#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; 13:28 GMT TreeBASE (cc) 1994-2008 Study reference: Derelle R., Torruella G., Klimeš V., Brinkmann H., Kim E., Vlček &., Lang B.F., & EliᚠM. 2015. Bacterial proteins pinpoint a single eukaryotic root. Proceedings of the National Academy of Sciences of the United States of America, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16424] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=80; TAXLABELS Acanthamoeba_castellanii Acrasis_kona Acropora_digitifera Agrobacterium_tumefaciens Amphimedon_queenslandica Andalucia_godoyi Aplanochytrium_kerguelense Arabidopsis_thaliana Batrachochytrium_dendrobatidis Bigelowiella_natans Bolidomonas_pacifica Burkholderia_ambifaria Capsaspora_owczarzaki Chlorella_variabilis Chondrus_crispus Collodictyon_triciliatum Cryptomonas_paramecium Desulfovibrio_vulgaris Dictyostelium_discoideum Ectocarpus_siliculosus Ephydatia_muelleri Escherichia_coli Eutreptiella_gymnastica Filamoeba_nolandi Galdieria_sulphuraria Geobacter_metallireducens Gonapodya_prolifera Goniomonas_avonlea Guillardia_theta Heterosigma_akashiwo Homo_sapiens Jakoba_libera Karenia_brevis Leishmania_major Lingulodinium_polyedrum Lottia_gigantea Magnetospirillum_magneticum Malawimonas_californiana Malawimonas_jakobiformis Micromonas_sp Monosiga_brevicollis Monosiga_ovata Mortierella_verticillata Myxococcus_xanthus Naegleria_gruberi Nematostella_vectensis Oryza_sativa Ostreococcus_lucimarinus Oxytricha_trifallax Paramecium_tetraurelia Pelagibacter_ubique Perkinsus_marinus Phanerochaete_chrysosporium Physarum_polycephalum Physcomitrella_patens Phytophthora_infestans Planctomyces_limnophilus Plasmodium_falciparum Platyophrya_macrostoma Polysphondylium_pallidum Puniceispirillum_marinum Reclinomonas_americana Rhizopus_oryzae Rhodopirellula_baltica Rickettsia_conorii Salpingoeca_rosetta Saprolegnia_parasitica Schizochytrium_aggregatum Seculamonas_ecuadoriensis Solibacter_usitatus Spizellomyces_punctatus Stereomyxa_ramosa Tetrahymena_thermophila Tetraselmis_astigmatica Thalassiosira_pseudonana Thecamonas_trahens Toxoplasma_gondii Tuber_melanosporum Ustilago_maydis Yarrowia_lipolytica ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=77; TAXLABELS Acanthamoeba_castellanii Acrasis_kona Acropora_digitifera Amphimedon_queenslandica Andalucia_godoyi Aplanochytrium_kerguelense Arabidopsis_thaliana Azospirillum_sp Batrachochytrium_dendrobatidis Bigelowiella_natans Bolidomonas_pacifica Capsaspora_owczarzaki Chlorella_variabilis Chondrus_crispus Collodictyon_triciliatum Cryptomonas_paramecium Dictyostelium_discoideum Ectocarpus_siliculosus Ephydatia_muelleri Eutreptiella_gymnastica Filamoeba_nolandi Galdieria_sulphuraria Gonapodya_prolifera Goniomonas_avonlea Granulibacter_bethesdensis Guillardia_theta Heterosigma_akashiwo Homo_sapiens Jakoba_libera Karenia_brevis Leishmania_major Lingulodinium_polyedrum Lottia_gigantea Magnetospirillum_magneticum Malawimonas_californiana Malawimonas_jakobiformis Maricaulis_maris Micromonas_sp Monosiga_brevicollis Monosiga_ovata Mortierella_verticillata Naegleria_gruberi Nematostella_vectensis Oryza_sativa Ostreococcus_lucimarinus Oxytricha_trifallax Paramecium_tetraurelia Parvibaculum_lavamentivorans Parvularcula_bermudensis Perkinsus_marinus Phanerochaete_chrysosporium Physarum_polycephalum Physcomitrella_patens Phytophthora_infestans Plasmodium_falciparum Platyophrya_macrostoma Polysphondylium_pallidum Reclinomonas_americana Rhizopus_oryzae Rhodospirillum_centenum Rhodospirillum_rubrum Roseomonas_cervicalis Salpingoeca_rosetta Saprolegnia_parasitica Schizochytrium_aggregatum Seculamonas_ecuadoriensis Spizellomyces_punctatus Starkeya_novella Stereomyxa_ramosa Tetrahymena_thermophila Tetraselmis_astigmatica Thalassiosira_pseudonana Thecamonas_trahens Toxoplasma_gondii Tuber_melanosporum Ustilago_maydis Yarrowia_lipolytica ; END; BEGIN TREES; TITLE 'Eukaryotic root consensus CAT-GTR result from ALPHA-PROT filtered dataset'; LINK TAXA = Taxa2; TRANSLATE 1 Acanthamoeba_castellanii, 2 Acrasis_kona, 3 Acropora_digitifera, 4 Amphimedon_queenslandica, 5 Andalucia_godoyi, 6 Aplanochytrium_kerguelense, 7 Arabidopsis_thaliana, 8 Azospirillum_sp, 9 Batrachochytrium_dendrobatidis, 10 Bigelowiella_natans, 11 Bolidomonas_pacifica, 12 Capsaspora_owczarzaki, 13 Chlorella_variabilis, 14 Chondrus_crispus, 15 Collodictyon_triciliatum, 16 Cryptomonas_paramecium, 17 Dictyostelium_discoideum, 18 Ectocarpus_siliculosus, 19 Ephydatia_muelleri, 20 Eutreptiella_gymnastica, 21 Filamoeba_nolandi, 22 Galdieria_sulphuraria, 23 Gonapodya_prolifera, 24 Goniomonas_avonlea, 25 Granulibacter_bethesdensis, 26 Guillardia_theta, 27 Heterosigma_akashiwo, 28 Homo_sapiens, 29 Jakoba_libera, 30 Karenia_brevis, 31 Leishmania_major, 32 Lingulodinium_polyedrum, 33 Lottia_gigantea, 34 Magnetospirillum_magneticum, 35 Malawimonas_californiana, 36 Malawimonas_jakobiformis, 37 Maricaulis_maris, 38 Micromonas_sp, 39 Monosiga_brevicollis, 40 Monosiga_ovata, 41 Mortierella_verticillata, 42 Naegleria_gruberi, 43 Nematostella_vectensis, 44 Oryza_sativa, 45 Ostreococcus_lucimarinus, 46 Oxytricha_trifallax, 47 Paramecium_tetraurelia, 48 Parvibaculum_lavamentivorans, 49 Parvularcula_bermudensis, 50 Perkinsus_marinus, 51 Phanerochaete_chrysosporium, 52 Physarum_polycephalum, 53 Physcomitrella_patens, 54 Phytophthora_infestans, 55 Plasmodium_falciparum, 56 Platyophrya_macrostoma, 57 Polysphondylium_pallidum, 58 Reclinomonas_americana, 59 Rhizopus_oryzae, 60 Rhodospirillum_centenum, 61 Rhodospirillum_rubrum, 62 Roseomonas_cervicalis, 63 Salpingoeca_rosetta, 64 Saprolegnia_parasitica, 65 Schizochytrium_aggregatum, 66 Seculamonas_ecuadoriensis, 67 Spizellomyces_punctatus, 68 Starkeya_novella, 69 Stereomyxa_ramosa, 70 Tetrahymena_thermophila, 71 Tetraselmis_astigmatica, 72 Thalassiosira_pseudonana, 73 Thecamonas_trahens, 74 Toxoplasma_gondii, 75 Tuber_melanosporum, 76 Ustilago_maydis, 77 Yarrowia_lipolytica; TREE Fig._1L = [&R] ((((35:0.209927,36:0.176787):0.339381,(15:0.443782,((1:0.229814,69:0.37297):0.229987,(21:0.386935,(52:0.302086,(17:0.150412,57:0.113036):0.320413):0.117817):0.069533):0.075662):0.019851):0.016939,(73:0.711486,(((23:0.280967,(9:0.174416,67:0.100429):0.092988):0.03402,((41:0.190197,59:0.24274):0.025215,((51:0.206038,76:0.21019):0.141337,(75:0.244817,77:0.278266):0.169636):0.059534):0.052989):0.160917,(12:0.276556,((40:0.249166,(39:0.177017,63:0.176534):0.13412):0.122789,((4:0.243458,19:0.222454):0.105193,((3:0.116277,43:0.1212):0.096586,(28:0.205226,33:0.243333):0.045358):0.027621):0.094392):0.039933):0.093605):0.087557):0.039559):0.0097585,((((37:0.265331,49:0.259966):0.0942,(48:0.207871,68:0.241324):0.039084):0.106432,((34:0.204426,61:0.22111):0.060122,((8:0.138073,60:0.169054):0.076905,(25:0.184018,62:0.186928):0.148638):0.021915):0.04477):0.389822,((((2:0.3775,42:0.371499):0.431131,(20:0.589132,31:0.831043):0.387499):0.129356,(5:0.382492,(58:0.221506,(29:0.300784,66:0.163434):0.039098):0.110867):0.038443):0.051331,(((24:0.344027,(16:0.135613,26:0.15704):0.291874):0.15229,((14:0.316701,22:0.29737):0.192436,((53:0.115002,(7:0.080146,44:0.083059):0.106439):0.129263,((13:0.241933,71:0.217991):0.058454,(38:0.122997,45:0.171971):0.140001):0.043144):0.126412):0.030128):0.017323,((10:0.568827,((6:0.23119,65:0.211937):0.179341,((54:0.139348,64:0.126148):0.207923,((11:0.200606,72:0.270684):0.155743,(18:0.316322,27:0.226205):0.040618):0.089324):0.057873):0.096607):0.026227,((46:0.485011,(56:0.281611,(47:0.295876,70:0.381348):0.116991):0.142569):0.35799,((55:0.636646,74:0.280487):0.239319,(50:0.399663,(30:0.208343,32:0.104318):0.217529):0.15819):0.201117):0.140142):0.033242):0.024232):0.015371):0.0097585); END;