#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 May 19, 2024; 15:13 GMT TreeBASE (cc) 1994-2008 Study reference: Aguilera F., Mcdougall C., & Degnan B.M. 2013. Origin, evolution and classification of type-3 copper proteins: Lineage-specific gene expansions and losses across the Metazoa. BMC Evolutionary Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13985] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=179; TAXLABELS Agaricus_bisporus_tyr Amphimedon_queenslandica_tyr Anopheles_gambiae_tyr1 Anopheles_gambiae_tyr2 Anopheles_gambiae_tyr3 Anopheles_gambiae_tyr4 Anopheles_gambiae_tyr5 Anopheles_gambiae_tyr6 Anopheles_gambiae_tyr7 Anopheles_gambiae_tyr8 Anopheles_gambiae_tyr9 Aplysia_californica_Hc Aspergillus_aculeatus_tyr Aspergillus_nidulans_tyr1 Aspergillus_nidulans_tyr2 Bacillus_megaterium_tyr1 Bacillus_megaterium_tyr2 Bombyx_mori_tyr1 Bombyx_mori_tyr2 'Branchiostoma floridae tyr1/2a' 'Branchiostoma floridae tyr1/2b' Branchiostoma_floridae_tyrA1 Branchiostoma_floridae_tyrB1 Branchiostoma_floridae_tyrC1 Branchiostoma_floridae_tyra Branchiostoma_floridae_tyrb Branchiostoma_floridae_tyrc Branchiostoma_floridae_tyrd Branchiostoma_floridae_tyre Branchiostoma_floridae_tyrf Branchiostoma_floridae_tyrg Branchiostoma_floridae_tyrh Branchiostoma_floridae_tyri Branchiostoma_floridae_tyrj Branchiostoma_floridae_tyrk Branchiostoma_floridae_tyrl Branchiostoma_floridae_tyrm Brugia_malayi_TYR1 Brugia_malayi_TYR2 Brugia_malayi_TYR3 Brugia_malayi_TYR4 Caenorhabditis_briggsae_TYR1 Caenorhabditis_briggsae_TYR2 Caenorhabditis_briggsae_TYR3 Caenorhabditis_briggsae_TYR4 Caenorhabditis_briggsae_TYR5 Caenorhabditis_briggsae_TYR6 Caenorhabditis_elegans_TYR1 Caenorhabditis_elegans_TYR2 Caenorhabditis_elegans_TYR3 Caenorhabditis_elegans_TYR4 Caenorhabditis_elegans_TYR5 Caenorhabditis_remanei_TYR1 Caenorhabditis_remanei_TYR2 Caenorhabditis_remanei_TYR3 Caenorhabditis_remanei_TYR4 Caenorhabditis_remanei_TYR5 Candidatus_nitrosopumilus_tyr Capitella_teleta_tyr1 Capitella_teleta_tyr2 Ciona_intestinalis_HcA Ciona_intestinalis_HcB Ciona_intestinalis_HcC Ciona_intestinalis_HcD Ciona_intestinalis_HcE Ciona_intestinalis_HcF Ciona_intestinalis_HcG Ciona_intestinalis_HcH Ciona_intestinalis_HcI Ciona_intestinalis_tyr Ciona_intestinalis_tyr1 'Ciona intestinalis tyr1/2a' 'Ciona intestinalis tyr1/2b' Ciona_intestinalis_tyr2 Ciona_intestinalis_tyr3 Ciona_intestinalis_tyr4 Clonorchis_sinensis_tyr2 Clonorchis_sinensis_tyr3 Clonorchis_sinensis_tyr4 Clonorchis_sinensis_tyr5 Clonorhis_sinensis_tyr1 Daphnia_pulex_tyr Dictyostelium_discoideum_tyr1 Dictyostelium_discoideum_tyr2 Dictyostelium_fasciculatum_tyr Drosophila_melanogaster_tyr1 Drosophila_melanogaster_tyr2 Drosophila_melanogaster_tyr3 Ectocarpus_siliculosus_tyr1 Ectocarpus_siliculosus_tyr10 Ectocarpus_siliculosus_tyr11 Ectocarpus_siliculosus_tyr12 Ectocarpus_siliculosus_tyr13 Ectocarpus_siliculosus_tyr14 Ectocarpus_siliculosus_tyr15 Ectocarpus_siliculosus_tyr16 Ectocarpus_siliculosus_tyr17 Ectocarpus_siliculosus_tyr18 Ectocarpus_siliculosus_tyr2 Ectocarpus_siliculosus_tyr3 Ectocarpus_siliculosus_tyr4 Ectocarpus_siliculosus_tyr5 Ectocarpus_siliculosus_tyr6 Ectocarpus_siliculosus_tyr7 Ectocarpus_siliculosus_tyr8 Ectocarpus_siliculosus_tyr9 Epiperipatus_sp_Hc Euphrynichus_bacillifer_HcA Euphrynichus_bacillifer_HcB Glycine_max_CO1 Glycine_max_CO10 Glycine_max_CO11 Glycine_max_CO12 Glycine_max_CO2 Glycine_max_CO3 Glycine_max_CO4 Glycine_max_CO5 Glycine_max_CO6 Glycine_max_CO7 Glycine_max_CO8 Glycine_max_CO9 Homo_sapiens_TYR Homo_sapiens_TYRP1 Homo_sapiens_TYRP2a Homo_sapiens_TYRP2b Hydra_magnipapillata_tyr Illex_argentinus_tyr1 Illex_argentinus_tyr2 Limulus_polyphemus_HcA Limulus_polyphemus_HcB Lottia_gigantea_Hc Lottia_gigantea_tyr1 Lottia_gigantea_tyr2 Mastigoproctus_giganteus_HcA Mastigoproctus_giganteus_HcB Megathura_crenulata_Hc Mus_musculus_Tyr Mus_musculus_Tyrp1 Mus_musculus_Tyrp2 Nematostella_vectensis_tyr1 Nematostella_vectensis_tyr2 Nematostella_vectensis_tyr3 Nematostella_vectensis_tyr4 Neurospora_crassa_tyr1 Neurospora_crassa_tyr2 Neurospora_crassa_tyr3 Neurospora_tetrasperma_tyr1 Neurospora_tetrasperma_tyr2 Neurospora_tetrasperma_tyr3 Nitrosomonas_europeae_tyr Nucula_nucleus_Hc Oryza_sativa_CO Phragmatopoma_californica_tyr Pinctada_fucata_tyr1 Pinctada_fucata_tyr2 Pinctada_fucata_tyr3 Pinctada_fucata_tyr4 Polysphondylium_pallidum_tyr1 Polysphondylium_pallidum_tyr2 Saccoglossus_kowaleksii_Hc Saccoglossus_kowalevskii_tyra Saccoglossus_kowalevskii_tyrb Saccoglossus_kowalevskii_tyrc Saccoglossus_kowalevskii_tyrd Schistosoma_japonicum_tyr Schistosoma_mansoni_tyr1 Schistosoma_mansoni_tyr2 Schistosoma_mansoni_tyr3 Schistosoma_mansoni_tyr4 Schmidtea_mediterranea_tyr Sepia_officinalis_Hc Sepia_officinalis_tyr Streptomyces_tsukubaensis_tyr Streptomyces_venezuelae_tyr Suberites_domuncula_tyr Tribolium_castaneum_tyr1 Tribolium_castaneum_tyr2 Tribolium_castaneum_tyr3 Vitis_vinifera_CO ; END; BEGIN TREES; TITLE Type_3_copper_proteins_Maximum_Likelihood; LINK TAXA = Taxa; TREE bootstrap_9 = [&R] ((((((((((((((((((Caenorhabditis_elegans_TYR4:0.030664,Caenorhabditis_remanei_TYR4:1.0E-6):0.017904,Caenorhabditis_briggsae_TYR4:0.0):0.044167,(Caenorhabditis_briggsae_TYR6:0.012134,Caenorhabditis_elegans_TYR5:0.086414):0.725642):0.266918,((Caenorhabditis_remanei_TYR3:0.036884,Caenorhabditis_briggsae_TYR3:0.0):0.057671,Caenorhabditis_elegans_TYR3:1.0E-6):0.040623):0.097202,(((Caenorhabditis_elegans_TYR2:0.0,Caenorhabditis_remanei_TYR2:0.0):0.037541,Caenorhabditis_briggsae_TYR2:0.038841):0.030984,(Brugia_malayi_TYR4:0.110814,Brugia_malayi_TYR2:0.415616):0.089843):0.113751):0.036624,(((((Caenorhabditis_remanei_TYR1:0.0,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.052842):0.036107,Caenorhabditis_elegans_TYR1:1.0E-6):0.06358,Brugia_malayi_TYR3:0.211771):0.1049,Brugia_malayi_TYR1:0.132551):2.0E-6,Caenorhabditis_remanei_TYR5:0.868444):0.027418):0.194092,((((Pinctada_fucata_tyr3:0.010334,Pinctada_fucata_tyr2:0.0):0.138514,Pinctada_fucata_tyr4:0.187256):0.209935,((Sepia_officinalis_tyr:0.067866,(Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):2.0E-6):0.626885,Lottia_gigantea_tyr1:0.265747):0.167351):0.258701,Pinctada_fucata_tyr1:0.517052):0.017606):0.172926,Lottia_gigantea_tyr2:0.869596):0.072189,(Ectocarpus_siliculosus_tyr14:0.070829,(((Ectocarpus_siliculosus_tyr16:0.026261,(Ectocarpus_siliculosus_tyr17:0.020227,Ectocarpus_siliculosus_tyr18:0.127085):0.038919):0.078607,Ectocarpus_siliculosus_tyr15:0.095046):0.113847,(((Ectocarpus_siliculosus_tyr1:5.0E-6,((Ectocarpus_siliculosus_tyr3:2.0E-6,(Ectocarpus_siliculosus_tyr5:0.284372,Ectocarpus_siliculosus_tyr6:0.165207):0.384566):0.134361,Ectocarpus_siliculosus_tyr2:0.044141):0.170725):0.228508,Ectocarpus_siliculosus_tyr4:0.238994):0.580222,(((Ectocarpus_siliculosus_tyr8:0.185781,((Ectocarpus_siliculosus_tyr10:0.17079,Ectocarpus_siliculosus_tyr11:0.053277):0.096842,Ectocarpus_siliculosus_tyr9:0.068617):6.0E-6):0.537381,Ectocarpus_siliculosus_tyr7:0.046718):0.953021,(Ectocarpus_siliculosus_tyr13:3.0E-6,Ectocarpus_siliculosus_tyr12:0.15462):0.347387):0.375175):0.269794):0.004686):0.807758):0.073221,(((((Branchiostoma_floridae_tyrj:2.0E-6,Branchiostoma_floridae_tyrk:0.044913):0.414865,((Branchiostoma_floridae_tyrl:0.32171,(Branchiostoma_floridae_tyra:1.0E-6,Branchiostoma_floridae_tyrb:0.02936):0.075404):0.05118,(((Branchiostoma_floridae_tyrc:0.0,Branchiostoma_floridae_tyrd:0.018184):0.265098,Branchiostoma_floridae_tyrg:0.128817):0.071201,(Branchiostoma_floridae_tyrh:0.010345,((Branchiostoma_floridae_tyre:1.0E-6,Branchiostoma_floridae_tyri:0.244701):0.06161,Branchiostoma_floridae_tyrf:0.135636):0.040531):0.047424):0.088425):0.112827):0.060773,(((Agaricus_bisporus_tyr:0.807026,((Glycine_max_CO1:3.0E-6,(Glycine_max_CO2:1.0E-6,(((Glycine_max_CO5:0.160089,(Glycine_max_CO6:0.104301,Glycine_max_CO7:0.016744):0.272548):0.129349,((Oryza_sativa_CO:0.267503,Vitis_vinifera_CO:0.282468):0.088862,((((Glycine_max_CO12:0.026841,Glycine_max_CO11:1.0E-6):0.030894,Glycine_max_CO9:0.031528):0.031595,Glycine_max_CO8:0.103838):0.048536,Glycine_max_CO10:0.142008):0.018106):0.020815):0.164218,(Glycine_max_CO3:0.11855,Glycine_max_CO4:0.03554):0.134729):0.165847):0.035302):0.969411,Aspergillus_aculeatus_tyr:0.500441):0.179815):0.202421,((((Neurospora_tetrasperma_tyr2:0.075755,Neurospora_crassa_tyr2:1.0E-6):0.327522,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.0):0.3735):0.129206,(Neurospora_crassa_tyr1:0.018039,Neurospora_tetrasperma_tyr1:3.0E-6):0.600112):0.387558,((((Aplysia_californica_Hc:0.303149,(Megathura_crenulata_Hc:0.08959,Sepia_officinalis_Hc:0.289927):0.154449):0.083636,Nucula_nucleus_Hc:0.184182):0.384713,((Ciona_intestinalis_HcA:5.0E-6,((Ciona_intestinalis_HcD:0.007324,Ciona_intestinalis_HcC:0.131621):0.098239,Ciona_intestinalis_HcB:0.006084):0.296559):0.052637,(((Ciona_intestinalis_HcE:0.06271,(Ciona_intestinalis_HcG:0.12794,Ciona_intestinalis_HcF:0.033523):0.106921):0.130654,Ciona_intestinalis_HcH:0.193817):0.054939,Ciona_intestinalis_HcI:0.128108):0.190742):0.503097):0.402478,Lottia_gigantea_Hc:0.500924):0.129569):0.234997):0.297806,((Clonorchis_sinensis_tyr3:0.344607,((((Schistosoma_mansoni_tyr1:0.0,Schistosoma_mansoni_tyr4:0.0):1.0E-6,Schistosoma_mansoni_tyr3:0.085162):0.074712,Schistosoma_japonicum_tyr:0.192189):0.252617,(Clonorchis_sinensis_tyr5:0.027104,Clonorchis_sinensis_tyr4:0.104316):0.324206):0.102432):0.029927,(Clonorchis_sinensis_tyr2:0.314699,Schistosoma_mansoni_tyr2:0.441646):0.330031):0.143806):0.356886):0.085556,(((Capitella_teleta_tyr1:0.316269,Capitella_teleta_tyr2:0.359019):0.239731,((Clonorhis_sinensis_tyr1:0.196617,Schmidtea_mediterranea_tyr:0.5148):0.214304,(((Saccoglossus_kowalevskii_tyrd:0.085612,Saccoglossus_kowalevskii_tyrc:0.080314):0.163651,Branchiostoma_floridae_tyrm:0.510398):0.060772,(Saccoglossus_kowalevskii_tyrb:1.0E-6,Saccoglossus_kowalevskii_tyra:0.045614):0.209122):0.075082):0.017117):0.048326,(((((Mus_musculus_Tyrp2:0.071707,(Homo_sapiens_TYRP2b:0.0,Homo_sapiens_TYRP2a:0.0):0.028875):0.220123,('Ciona intestinalis tyr1/2a':0.108357,'Ciona intestinalis tyr1/2b':0.078132):0.058017):0.127765,(Mus_musculus_Tyrp1:0.048624,Homo_sapiens_TYRP1:0.029093):0.25549):0.089495,('Branchiostoma floridae tyr1/2a':0.038172,'Branchiostoma floridae tyr1/2b':1.0E-6):0.133361):0.39128,(Ciona_intestinalis_tyr:0.488064,(((Branchiostoma_floridae_tyrB1:0.0,Branchiostoma_floridae_tyrC1:0.0):0.140125,Branchiostoma_floridae_tyrA1:0.296402):0.247593,(Homo_sapiens_TYR:0.087119,Mus_musculus_Tyr:0.013157):0.22973):0.102937):0.1275):0.06709):0.115723):0.132775,Suberites_domuncula_tyr:0.737569):0.118231):0.07905,(Phragmatopoma_californica_tyr:0.545147,(((((Streptomyces_tsukubaensis_tyr:0.253873,Streptomyces_venezuelae_tyr:0.074231):0.071289,(Dictyostelium_discoideum_tyr2:1.0E-6,Dictyostelium_discoideum_tyr1:0.00898):0.715732):0.1305,((Bacillus_megaterium_tyr1:0.0,Bacillus_megaterium_tyr2:0.0):0.434117,(Nitrosomonas_europeae_tyr:0.477251,Candidatus_nitrosopumilus_tyr:0.439907):1.5E-5):0.165999):0.042797,((Nematostella_vectensis_tyr2:0.792106,((Nematostella_vectensis_tyr4:0.479086,Nematostella_vectensis_tyr3:0.137901):0.093799,Nematostella_vectensis_tyr1:0.699197):0.209164):0.228613,Hydra_magnipapillata_tyr:0.334061):0.568916):0.179564,Polysphondylium_pallidum_tyr1:0.474961):0.217572):9.0E-6):3.282612,Epiperipatus_sp_Hc:0.364093):0.237888,((Anopheles_gambiae_tyr9:0.620588,Anopheles_gambiae_tyr7:0.179221):0.054044,(Anopheles_gambiae_tyr2:0.097241,((((((((Tribolium_castaneum_tyr3:0.0,Tribolium_castaneum_tyr2:0.0):0.045556,(((Drosophila_melanogaster_tyr1:0.131078,Bombyx_mori_tyr1:0.132678):0.051111,Drosophila_melanogaster_tyr2:0.089583):0.021624,Anopheles_gambiae_tyr1:0.145214):0.050508):0.022195,Tribolium_castaneum_tyr1:0.183156):0.125214,(Drosophila_melanogaster_tyr3:0.185701,Bombyx_mori_tyr2:0.20306):0.034196):0.040934,Daphnia_pulex_tyr:0.332855):0.041083,(Anopheles_gambiae_tyr4:0.060037,Anopheles_gambiae_tyr5:0.152554):0.204961):0.143865,(Anopheles_gambiae_tyr3:0.07016,Anopheles_gambiae_tyr6:0.046935):0.171395):0.084637,Anopheles_gambiae_tyr8:0.215527):0.024271):0.026534):0.108968):0.22451,(Limulus_polyphemus_HcB:0.043651,((Euphrynichus_bacillifer_HcB:0.038482,Mastigoproctus_giganteus_HcB:0.052098):0.086421,((Euphrynichus_bacillifer_HcA:0.191286,Mastigoproctus_giganteus_HcA:0.192643):1.1E-5,Limulus_polyphemus_HcA:0.070287):0.118901):0.030963):0.293019):0.240508,(Polysphondylium_pallidum_tyr2:0.151967,Dictyostelium_fasciculatum_tyr:0.038309):1.118809):0.220947,(((Ciona_intestinalis_tyr4:0.0,(Ciona_intestinalis_tyr3:0.0,Ciona_intestinalis_tyr2:0.0):0.0):0.282406,Saccoglossus_kowaleksii_Hc:0.357533):0.235539,Ciona_intestinalis_tyr1:0.044953):0.581396):0.350186,Amphimedon_queenslandica_tyr:0.400899):0.582867,Aspergillus_nidulans_tyr2:0.0,Aspergillus_nidulans_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61673] END;