_brevicompactum Trichoderma_brunneoviride Trichoderma_candidum Trichoderma_caribbaeum Trichoderma_catoptron Trichoderma_ceraceum Trichoderma_ceramicum Trichoderma_cerinum Trichoderma_chlorosporum Trichoderma_chromospermum Trichoderma_cinereoflava Trichoderma_cinnamomeum Trichoderma_citrinoviride Trichoderma_costaricensis Trichoderma_crassum Trichoderma_cremeum Trichoderma_cuneisporum Trichoderma_dingleyae Trichoderma_dorotheae Trichoderma_erinaceus Trichoderma_estonicum Trichoderma_evansii Trichoderma_fertile Trichoderma_gamsii Trichoderma_gelatinosum Trichoderma_ghanense Trichoderma_hamatum01 Trichoderma_hamatum02 Trichoderma_hamatum03 Trichoderma_harzianum01 Trichoderma_harzianum02 Trichoderma_harzianum03 Trichoderma_harzianum04 Trichoderma_harzianum05 Trichoderma_harzianum06 Trichoderma_harzianum07 Trichoderma_harzianum08 Trichoderma_harzianum09 Trichoderma_harzianum10 Trichoderma_helicum Trichoderma_intricatum Trichoderma_koningii Trichoderma_koningiopsis Trichoderma_lieckfeldtiae Trichoderma_longibrachiatum Trichoderma_longipile Trichoderma_martiale Trichoderma_melanomagnum Trichoderma_minutisporum Trichoderma_novaezelandiae Trichoderma_oblongisporum Trichoderma_ovalisporum01 Trichoderma_ovalisporum02 Trichoderma_pachybasioides Trichoderma_parapiluliferum Trichoderma_parareseei Trichoderma_parestonicum Trichoderma_paucisporum Trichoderma_petersenii Trichoderma_pleuroticola Trichoderma_pleurotum Trichoderma_protrudens Trichoderma_pseudokoningii Trichoderma_pubescens Trichoderma_reesei Trichoderma_rogersonii Trichoderma_rossicum Trichoderma_saturnisporum Trichoderma_sinuosum Trichoderma_spirale01 Trichoderma_spirale02 Trichoderma_spirale03 Trichoderma_stilbohypoxyli Trichoderma_strictipile Trichoderma_strigosum Trichoderma_stromaticum Trichoderma_surrotundum Trichoderma_thailandicum Trichoderma_thelephoricola Trichoderma_theobromicola Trichoderma_tomentosum Trichoderma_turrialbense Trichoderma_velutinum Trichoderma_victoriensis Trichoderma_virens Trichoderma_virescentiflava Trichoderma_viride Trichoderma_viridescens ; END; BEGIN TREES; TITLE 'Maximum Likelihood, multilocus result'; LINK TAXA = Taxa; TREE Best_ML_tree = [&R] (Sphaerostilbella:0.24898397,((((((Hypocrea_crystalligena:0.10071914,Hypocrea_megalocitrina:0.0027856):0.02575729,Hypocrea_psychrophila:0.07026088):0.04254849,(((Hypocrea_americana:1.0E-8,(Hypocrea_protopulvinata:0.00657285,Hypocrea_pulvinata:0.00672979):0.00435999):0.01780547,Hypocrea_pseudostraminea:0.02473138):0.01144112,(((Hypocrea_decipiens:0.07036936,Hypocrea_eucorticioides:0.01792213):0.01650497,Hypocrea_microcitrina:0.00976545):0.0158276,(Hypocrea_sulfurea:0.00270704,Trichoderma_victoriensis:0.00704462):0.03322119):0.00669528):0.05325916):0.01804319,(((((Hypocrea_voglmayrii:0.0573716,(Hypocrea_neorufa:0.03411767,(((Trichoderma_rogersonii:0.01772506,Trichoderma_austrokoningii:0.03301357):0.01102887,(Trichoderma_strigosum:0.02635164,(Trichoderma_erinaceus:0.02645443,(((Trichoderma_atroviride:0.01650132,(Trichoderma_viride:0.01027961,Trichoderma_martiale:0.00997208):0.00250538):7.5193E-4,((Trichoderma_viridescens:0.01432431,Trichoderma_gamsii:0.01512006):8.4162E-4,Trichoderma_stilbohypoxyli:0.02972879):0.0012712):0.0024389,(((((Trichoderma_ovalisporum01:0.00151118,Trichoderma_ovalisporum02:0.00169971):0.0083287,(((Trichoderma_caribbaeum:0.00677735,Trichoderma_dorotheae:0.00537002):0.00322629,Trichoderma_petersenii:0.01183202):0.00218084,Trichoderma_intricatum:0.01679151):9.8195E-4):0.0010745,(Trichoderma_koningiopsis:0.0104912,Trichoderma_koningii:0.0122227):0.00152016):0.00410649,Trichoderma_dingleyae:0.01265232):0.00816446,Hypocrea_chionea:0.02116275):0.00711665):0.00389789):0.00525939):0.00238924):0.01513557,((((Trichoderma_paucisporum:0.01223833,Trichoderma_theobromicola:0.00545909):0.01137505,(((Trichoderma_hamatum01:0.00381667,(Trichoderma_hamatum03:0.00102478,Trichoderma_hamatum02:0.00442671):0.00100974):0.01147164,(Trichoderma_pubescens:0.00798398,Trichoderma_evansii:0.01015653):0.00409358):0.00224736,Hypocrea_flaviconidia:0.02697431):0.00593061):0.00251281,(Trichoderma_asperellum:0.00730036,Trichoderma_asperelloides:0.00743257):0.01923806):0.00311162,Trichoderma_lieckfeldtiae:0.02560214):0.00485449):0.00867759):0.01579192):0.03697623,((Trichoderma_minutisporum:0.02878186,(Hypocrea_pillulifera:0.0325374,(Trichoderma_pachybasioides:0.02345657,Trichoderma_parapiluliferum:0.0190534):0.01638366):0.00501127):0.00416763,(Hypocrea_alutacea:0.06107639,Hypocrea_placentula:0.02102544):0.00419796):0.00918773):0.01436487,(Hypocrea_leucopus:0.03622835,(Hypocrea_nybergiana:0.02501474,Hypocrea_seppoi:0.02483508):0.0071626):0.02397511):0.01602019,((Hypocrea_lutea:0.01680884,Trichoderma_melanomagnum:0.05863191):0.05257448,((Trichoderma_brevicompactum:0.03342462,(Trichoderma_turrialbense:0.01133016,(Trichoderma_arundinaceum:0.01881491,Trichoderma_protrudens:0.01667593):0.00447026):0.00989566):0.01841268,Hypocrea_rodmanii:0.0253131):0.00956467):0.01057707):0.0028791,(Hypocrea_subalpina:0.14969433,(Hypocrea_avellanea:0.07887768,Hypocrea_delicatula:0.04919956):0.02735826):0.03735793):0.00208872):0.01719353,(((Trichoderma_novaezelandiae:0.04380939,((Trichoderma_citrinoviride:0.01483993,Trichoderma_longibrachiatum:0.01108648):0.01148854,(Hypocrea_andinensis:0.03408269,((Trichoderma_ghanense:0.02152728,(Trichoderma_pseudokoningii:0.00864888,Trichoderma_saturnisporum:1.0E-8):0.01863226):0.00235218,(Trichoderma_reesei:0.00888584,Hypocrea_patella:0.15372062,Trichoderma_parareseei:0.00545345):0.02836446):0.00647286):0.00596444):0.02867635):0.07874816,((Trichoderma_rossicum:0.01182735,Trichoderma_stromaticum:0.02141303):0.0263992,(Trichoderma_helicum:0.06717731,(((Trichoderma_crassum:0.00253379,Trichoderma_virens:0.00560443):0.02312982,(Trichoderma_catoptron:0.02578801,(((Trichoderma_cerinum:0.00954015,Trichoderma_tomentosum:0.00629542):0.00532542,(Trichoderma_atrogelatinosum:1.0E-8,Trichoderma_ceraceum:1.0E-8):0.01830339):0.00593438,((Trichoderma_cinnamomeum:0.02438837,(Trichoderma_velutinum:0.01252735,Hypocrea_straminella:0.01230899):0.0041542):0.00824212,((((Trichoderma_pleuroticola:0.01176545,(Trichoderma_amazonicum:0.00473883,Trichoderma_pleurotum:0.00531276):0.00257239):0.00881762,(Trichoderma_aggressivum:0.01259138,((Hypocrea_alni:0.01186243,(Hypocrea_tawa:0.01482169,Hypocrea_parepimyces:0.01686269):0.0014403):0.00299101,Hypocrea_epimyces:0.01401495):0.00351772):0.00187879):0.0060413,(((Trichoderma_harzianum02:0.01201091,Trichoderma_harzianum03:0.01089153):0.00253006,(((Trichoderma_harzianum06:0.00783346,(Trichoderma_harzianum01:0.01051592,(Trichoderma_harzianum07:0.0097506,Trichoderma_harzianum04:0.00284298):0.00811605):9.2602E-4):0.00378146,(Trichoderma_harzianum05:0.01166238,Trichoderma_harzianum09:0.00984129):0.00108162):0.00130937,Trichoderma_harzianum08:0.01116854):0.00163139):0.0012958,Trichoderma_harzianum10:0.01510125):0.0096108):0.00394243,(Hypocrea_dacrymycella:0.03478044,Trichoderma_brunneoviride:0.02541627):0.009329):0.00107845):0.00361691):0.00399653):0.00879925):0.00396224,((Hypocrea_nigrovirens:0.06436995,((Trichoderma_gelatinosum:0.03238468,Trichoderma_chromospermum:0.07144594):0.00892138,Hypocrea_sulawesensis:0.08398376):0.01538996):0.00882035,(Hypocrea_phyllostachydis:0.04576274,(((((((Trichoderma_sinuosum:0.00769098,Trichoderma_surrotundum:0.0062366):7.1375E-4,Trichoderma_cremeum:0.00418284):0.00722611,Trichoderma_thelephoricola:0.01349293):0.00285049,Trichoderma_chlorosporum:0.0068472):0.01326901,Trichoderma_costaricensis:0.03743345):0.01555447,((Trichoderma_aureoviride:0.04725425,Trichoderma_candidum:0.03091657):0.0215653,(Hypocrea_aeruginea:0.05131041,(Hypocrea_spinulosa:0.01765362,Hypocrea_danica:0.04011238):0.02058575):0.02873167):0.00954416):0.00786832,(Trichoderma_virescentiflava:0.00454757,Trichoderma_thailandicum:0.00853372):0.03246533):0.01954743,((Trichoderma_ceramicum:0.00499312,(Trichoderma_estonicum:0.00608369,Trichoderma_parestonicum:0.00767362):0.00256609):0.01550199,((Trichoderma_spirale01:0.05527208,(Trichoderma_spirale03:0.00993731,Trichoderma_spirale02:0.0086408):0.00367235):0.02325138,((Trichoderma_fertile:0.00287352,Trichoderma_strictipile:7.8077E-4):0.02457009,(Trichoderma_cuneisporum:0.00586757,Trichoderma_longipile:0.00425735):0.01020507):0.00351065):0.00436822):0.00331088):0.00316911):5.8721E-4):0.0024518):0.00737636):0.00641717):0.0057807,(Hypocrea_semiorbis:0.02841395,((Trichoderma_oblongisporum:0.00948325,Hypocrea_moravica:0.02219676):0.00811345,Hypocrea_fomiticola:0.02709941):0.00347725):0.01831801):0.01546659):0.03040345,(Hypocrea_parmastoi:0.12000149,(Trichoderma_cinereoflava:0.09178458,Hypocrea_alcalifuscescens:0.11198549):0.09089744):0.02474404):0.06357668,Hypomyces:0.23537421); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr60735] END;