#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 24, 2024; 14:34 GMT TreeBASE (cc) 1994-2008 Study reference: Cohen B.L., Baker A., Blechschmidt K., Dittmann D., Furness R., Gerwin J., Helbig A., De korte J., Marshall H., Palma R., Peter H., Ramli R., Siebold I., Willcox M., Wilson R., & Zink R. 1997. Enigmatic phylogeny of skuas (Aves: Stercorariidae). Proceedings of the Royal Society B, 264(1379): 181-190. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S600] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=10; TAXLABELS Catharacta_antarctica Catharacta_chilensis Catharacta_hamiltoni Catharacta_lonnbergi Catharacta_maccormicki Catharacta_skua Larus_canus Stercorarius_longicaudus Stercorarius_parasiticus Stercorarius_pomarinus ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=5; TAXLABELS Catharacta_chilensis Larus_fuscus Stercorarius_longicaudus Stercorarius_parasiticus Stercorarius_pomarinus ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2245] TITLE cytb; LINK TAXA = Taxa1; DIMENSIONS NCHAR=1020; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 1000 1010 1020 1030 1040 1050 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Catharacta_antarctica GGATCTCTACTAGGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACCGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAATGGAGCCTCATTTTTCTTCATCTGCATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTATACAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTT?GTAGGATATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCTACAGTCATTACCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCCTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTAGGAATTGTCTCAAATTGCGACAAAATCCCATTCCACCCCTACTTCTCACTAAAAGATATCCTAGGGTTCATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCGCATATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACCTTCCGCCCACTCTCACAAATTCTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA Catharacta_chilensis GGATCTCTACTAGGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACCGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAATGGAGCCTCATTTTTCTTCATCTGCATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTA{CT}ACAAAGAAACCTGAAACACTGGCGTTATCCTCTTACT{AG}ACCCTAATAGCAACTGCCTTCGTAGGATATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCTACAGTCATTACCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCCTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGC{CT}CTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTAGGAATTGTCTCAAATTGCGAC{AG}AAAT{CG}CCATTCC{AG}CCCCTACTTC{AT}CACTA{AG}AAGATATCCTAGGGTTCATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCACATATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACCTTCCGCCCACTCTCACAAAT{CT}CTATTCTGAACCTTAGTC{AG}C{CT}AACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA Catharacta_hamiltoni GGATCTCTACTAAGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACCGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAATGGAGCCTCATTTTTCTTCATCTGCATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTATACAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGATATGT????????????????????????????????????????????CCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCCTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTAGGAATTGTCTCAAATTGCGACAAAATCCCATTCCACCCCTACTTCTCACTAAAAGATATCCTAGGGTTCATTATCATATTCCTTCCA{CT}TAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCACATATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACCTTCCGCCCACTCTCACAAATTCTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA Catharacta_lonnbergi GGATC{CT}CTACTAGGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACCGCAGACACAACCTTAGCCTTCACATC{CT}GTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAATGGAGCCTCATTTTTCTTCATCTGCATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTA{CT}ACAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGATATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCTACAGTCATTACCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCCTGAGGTGG{CT}TTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTAGGAATTGTCTCAAATTGCGACAAAATCCCATTCCA{CT}CCCTACTTC{AT}CACTAAAAGATATCCTAGGGTTCATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCACATATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACCTTCCGCCCACTCTCACAAAT{CT}CTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA Catharacta_maccormicki GGATCTCTACTA{AG}GTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACCGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAATGGAGCCTCATTTTTCTTCATCTGCATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTATACAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGATATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCTACAGTCATTACCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCCTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTAGGAATTGTCTCAAATTGCGACAAAATCCCATTCCATCCCTACTTCTCACTAAAAGATATCCTAGGGTTCATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCACATATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACCTTCCGCCCACTCTCACAAATTCTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA Catharacta_skua GGATCTCTACTAGGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACTGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAACGGAGCCTCATTTTTCTTCATCTGTATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTATATAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGGTATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCCACAGTCATTACCAACCTATTCTCGGCAATCCCCTACATCGGCCAAACCCTTGTAGAATGGGCTTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCC{AG}CTAG?AATTGTCTCAAATTGCGACAAAATCCCATTCCACCCCTACTTCTCACTAAAAGACATCCTAGGATTTATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCTAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCCCCACACATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACTTTCCGCCCACTTTCACAAATTCTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCCTAGAA Larus_canus GGGTCCCTACTAGGCATTTGCCTGCTAACACAAATCCTAACAGGACTCCTGCTAGCTATACACTACACCGCAGACACAACCCTAGCCGTCTCATCCGTCGCCCACACATGTCGAAACGTACAATATGGCTGACTAATCCGAAACCTCCACGCAAACGGAGCATCATTCTTCTTTATTTGTATCTACCTACACATCGGACGAGGATTCTACTATGGCTCATACCTCTATAAAGAAACCTGAAATACAGGAGTTATTCTCCTCTTAACCCTAATAGCAACTGCCTTCGTAGGATATGTCC??????????????????????????????????????????CCAACCTATTCTCAGC??TCCCATACATCGGCCAAACCCTCGTAGAATGAGCCTGAGGTGGCTTCTCAGTGGACAACCCAACACTAACCCGATTCTTCGCCCTCCATTTCCTACTTCCATTCATAATCGCAGGTCTTACCTTCATCCACCTAACCTTTCTTCACGAATCAGGGTCAAACAATCCACTGGGTATTCAATCAAACTGTGACAAAATCCCATTCCACCCTTACTTCTCGCTCAAAGACATCCTAGGATTCATTATCATATTCTTACCACTAACAACATTGACTCTATTCTCACCCAACCTGCTAGGTGACCCAGAAAACTTTACTCCAGCAAACCCACTCGTTACACCCCCACACATTAAACCCGAATGATACTTCCTATTCGCATACGCTATCTTACGCTCAATCCCCAACAAACTAGGGGGCGTATTAGCCTTTGCAGCATCCGTACTAGTACTATTCTTAAGCCCCCTCCTCCACAAATCTAAGCAACGTACAATAACCTTCCGTCCCCTCTCACAACTCCTATTCTGAATCCTAGTTACTAACCTCTTCATCCTAACATGAGTAGGCAGTCAACCCGTAGAGCATCCCTTTATCATCATTGGACAACTGGCTTCCTTAACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGGCCCTAGGA Stercorarius_longicaudus GGATCCCTACTAGGCATTTGTCTACTAACACAAATCCTAACAGGCCTACTACTAGCAATGCACTATACAGCAGACACAACTTTAGCCTTCACATCCGTTGCCCATACATGCCGCAACGTCCAATACGGCTGACTAATCCGAAACCTCCATGCAAACGGAGCCTCATTCTTCTTCATCTGCATCTACCTGCACATTGGACGAGGATTTTACTACGGCTCATACCTATATAAAGAAACCTGAAACACCGGTGTCATCCTCTTATTAACCCTAATAGCAACTGCCTTTGTAGGATATGTCCTACCATGAGGACAAATATCATTTTGAGGAGCTACAGTCATCACCAACCTATTCTCAGCAATTCCCTACATCGGTCAAACCCTTGTAGAATGGGCCTGGGGTGGCTTTTCAGTAGATAACCCAACACTAACTCGATTTTTTGCCCTCCATTTCCTCCTCCCATTCGTAATTGCAGGCCTTACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCACTGGGAATTGTCTCAAACTGCGATAAAATCCCATTCCACCCTTACTTCTCGCTAAAAGATATCCTAGGATTTATCATCATATTCCTTCCACTAACAACCCTCGCCCTATTCTCACCTAATCTACTAGGTGACCCAGAAAACTTCACTCCAGCAAACCCACTAGTTACGCCTCCACATATTAAACCTGAATGGTACTTTCTGTTTGCCTATGCCATCTTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCCTAGCCGCCTCAGTA{CT}TAGTCCTATTCCTAACCCCCCTTCTCCATAAATCCAAACAGCGCACAATAACCTTCCGCCCACTCTCACAGTTACTATTCTGAACCTTAGTCGCTAACCTCTTTATCCTGACCTGGGTGGGCAGCCAACCCGTAGAACATCCATTCATTATCATCGGACAGTTAGCCTCCCTCACCTACTTCACTATCCTATTACTCCTATTTCCCATCATCGGGACCTTAGAA Stercorarius_parasiticus GGATCCCTGCTAGGTATCTGCCTACTAACACAGATCCTTACAGGTCTGCTACTAGCAATACACTATACAGCAGACACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGCAACGTCCAATACGGCTGACTAATCCGAAACCTTCATGCAAACGGAGCCTCATTCTTCTTCATCTGCATCTACCTGCACATTGGACGAGGATTTTACTATGGCTCATACCTATATCAAGAAACTTGAAACACTGGTGTCATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGGTACGTCCTACCATGAGGACAAATATCATTTTGAGGGGCTACAGTCATCACCAACCTATTCTCAGCAATTCCCTACATCGGCCAGACCCTTGTAGAATGAGCCTGAGGAGGCTTTTCAGTAGACA{AG}CCCAACATTAACCCGATTTTTTGCCCTCCATTTCCTTCTCCCATTCGTAATCGCAGGCCTTACCCTAATCCACCTTACCTTCCTCCATGAATCTGGATCAAACAACCCGCTAGGAATTGTCTCAAACTGCGACAAAATCCCATTCCATCCATACTTCTCGCTA{AG}AAGATATCCTAGGGTTTATCATCATACTCTTCCCACTAATAACCCTCGCTCTATTCTCACCTAATCTACTAGGTGACCCAGAAAACTTTACCCCGGCAAACCCGCTAGTTACACCTCCACATATTAAGCCTGAGTGGTACTTCCTGTTTGCATATGCCATCCTACGCTCGATTCCCAACAAACTAGGAGGCGTCCTAGCTCTAGCTGCCTCAGTATTAGTCCTATTCCTAACCCCCCTTCTCCATAAATCCAAACAACGCACAATAACCTTCCGCCCACTCTCACAGCTCCTATTCTGAACCTTAGTCGCTAATCTCTTCATCCTAACATGAGTAGGTAGCCAACCCGTAGAACATCCATTCATTATCATCGGACAGCTAGCCTCCTTCACTTACTTCGCTACCCTATTATTCCTATTCCCCATCATCGGGACCTTAGAA Stercorarius_pomarinus GGATCTCTACTAGGTATCTGCCTACTGACGCAAATCCTAACAGGCCTACTACTAGCAATACACTACACTGCAGA{CT}ACAACCTTAGCCTTCACATCCGTTGCTCACACATGCCGAAACGTCCAATATGGTTGACTAATCCGAAACCTCCATGCAAACGGAGCCTCATTTTTCTTCATCTGTATCTACCTACACATCGGACGAGGATTTTACTACGGCTCATACCTATATAAAGAAACCTGAAACACTGGCGTTATCCTCTTACTAACCCTAATAGCAACTGCCTTCGTAGGGTATGTCCTACCATGAGGACAAATATCATTTTGAGGGGCCACAGTCATTACCAACCTATTCTCAGCAA{CT}CCCCTACATCGGCCAAACCCTTGTAGAATGGGCTTGAGGTGGTTTCTCAGTAGACAACCCAACACTAACTCGATTTTTCGCTCTCCACTTCCTTCTCCCATTCATAATTGCAGGTCTCACCCTAATCCACCTCACCTTCCTCCACGAATCCGGATCAAACAATCCGCTAGGAATTGTCTCAAATTGCGACAAAATCCCATTCC{AG}CCCCTACTTCTCACTA{AG}AAGACATCCTAGGG{CT}TTATTATCATATTCCTTCCATTAGCAACCCTCGCCCTATTCTCACCCAACCTACTAGGTGACCCAGAGAACTTCACCCCAGCAAACCCACTAGTTACACCTCCACACATCAAACCCGAGTGATACTTCCTATTTGCATACGCCATCCTACGCTCAATCCCCAACAAACTAGGAGGTGTCCTAGCCTTAGCCGCCTCAGTACTAGTTCTATTCCTAATCCCCCTCCTTCACAAATCCAAACAGCGTACAATAACTTTCCGCCCACTTTCACAAATTCTATTCTGAACCTTAGTCGCCAACCTCCTTATCCTAACATGAGTGGGCAGCCAACCCGTAGAACATCCATTCATCATCATTGGACAACTAGCCTCCCTCACCTACTTCACCATCCTACTACTCCTATTCCCTGCCATCGGGACCTTAGAA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = cytb) = N: 1-1020; CODONPOSSET CodonPositions (CHARACTERS = cytb) = N: 1-1020; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2247] TITLE 12S; LINK TAXA = Taxa1; DIMENSIONS NCHAR=394; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Catharacta_antarctica ????????CTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGTCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCCATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGCGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Catharacta_chilensis ????????CTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGTCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCCATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Catharacta_hamiltoni GCCTAGCCCTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGTCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCCATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Catharacta_lonnbergi ???????????????CTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGTCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCCATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Catharacta_maccormicki ????????CTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCC?TGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCCATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Catharacta_skua ????????CTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACAAGACAGGTCAAGGTATAGCCTATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCCTTTAAGTTGGCCCTGGGGCACG Larus_canus GCCTAGCCCTAAATCTCGATGCTTGCCGTACCAAAGCATCCGCCCGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCATCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTCGCCAAAGCAGCCTACATACCGCCGTCGCCAGCTCACCTTCCCTGAAAGCCCAATAGTGAGCACAATAGCCCAACCTGCTAGTAAGACAGGTCAAGGTATAGCCCATGAGGTGGAAGAAATGGGCTACATTTTCTACGATAGAAAA????????????????????????????????????????????????????????????????????????????????????????????? Stercorarius_longicaudus ????????????????????????????????AAAGCATCCGCCCGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCCCTTGCCAGAACAGCCTACATACCGCCGTCGCCAGCTCACCTCCCCTGAGAGCTCAACAGTGAGCACAATAGCCTAACCCGCTAACAAGACAGGTCAAGGTATAGCCTATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGG????????????????????????????????????? Stercorarius_parasiticus GCCTAGCCCTAAATCCTGATGCTTACCATACCAAAGCATCCGCCTGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATCCACCCGACCACCCCTTGCCAGAACAGCCTACATACCGCCGTCGCCAGCTCACCTCTCCTGAGAGCCCAACAGTGAGCACAATAGCCTAACCCACTAACAAGACAGGTCAAGGTATAGCTCATGGGGTGGAAGAAATGGGCTACATTTTCTATAGTAGAAAACCTACGAAAGAGGGTATGAAATAG-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGAGTCCCCTTTAAGTTGGCCCTGAGGCACG Stercorarius_pomarinus GCCTAGCCCTAAATCCTGATGCTTACCGTACCAAAGCATCCGCCTGGGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAACCCACGATTCACCCGACCACCTCTTGCCAGAGCAGCCTACATACCGCCGTCGCCAGCTCACCTCCCC??AGAGCCCAACAGTGAGCACAATAGCCCAACCCACTAACCAGACAGGTCAAGGTATAGCCTATGGGGTGGAAGAAATGGGCTACATTTTCTACAATAGAAAACCTACGAAAGAGGGTATGAAATAA-CCCCCGGAAGGCGGATTTAGCAGTAAAGGGGAACAATAGGGCCCCC?????????????????????? ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 12S) = N: 1-394; CODONPOSSET CodonPositions (CHARACTERS = 12S) = N: 1-394; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2246] TITLE RFLP; LINK TAXA = Taxa2; DIMENSIONS NCHAR=79; FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -; CHARSTATELABELS 1 AvaI, 2 AvaI, 3 AvaI, 4 AvaI, 5 AvaI, 6 AvaI, 7 AvaI, 8 BamH1, 9 BamH1, 10 BamH1, 11 BamH1, 12 BamH1, 13 BamH1, 14 BclI, 15 BclI, 16 BclI, 17 BclI, 18 BclI, 19 BclI, 20 BclI, 21 BglI, 22 BglI, 23 BglI, 24 BglI, 25 BglI, 26 BglI, 27 BglI, 28 BstEII, 29 BstEII, 30 BstEII, 31 BstEII, 32 BstEII, 33 BstEII, 34 BstEII, 35 EcoRI, 36 EcoRI, 37 EcoRI, 38 EcoRI, 39 HaeII, 40 HaeII, 41 HaeII, 42 HaeII, 43 PstI, 44 PstI, 45 PstI, 46 PstI, 47 PstI, 48 PstI, 49 PstI, 50 PstI, 51 PvuII, 52 PvuII, 53 PvuII, 54 PvuII, 55 PvuII, 56 PvuII, 57 PvuII, 58 SacI, 59 SacI, 60 SacI, 61 SacI, 62 SacI, 63 SacI, 64 SacI, 65 SacI, 66 SacII, 67 SacII, 68 SacII, 69 SalI, 70 SalI, 71 XbaI, 72 XbaI, 73 XbaI, 74 XbaI, 75 XbaI, 76 XhoI, 77 XhoI, 78 XhoI, 79 XhoI, ; MATRIX [ 10 20 30 40 50 60 70 ] [ . . . . . . . ] Catharacta_chilensis 1101100110000111110011100111111100111111001000000010000001100000011010100000000 Larus_fuscus 1110001100011100100010100000100101000011001001111000011110000111111010000110000 Stercorarius_longicaudus 1110000100011110111101011001110100111011001111111111100001001000011011101001100 Stercorarius_parasiticus 1101010100010110100011010001110000111011111001000111000001010000011110101001011 Stercorarius_pomarinus 1101100111100111110011100111110110111111001010000010000001100000011010110000000 ; END; BEGIN TREES; TITLE Tb5656; LINK TAXA = Taxa2; TRANSLATE 1 Larus_fuscus, 2 Stercorarius_pomarinus, 3 Stercorarius_parasiticus, 4 Stercorarius_longicaudus, 5 Catharacta_chilensis; TREE RFLP_2 = [&R] (1,(((5,2),3),4)); TREE RFLP_1 = [&R] (1,((5,2),(4,3))); END; BEGIN TREES; TITLE Tb5655; LINK TAXA = Taxa1; TRANSLATE 1 Stercorarius_pomarinus, 2 Stercorarius_parasiticus, 3 Stercorarius_longicaudus, 4 Catharacta_skua, 5 Catharacta_maccormicki, 6 Catharacta_lonnbergi, 7 Catharacta_hamiltoni, 8 Catharacta_chilensis, 9 Catharacta_antarctica, 10 Larus_canus; TREE Fig._1 = [&R] (((((9,8,7,6),5),(4,1)),(2,3))Stercorariidae,10); END;