#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 25, 2024; 7:46 GMT TreeBASE (cc) 1994-2008 Study reference: Yokoyama A., Takahashi F., Kataoka H., Hara Y., & Nozaki H. 2011. Evolutionary analyses of the nuclear-encoded photosynthetic gene psbO from tertiary plastid-containing algae in Dinophyta. Journal of Phycology, 47. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11256] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=28; TAXLABELS Amphidinium_carterae Aureococcus_anophagefferens Botrydium_granulatum Chaetoceros_gracilis Chroomonas_caudata Cryptomonas_ovata Cyanidioschyzon_merolae Dixoniella_grisea Emiliania_huxleyi Fucus_distichus Galdieria_sulphuraria Guillardia_theta Heterocapsa_triquetra Heterosigma_akashiwo Isochrysis_galbana Karenia_brevis Karlodinium_veneficum Kryptoperidinium_foliaceum Neorhodella_cyanea Pavlova_lutheri Phaeodactylum_tricornutum Porphyra_yezoensis Porphyridium_purpureum Prymnesium_parvum Pyrenomonas_helgolandii Thalassiosira_pseudonana Vaucheria_frigida Vaucheria_litorea ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M7951] TITLE Dinophyta_pbsO; LINK TAXA = Taxa1; DIMENSIONS NCHAR=219; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=X GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 ] [ . . . . . . . . . . . . . . . . . . . . . ] Amphidinium_carterae ARA--ITSEQFEQLTYEQVKGSGLANRCPTVERMKKMCFEPKSFAVEAEFVNTRLVTRQTYTLEQIEGQLKLTFVEEDGIDFAASTVQLPNGERVPFLFTMKKLVAKGFKPGFTWGGEYEVPSYRTGGFLDPKGRGMYSGYDQAVALPALQAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Aureococcus_anophagefferens ANA--ITSEVRNQLSYEQVKGTGLANRCNEVVSLVDVCLEPKTWQVEEQFVNTKLMTRQTYTLDGISGKLSITFTEEDGIDYAPTTVQLPGGERVPFLFTVKELVAKGFKPGYEFGGTFKVPSYRTGLFLDPKGRGMTTGYDQAQALAASQTDSQGELEGEINKVFDVFDGTIEFAVSQVNAAEGEIGGVFVSSQASDTDLGSKTPKKVLSKGIFYGRV Botrydium_granulatum AEA--ITKDQIDSLSYMQVKGTGLANRCPEVVKIVDLCIEPKVFQVLEEYVNTKLMTRQTYTLYGIEGDLTLVFTEKDGIDYAATTVQLPGGERVPFLFTVKELVAKAVAPGFQFGGAFKTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDKELFDENNKTFDVTDGQIEFEVNRVDAEAGEIGGVFVSKQKGDTDMGSKVPKDMLVKGIFYGRL Chaetoceros_gracilis AQA--LTKSQINELSYLQVKGTGLANRCAEVVKLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLDAIEGPITITFNEKEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFNTPSYRTGLFLDPKGRGGTTGYDMAVALPALQLEGDAELFGENNKVFDITQGRIEMEVNKVNAEDSEIGGVFVATQLSDTDMGSKTPKKVLTKGIFYAKV Chroomonas_caudata ADA--LTTQDIKSLTYLQIKGTGLANRCPEVSKIVDMCLEPKSWQIEEEFVDTKLMNRATYTLTGIEGPLVLVFYEKEGIDYAPTTVQLPGGERVPFLFNVKELVASFIKAGVEFGGNFRTPSYRTGLFLDPKGRGGTTGYDMAVALPALEAEGQSELFAETNKVFQVTDGSIEMAITKVDATTGEFSGVFVSEQLSDTDMGSKAPKKVLLKGIVFAKV Cryptomonas_ovata ADA--LTTQDIRDLTYGQIKGTGIANRCPEVAKIVDLCLEPKSFQIEEEFVDTKLMTRATYSLTGVEGPLFLTFLEKGGIDYAPATVQLPGGERVPFMFTIKQLEAKSIAPGTEFGGTFTVPSYRSGLFLDPKGRGGTTGYDNAGALVALEAEGQEELFKETNKVYQVTDGSIEFAVNKVDGASGEFSGVFVSEQLSDTDMGSKAPKKVLLKGILFGRV Cyanidioschyzon_merolae VQA--LTAQDVRQLSYEQVKGTGLANRCPEVVKVVDLCLEPKQFLVEEEFVDTKLMTRATYTLANIEGELVWKFIEKDGMDYAATTVQIPGGERVPFLFSIKKLVASLISTSTELGGEFKVPSYRTGMFLDPKGRGMANGYDMAVALPALEAVGQEVLRKENDKVFQETSGRIELAVNKVDPTSNEIGGVFVSEQLSDTDMGAKEPKKLLLKGVFYARI Dixoniella_grisea AQA--LTSADIRGLSYEQIKGTGLANRCPEVDKIVDMCIEPKSFQVEEEYVDTKLMTRATYTLTGITGPLELTFTEVDGIDYAATTVQLPGGERVPFLFTVKELVAKAISTATEFGGDFKVPSYRAGTFLDPKGRGMTTGYDMAVALPAMEAEGQEELFKETNKVFQVTDGSIEMAVNKVDPETGEFAGVFVSEQLSDTDMGAKAPKKLLLKGVFYARV Emiliania_huxleyi ASAGPFTRTDIASLTYQQIKGTGLANTCPVVEKIDEFCLEPTSFQVLEEAVDTKVTTRQTYVLTGMEGDLVLTFLEKDGIDYAPTTVQLPGGERVPFLFTVKNLVAQSISPGLKMSGGFNVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFKENNKKFDVGRGSIELKVTSVNAELGEFGGVFVQKQPSDTDLGSKVPKELLLKGQFFGTV Fucus_distichus SEA--VTRDTLDALSYTQVKGTGLANRCPEVREIIDMCIEPKQFQVLSRMIDTKLMTRETYTLYGIEGNFGLTFEEKDGIDYAATTIQSN-YERIPFLFTVKDLVAKAVKPGFQMGGGFRTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDAELFKENNKVFDVTDGNIEFEVNKVDKEAGEIGGVFVSKQKGDTDMGSKVPKDILVKGIFYARI Galdieria_sulphuraria SLA--LTRSDIRSLTYDQVKGTGIASRCPEVDKLVDLCLEPKSFQVEEEFVDAKLVTRATYTLSNIEGTLNLVFRERDGLDYAACTVQLPGGERVPFLFSIKKLVAKAINTATEFGGQFKVTGYRTGLFLDPKGRGGTSGYDMAVALPAREAEGQDDLLRENNKTFDVTDGSIEMAVNKLDPTSGEIAGVFVSEQLSDTDMGAKDPKKLLLKGIFYARV Guillardia_theta ANA--LTSKDINNLTYEEVKGTGIANRCPEVEKITDLCIEPKSFQIETEFVDTKLVTRATYSLAGVEGPLFLTFQEKEGLDYAATTVQLPGGERVPFFFTIKELVAKAISPGTEFGGTFTVPSYRSGLFLDPKGRGATTGYDMAQALPAFEAEGQAELFKENNKVFQVTDGSMEFAVNKVDGQTGEFSGVFVSEQLSDTDMGSKAPKKVLIKGIVYGKV Heterocapsa_triquetra AKA--ITAEQFSQLTYAQVRGSGLANRCPTVERMQNFCLEPKSFAIEFEFVTTKLTTRQTYTLAFIEGALKITFTEQDGMDFAATTVKMPDGEYVPFLFSCKQLIAKGFKPGFTWGGEFNVPSYRTGGFLDPKGRGMYTGYDQAVALPALQAGGQEELFKETNKVFDIGKGAIEMEVNKVNQELGEIGGVFVSKQPSDTDMGAKAPKTVLLKGIFYGKI Heterosigma_akashiwo AFA--ITKAESNSLDYLQVKGTGLANRCSEVIQLVDLCIEPKTFQVEEEFVNTKLMTRQTYTLDGISGTISIVFTEEDGIDYAASTVQKPGGERVPFLFTVKELVATAIAPGFQMGGKFTVPSYRTGLFLDPKGRGMSTGYDMAVALPGKQSEGDAELFKENNKVFDVLGGQIEFEVNRVNAEEGEIGGVFVSTQASDTDMGGKEPQTILLKGIFYGRI Isochrysis_galbana ASAGPFTREDIASLTYLQIKGTGLANTCPIVQKIEEFCLEPTSFQVLEEAVDTKVTTRQTYVLTGIDGDLVLTFLEKDGIDYAATTVQLPGGERVPFLFTVKNLVAQSISPGLKMAGSFTVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFKENDKKFDVGTGTIEMKVTAVNAELGEFGGVFVQKQPSDTDLGSKQPKEVLLKGQFFGTV Karenia_brevis ALAGPFTRDDLASLTYDQVKGSGLANTCPKVNLSD-FCLEPTSFAILEEPVPSKVTTRQTYVLDGIEGTLSLKFVETDGIDYAPTTIQLPGGERVPFLFTVKNLVATAIAPGFTMSGPFMVPSYRTGLFLDPKGRGTTTGYDQAVALPAMQAGGDEEMFKENDKKFDVGKGSIELKVTQVNTELKEIGGVFVHKQPGDTDLGSKEPKEILLKGNWFATV Karlodinium_veneficum AKAGPFTRTELNSLTYQQIKGTGLANTCPKVE-------------------KEKVTTRQTYTLTGIEGKLSLTFTEQDGIDYAATTVQRPGGERVPFLFTVKNLVAQALEPGFEWGGKFVVPSYRTGLFLDPKGRGITTGYDQAVALPALQAGGDEALYAENNKKFDVLAGNIEMKVTSVNSELGEIGGVFVQQQPSDTDLGGKTPITLQLKGSWFATV Kryptoperidinium_foliaceum AQA--LTKSEINELTYLQVKGTGLANRCPEVVKLVDMCIEPKAWAVEEEFVNSKVVTRQTYTLDGIEGVLSIVFKEKEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFSVPSYRTGLFLDPKGRGGTTGYDMAVALPGLQSEGDDDLFKENNKTFDVTTGRIEMEVNKVNADEQEIGGVFVATQLGDTDMGSKVPKKILTKGIFYARV Neorhodella_cyanea AQA--LTTSDIRGLSYDQVKGTGLANRCPEVDKTVDMCIEPKSFQVEEEYVDTKLMTRATYTLTGIEGPLTLTFVEKDGIDYAATTVQLPGGERVPFLFTVKELVAKGISTATEFGGDFRVPSYRTGLFLDPKGRGGVTGYDMAVALPGKEAEGQDDIFKETNKVFQITDGSIEMAVNKIDVETKEFAGVFVSEQLSDTDMGAKTPKKVLLKGVFYGRL Pavlova_lutheri AQA--LSKETYNSLTYDQIKGTGLANKCPDVTKFDEFCMQPTEVSILETIIPSKMMTRQTGTLAMVEGDLVVVLKEKDGIDYAASTVQTPGGERVPYLFTVKGLIAKGVKPGLKLSGDYIVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDDELFKENNKKFEVLSGSTELTVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Phaeodactylum_tricornutum ANA--LTKSQINELSYLQVKGTGLANRCPEVVRLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLDGIEGALKIVFQEQEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFNTPSYRTGLFLDPKGRGGTTGYDMAVALPGLQSEGDDDLFKENNKTFDITTGRIEMEVNKVNAEEQEIGGVFVATQLSDTDMGSKVPKKVLTKGIFYARV Porphyra_yezoensis AAA--LTSADIRSLTYEQVKGTGLANRCPEVDKLVDLCLEPKSFQVEEEFVDTKLMTRATYTLSGIEGILRLVFEEKEGIDYAATTVQLPGGERLPFLFTIKQLVAKAISTATEFGGTYRVPSYRTGGFLDPKGRGMVTGYDMAVGLPAMEAEGQTKLFKETNKVFEVTDGEIEMAVNKLDAASGELGGVFVAEQLSDTDMGAKAPKNVLVKGVFYGRV Porphyridium_purpureum VQA--FTEEDFRQLSYEQVKGTGLANRCPEVDKIVDMCIEPKSFQVEDEFVDTKLMTRATYTLTGIEGPLTLEFQEKDGIDYAATTVQLPGGERVPFLFTVKELVATAIGSGTEFGGEFTVPSYRTGLFLDPKGRGGVTGYDMAVALPGMMAEGQDELFKETNKVFQVTKGEIEMGVQKVDPSTNEIAGVFVSEQLTDTDMGAKAPKNILLKGVFYARI Prymnesium_parvum ASAGPFTRSEIASLTYEQIKGTGLANTCPIVEKIDEFCLEPTSFQVLEEAVNTKVTTRQTYVLTGIEGDLTLKFTEKDGIDYAPTTVQLPGGERVPFLFTVKNLIATSIESGTKLAGKFTVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFAENNKKFDVGSGSIELKVTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Pyrenomonas_helgolandii ANA--LSSADVRSLTYQQIKGTGLANRCPEVEKITDLCLEPKSFQIEEEFVDTKLMTRATYTLAGVEGPLFLTFLEKEGIDYAATTVQLPGGERVPFMFTVKDLEAKSISAGTEFGGTFKVPSYRSGLFLDPKGRGGTTGYDMAQALPGMEAEGQEELFKETNKVFQVTDGTIEFAVNKVDAATGEFSGVFVSEQLSDTDMGSKAPKKVLLKGIIFGKV Thalassiosira_pseudonana AQA--ITKSELNQLSYLQVKGTGLANRCSEVIRLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLEGIEGSLKIVFTEEEGIDYAPTTVQLPGGERVPFLFTVKELVATGFKPGFQMGGDFSVPSYRTGLFLDPKGRGGVTGYDMAVALPGLQSEGDAELFKENNKTFEVGNGRIEMEVNKVNAEESEIGGVFVASQSGDTDMGSKVPKKILTKGIFYAKI Vaucheria_frigida ADA--ITKDQIDSLSYMQVKGTGLANRCPEVIKLMDLCIEPKVFQVLEEYVNTKLMTRQTYTLYGIEGSFALTFREKDGIDYAATTVQLPGGERVPFLFTVKELVAKAVAPGFQFGGGFSTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDKEMFKENNKTFDVTKGQIEFEVNRVDASAGEIGGVFVSNQKGDTDMGSKTPKDVLVKGIFYGRL Vaucheria_litorea VEA--ITKDQIESLSYLQVKGTGLANRCPEVFKIVDMCIEPKTFQVLEEYVNTKLMTRQTYTLYGIDGSFAITFREKDGIDYAATTIQLPGGERVPFLFTVKELVAQAVTPGLQFGGPFSTPSYRTGLFLDPKGRGGSTGYDMAVALPGKQSEGDAELFGENNKTFDVTKGNIEFEVNRVDPSNGEIGGVFVSKQKGDTDMGSKVPKDLLIKGIFYGRL ; END; BEGIN TREES; TITLE Dinophyta_pbsO_TB; LINK TAXA = Taxa1; TRANSLATE 1 Cyanidioschyzon_merolae, 2 Galdieria_sulphuraria, 3 Porphyra_yezoensis, 4 Porphyridium_purpureum, 5 Neorhodella_cyanea, 6 Dixoniella_grisea, 7 Guillardia_theta, 8 Pyrenomonas_helgolandii, 9 Cryptomonas_ovata, 10 Chroomonas_caudata, 11 Aureococcus_anophagefferens, 12 Heterosigma_akashiwo, 13 Vaucheria_litorea, 14 Vaucheria_frigida, 15 Botrydium_granulatum, 16 Fucus_distichus, 17 Phaeodactylum_tricornutum, 18 Chaetoceros_gracilis, 19 Thalassiosira_pseudonana, 20 Kryptoperidinium_foliaceum, 21 Karlodinium_veneficum, 22 Pavlova_lutheri, 23 Karenia_brevis, 24 Isochrysis_galbana, 25 Emiliania_huxleyi, 26 Prymnesium_parvum, 27 Heterocapsa_triquetra, 28 Amphidinium_carterae; TREE PAUP_1 = [&R] ((((((1:36.0,2:31.0):9.0,3:23.0):7.0,(4:27.0,(5:17.0,6:11.0):6.0):7.0):7.0,((7:22.0,(8:12.0,9:22.0):7.0):10.0,10:26.0):6.0):17.0,(11:42.0,((12:27.0,(((17:10.0,20:7.0):5.0,18:18.0):7.0,19:18.0):15.0):6.0,((13:19.0,(14:9.0,15:9.0):6.0):6.0,16:31.0):18.0):11.0):6.0):0.0,(((21:27.0,(23:38.0,((24:12.0,25:9.0):8.0,26:9.0):8.0):8.0):19.0,22:47.0):12.0,(27:35.0,28:20.0):17.0):10.0); END;