#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; 16:20 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=98; TAXLABELS Agaricus_bisporus_tyr Aplysia_californica_Hc Aspergillus_aculeatus_tyr Bacillus_megaterium_tyr1 Bacillus_megaterium_tyr2 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_TYR5 Caenorhabditis_elgans_TYR4 Caenorhabditis_remanei_TYR1 Caenorhabditis_remanei_TYR2 Caenorhabditis_remanei_TYR3 Caenorhabditis_remanei_TYR4 Caenorhabditis_remanei_TYR5 Candidatus_nitrosopumilus_tyr 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 Dictyostelium_discoideum_tyr1 Dictyostelium_discoideum_tyr2 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 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 Hydra_magnipapillata_tyr Illex_argentinus_tyr1 Illex_argentinus_tyr2 Lottia_gigantea_Hc Lottia_gigantea_tyr1 Lottia_gigantea_tyr2 Megathura_crenulata_Hc 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 Sepia_officinalis_Hc Sepia_officinalis_tyr Streptomyces_tsukubaensis_tyr Streptomyces_venezuelae_tyr Vitis_vinifera_CO ; END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = Taxa; TREE bootstrap_8 = [&R] ((((((((((Brugia_malayi_TYR2:0.296841,Brugia_malayi_TYR3:0.317843):0.029282,(Brugia_malayi_TYR1:0.159433,((((Caenorhabditis_briggsae_TYR2:0.010045,Caenorhabditis_remanei_TYR2:0.009508):0.009793,Caenorhabditis_elegans_TYR2:0.0):0.057165,Brugia_malayi_TYR4:0.230234):0.175033,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.067076,Caenorhabditis_remanei_TYR1:0.009022):0.02812,Caenorhabditis_elegans_TYR1:1.0E-6):0.089608):0.161856):0.090848):3.0E-6,(Caenorhabditis_remanei_TYR5:0.747043,((Caenorhabditis_briggsae_TYR4:1.0E-6,((Caenorhabditis_remanei_TYR4:0.0,Caenorhabditis_elgans_TYR4:0.0):0.022179,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.039716):0.013906,Caenorhabditis_elegans_TYR3:0.035728):0.29389):0.017172):0.06202,(Caenorhabditis_elegans_TYR5:0.031146,Caenorhabditis_briggsae_TYR6:0.0):1.024659):0.172786):0.086403):0.270373,((((Lottia_gigantea_Hc:0.803649,(((Neurospora_tetrasperma_tyr3:0.019282,Neurospora_crassa_tyr3:1.0E-6):0.260206,((Agaricus_bisporus_tyr:0.73626,(Neurospora_tetrasperma_tyr2:0.039241,Neurospora_crassa_tyr2:0.0):0.275862):0.056842,((Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.009693):0.798758,Aspergillus_aculeatus_tyr:0.473019):0.342754):0.227054):0.22136,((((Oryza_sativa_CO:0.264938,((((Glycine_max_CO12:0.080758,Glycine_max_CO11:0.0):0.0,(Glycine_max_CO10:0.092017,(Glycine_max_CO7:0.021221,Glycine_max_CO6:0.035184):0.169396):0.085213):0.093718,Glycine_max_CO9:0.033794):0.108061,Glycine_max_CO8:0.11156):0.052277):0.089797,Vitis_vinifera_CO:0.1757):1.0E-6,(Glycine_max_CO3:0.063172,Glycine_max_CO4:0.028268):0.291442):0.123811,((Glycine_max_CO2:0.009455,Glycine_max_CO1:0.0):0.199452,Glycine_max_CO5:0.20948):2.0E-6):1.00378):0.152035):0.345319,(((Nucula_nucleus_Hc:0.200755,(Megathura_crenulata_Hc:0.276113,Sepia_officinalis_Hc:0.197039):0.058304):0.116793,Aplysia_californica_Hc:0.056157):0.304236,(((Ciona_intestinalis_HcG:0.375978,(((Ciona_intestinalis_HcH:0.181084,Ciona_intestinalis_HcI:0.050472):0.196837,Ciona_intestinalis_HcE:0.001192):0.046544,Ciona_intestinalis_HcF:0.068843):0.073784):0.440712,(Ciona_intestinalis_HcB:0.131537,(Ciona_intestinalis_HcC:0.113968,Ciona_intestinalis_HcD:0.0):0.181868):9.9E-5):0.33393,Ciona_intestinalis_HcA:8.0E-6):0.674357):0.528808):0.270876,((Nematostella_vectensis_tyr1:0.823683,(Nematostella_vectensis_tyr2:1.46165,(Nematostella_vectensis_tyr4:0.232817,Nematostella_vectensis_tyr3:0.629708):0.189979):0.150625):0.046819,Hydra_magnipapillata_tyr:0.969019):0.824523):0.227649,(((Dictyostelium_discoideum_tyr2:0.009672,Dictyostelium_discoideum_tyr1:0.017875):0.718901,(Streptomyces_venezuelae_tyr:0.11816,Streptomyces_tsukubaensis_tyr:0.399288):0.148912):0.196047,(((Polysphondylium_pallidum_tyr1:0.599172,Nitrosomonas_europeae_tyr:0.825261):0.371216,(Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.219268):0.202638,Candidatus_nitrosopumilus_tyr:0.658758):0.042053):0.206182):0.200144):0.152511,(Lottia_gigantea_tyr1:0.499999,(((((Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.027491):0.152209,Pinctada_fucata_tyr4:0.140042):0.459032,Pinctada_fucata_tyr1:0.572671):0.009368,Lottia_gigantea_tyr2:0.586792):0.262684,Phragmatopoma_californica_tyr:0.446978):0.073629):0.036267):0.191963,((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:1.0E-6):2.0E-6,Sepia_officinalis_tyr:0.084027):0.643913):1.035889,(((Ectocarpus_siliculosus_tyr9:0.047337,(Ectocarpus_siliculosus_tyr11:0.028493,Ectocarpus_siliculosus_tyr10:0.276589):0.130228):0.047713,Ectocarpus_siliculosus_tyr7:0.645424):0.187616,Ectocarpus_siliculosus_tyr8:0.067384):0.49508):0.191206,(((Ectocarpus_siliculosus_tyr6:0.079529,Ectocarpus_siliculosus_tyr5:0.224171):0.36078,Ectocarpus_siliculosus_tyr4:0.319058):0.035652,((Ectocarpus_siliculosus_tyr2:0.027807,Ectocarpus_siliculosus_tyr3:0.104762):0.119231,Ectocarpus_siliculosus_tyr1:0.24466):0.095131):0.53855):0.315165,(Ectocarpus_siliculosus_tyr14:0.093441,(Ectocarpus_siliculosus_tyr18:0.084861,((Ectocarpus_siliculosus_tyr17:0.029562,Ectocarpus_siliculosus_tyr15:0.172893):0.074754,Ectocarpus_siliculosus_tyr16:0.058304):0.049793):0.119011):0.25943):0.405748,Ectocarpus_siliculosus_tyr13:1.0E-6,Ectocarpus_siliculosus_tyr12:0.123166); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61704] END;