#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 26, 2024; 16:22 GMT TreeBASE (cc) 1994-2008 Study reference: Fitch D. 1997. Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans. Systematic Biology, 46(1): 145-179. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S384] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=10; TAXLABELS Caenorhabditis_briggsae Caenorhabditis_elegans Caenorhabditis_remanei Caenorhabditis_sp._CB5161 Pellioditis_typica Pelodera_strongyloides Rhabditella_axei Rhabditis_blumi Rhabditis_myriophila Teratorhabditis_palmarum ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3980] TITLE 18S_rDNA; LINK TAXA = Taxa1; DIMENSIONS NCHAR=1795; 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 1060 1070 1080 1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200 1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320 1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440 1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560 1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670 1680 1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Caenorhabditis_briggsae GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTGTTCGGAA-TCCTAATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTAAACCCCAACGTAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGGACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTTATTGGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGAAACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATGATTCTTCGAGTATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAACTCGTAGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGTCCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-TGTTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAGGACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGACCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGACTCAGCGGGTTTTTC-?CTATGCCGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGCCTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTGGGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT Caenorhabditis_elegans GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTATCCGGGA-TCCTCATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTATACCCCAACGCAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGGACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTTATTGGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGAAACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATGATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTAGGTTACGTGCCGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTGGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGTTCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-CGCTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAGGACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGACCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGAGTCAGCGGGTTTTTC-?CTATGCCGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGCCTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTGGGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT Caenorhabditis_remanei GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTGTTCGGAA-TCCT-ATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTAAGCCCCAACGTAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGGACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCGGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTCATTGGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGAAACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATGATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGTCCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-TGTTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAGGACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGACCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGACTCAGCGGGTTTTTC-?CTATGCCGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGCCTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTGGGGACTGTGGCTCCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT Caenorhabditis_sp._CB5161 GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTATTCGGAA-TCCT-ATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTATACCCCAACGCAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTCTCGGACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCTATCAACTA-?GATGGTAGTCTATTGGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGAAACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATATAAATGATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTAGGTTACGTGTTGCAGT-??????TCGCC-????????CTCGTGCGTCAACTGTAGCCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGTTCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-GCTTTGCTTGTATAGCTCAT-CATGGAATAATGAAATAGGACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGACCGTAGTGAGACGCCCAATAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTCGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGAGTCAGCGGGTTTTTC-?CTATGCCGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGCCTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTGGGGACTGTCGCTTCGAGGTTTTCGGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAG?? Pellioditis_typica ????????????????????????????????????????????GAA-?ACTG-CGAA-CGG-???CTCATTAGAGCTTATACTAAGCTAG-CACCT-GCCTTTTA-GGATATCTTCGACAA-ATTGAAGCTAATACATGCAACCATGGCTC-?CTTCGGG-?GGTCGCA-ATAT-TAG-AACT-ACCAGT-?TTACTGGATA-?????GTTGACTTTAATTATCGTAGA-AATCGGCAGCGTGAGCT-CCGATGGGTGCAAGTTATGTACGCCCTATCACCCA-?GCAGGCTGTTTAACCGACAGCCAGGGGTATAACGGGTAACGGAGAACTAG-GTTCGTCTCCGGAGAAGAAGCCTTCGAAA-GGCTACTACATCCAAGGAAGGCAGCAGGCGCGTAACTTATCCA-?CTAC-ATCA-???GTGAG-?ATAGTAACTAGTCTTAACTATTAACTGACTTTTCAAGTTAGTTATGGTCCATGAGTTGAGCTTAAATAGCTCTTCGAGGATCAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGCGTAAATTATTACTGCTGCGGTTAAAAAGCTCGTAGTTGAATCT-AGACGTGTATTGTTGGCATGCTTTTGGCATTCATTTGTCATTGGCTTTAGCCTTCAACCGTCT-??TTGCTGGTTTTCTGTTGGTG-?TTCG-CATC-TTCAGTGGCCAGCGAGT-TACT-TTGACCAAATCAGAGTGCTCAAAACAGG-CGAAAGCTTGTATGATTTCT-CGAGGAATAACAGAATAGGACTTCG-GTTCT-TGTTGTTGGTTCCAGAATCG-TTTAATGGTTAAGAGGGACAATTCGGGGGCAGCCGTATCCTCGGGCGAGGGGTGAAATCCGTAGACCCTGAGGAGACGACCAATAGCGAAAGCAGCTGCCAAGAATGTCTCCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACTATACCAGCTCAT-??GACTAGTTGG?-GATGT-?AATGTCCACAACGG-GTCTGATCCGGAAACGAAAG-CTTTCGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTAGACTCAACACTGGGAAGCTCACCCGGTCTGGACACTATGAGGATTGACGGAACT-CGAA-GCTCCTTCTCGATTT-AGTGGCTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATCTGTCTGGTTTATTCCGGT-AACGATCGAGACTCTAGCCAACTCAATAGTTACTGGATC-GCAAGG-??ATCCAGGTAACTTC-TTAGAGGGATTAGTGGCGTTT-AGTCACACGAGAAGGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCCACACTGGGAGAATCATTAGGTGTC-???CATGGCCGAAAGGCT-TTGGT-??AATCCTTT-TGAACCTCTCCCGTGG-CCGGGATAGGGATTTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTCCTAGTAAGTGTG-AGTCATCAACTCACGTTGATTGCGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGAACT-?GAACTGTTTCGAGAAGGCTGAGGACTGACTTT-????GTTCACTTGTGTTCATTGTT-?GGGAATCAGTTGGATCGAATTGGTTTGAACCGGGCACAAGTCGTAACAAGGTAG?? Pelodera_strongyloides GATTAAGCCATGCAAGTAAAAGTGCCAACTTGTTCGTTCTTCGGAACTAAGTTGAACTACGGACTACTCATTGCAATGTTTTGAAAAAAGCTGAAAAGACGTGAAAGGGATATATACGGCAAATCTGGGTCTAATACAGAATACGTA-????????????????????CACCTAGCTATGGATAAAGAAATCG-???AAGAGAATGGCCGTCCACTTT-???????TTGCGGATTGACAGCCGGAACC???????????????????-AACACCATTTTCTG-???GTTGGTGGTGTA-?TTGGTGCAAATAGGACAAT-GGTTGCGGATGATAGTTGTCGGGCGTCGGAGAATACGCTTGAGAAACGGCGAATACTTCTAAGGAAGGCAGCAGGCTCGCAAATTACCCATACTTCTAATTTTGAGCGGGTGGTAGTGACAACAAATACCGAA-ACCTTCCTCATATGAGGAGCTATTGG-AATGATTTTCTTTTAAACCGAGATCGCAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAACTCCAGCTCTTAAAGTTTATACCATATCTGCTATGGTTGGCAAGTCTGT-GCCAGCAAGCCCGTACACAGCTCTTAAA-?GTTATACCAT-???ATCTGCTATGGTT-GGAATGCATTACTTTGGATTCTA-??TTTGCCGGTGCAGCTTCGGTTGCGCATGCCGGCGGAA-????TACT-CCGAGTCTCACGGAGTGTTCAAAACAAGACTTTTGCTTGAACGATCATTGCATGGGATATTGGAAAAGGACTATGTGCTCTTTATT-TTGGTTTCGGCCTAG??-TAATGGATAGCAGGGTCTG-CCGGGGGCGTACGTATCGTCCCGCGAGGGGTGAAATCCGTAGACCGTGACGAGACGACCAAGAGCGCAAGCATACGCCAAGAAAGAC-CCGCTAACCTCTGGCGAGAGCCTGACGATTAAAGACGATTAGATACCGTCGTAGTTTTATCTGTGAACGATGGGAACTGACTGAAGTTTTATGCGAAGTACTACAAGAGTTGTT-?TGAATT?-CCTGGAAACGTCGAGTGTCC-?CTCCAGGGGTAGTATTGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGCGCACCACCAGGAGTGGAGCCTGTGGCTTAATTTGACTCAACACGGAGAAACTTACCCAGCCATCACGTTTAGTGGATGGACCTGCGA-AAGT-GAGCGTTCTTGATTT-TACGAATAGTGGTGCATGGTCGATTTTAGTTCGTGGGTTGATCTCTCAGCTTAATTGCGTT-AACGAACAAGATACAAAAACCCCAAAAGGATT-????????????????ATCCAAGTGGGTTC???????-AACGGTTACTTCCAAATTTCTATGAAATTGTGCTATATCAGGTCTGT-ACGCTCTACGATGGCTGGGGCCGCACGCGTGCTACACTTAGGTCCGCAGCGAGTTCTTAATCACAGCGGGTAAACCCACTGT??CGAACCAATGCAATGGACCTTCGTGGATTGGGATTGTAATTTGCACGTTTGTCGGCTAATTCGATATCGTGAACAAGGAATTCCTAGTAAGCGTTCAGTCATCATCTCACACTGAATGCGTCCCTGCGCTTTGTACACACCGCCCGTCGCTACCGGGGACTCTGAGCTGCGGCGAGAAGT?????????????????????????????????????????????????????????????????????????????????????????????????? Rhabditella_axei GATTAAGCCATGCA-???????TGT?-ATAGTTCATTTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAGCAGATTTTAC-CTATTCCGAA-ATCTTATTTGGATAACTGCGGTAATTCTGGAGCTAATACATGCAATAAAGCCCATCCTTACGGGTGGGTGCAGATAT-TAG-TACAAACCAATCGTCTCTG-ACGAAGTTTGTTGACTCTGAATATCGTAGCTGATCGACGGTTT-ACCTGTCGACGATCGGAGAAGGAGTCTGCCCTATCAACCA-?GATGGTAGTCTATTAGTCTACCATGGTGATCACGGGTAACGGAGAATCAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGTAACTTATCCA-?CTACC-TTA-???GTGAG-?ATAGTGACTAAAAATAAAGAG-ACCAATCCTTT-GGATTGGTTATT-TCAATGAGTTGAGCTTAAATAGCTCTTCGAGGACCCAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTATAAATCGTCATTGCTGCGGTTAAAAAGCTCGTAGTTGGATTTGAGGCACGTACAGCGGT-??????TCGGC-????????TCTGCCG-TTAATCACTGTTGTGTCTAATTTGTTGGTTTTCTGTTGGTAACTTCGGTTCC-TTCAGTGGCTAGCAAGTTTACC-TTGATCAAATCAAAGCGCTCAAAGCAGG-CGATTGCTTGCATTTTGGAT-CATGGAATAATAAAATAGGATTTCG-ATTCTAT-TTATTGGTTTAAGAATTGAATTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCCCTGCGCGAGAGGTGAAATTCGTGGACCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACTATGCCATCTAGC-??GATCCGATAG?-GGTATT-CATGCCTTG??GGG-AGCT-TCCCGGAAACGAAAGTTTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGCCCGGACACCAGTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTACAGAAT-?TATTAA-??GTTCTGTTAACTTC-TTAGAGGGATAAGCGGTGTTT-AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAGAATCAGCTGGTTTTT-??CATTATCGAAAGATA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGTTTCGAGAAGACTGAGGACTGCTGCAGCGAGGCTC-?ACGC-TTTTCTGTTGCGGAAATCATTTTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTAGCT Rhabditis_blumi GACTAAGCCATGCA-???????TGT-CTCAGATCCCCATTTCACGGA-?ATCGGCGAA-CGG-???CTCAATATTACAGCTATCACT-TATTCGGTG-ATCCTT-?TGGATAACTGCGGAAATACTGGAGCTAATACATGCAACAT-GCCGTGTCTT-TGACACGGTGCAATTAT-TAG-TACAAATCAATCGCTTTCGGGCGTTGTTTGTTGACTCTGAATAACGTAGTTTATCGGTGGTTT-ATCTGCCGAAGTCCGAAATAGGTGTCTGCCCTATCAACT-??GACGGTAGTCTATTAGTCTACCGAGGTTATCACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGTAACTTATCCA-?CTACCAATA-???GTGAG-?ATAGCGACAGAAAATAAAAAG-ACCAGTCCTCT-GGATTGGTTATT-TCAATGAATTGAGTCTAAACAGCTCTTTGAGTAACAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTACACCGTTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATTTGAGTCGTTCGTTTGCGT-??????TGCTC-????????TTTG-AGCTTAACGTAGGCAGCGACTATTTTGCTGGTTTGCTGTTGTAGCTTTCGGGCTC-TTCAGTTGCTAGCGAGTTTACT-TTGAATAAATCAGAGTGTTCATGACAGG-TGTTTGCCTGAATGGTCTAT-CATGGAATAATAGAATAGGACTTCG-GTTCTGT-TTATTGGTTTCTGAACCGATGTAATGATTAACAGGAACAAACCGGGGGCATACGTATTTCTGCGCGAGAGGTGAAATTCGTGGACCGCAGAAGGACGCCTAAAAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCATGAGCGAAAGTTAGAGTTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACTATGCCATCTAGC-??GATCCAATGG?-GATGTT?-AAGTCTCGTTGGGGAGCT??-????AAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAACTGAAACTTAAAGAAATTGACGGAATGGCACCACCA???GTGGATTTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGCCCGGACACTGTTAGGATTGACAGA-TT-GATA-GCTCTTTCTTGATTC-GGTGGTTGGTGGTGCATGGCCGTTCTTGGTTGGTGGAGTGATTTGTCTGGTTGATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCTGAAT-?CTTCTA-??GTTCAGTAAACCTC-TTAGAGGCATAAGCGGTGTGA-AACCGCATGAGAGAGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTAATACACTGGGAGAATCAGCTGGCCATC-??CATTGCCGAAAGGTA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGT-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATCGCTAGTAAGTGTG-AGTCATCAGCTCATATTGATTACGTCCCTGCCATTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGTTTCGAGAAGTGTGAGGACTTTTGTTGCGGGGCTT-?CGGC-TCTTCTTCGAGAGAAATCATCCTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTA??? Rhabditis_myriophila GATTAAGCCATGCA-???????TGT-AAAAGTTCAACTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAGCAGCTATCATTCTCTTCGGAT-ATCCTTTATGGATAACTGCGGAAATTCTGGAGCTAATACATGCAACAAAACCTCGACTT-TGAAGAGGTGCAGATAT-TAG-TACAAACCAATCGTCTTCGGACGTTGTTTGTTGACTCTGAATATCGCAGTTTATCGGCAGGTA-ATCTACCGATAACCGAAAGAAGTGTCTGCCCTATCAACCA-?GATGGTAGTCTATTAGTCTACCATGGTTATTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGTAACTTATCCA-?CTACTT-CA-???GTGAG-?ATAGTGACTAAAAATAAAAAG-ACCAATCCTCACGGATCGGTTATT-TCAATGAGTTGAGCTTAAATAGCTCTTCGAGGATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTAAATCGTCATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTGAGTTGCATGCGTTGGT-??????TCCTC-????????TCTG-AGGTTAATCTTCGCTGCAACTATTTTGCTGGTTTTCTGCAGATAGCTTCGGCTTC-TGTAGTGGCTAGCGAGATTACT-TTGAATAAAACAGAGTGTTCAAAACAAG-CGATTGCTTGAATGCTCGAT-CATGGAATAATGGAATAGGACCTCG-GTTCTAT-TTATTGGTTCAAGAATTGAGGTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCC-TGCGCGAGAGGTGAAATTCGTGGACCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACTATGCCATCTAGC-??GATCCGGTGG?-GGTTAT?-TCGCCTCGCCGGGGAGCT-TCCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGCCCGGACACCGTTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCACGAT-?TTTCGG-??GTCGTGTGAACTTC-TTAGAGGGATAAGCGGTGTTT-AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAGGATCAGCTGGTCGCC-??AATTGCCGAAAGGTA-TTGGT-??AAACCGTT?-GAAACCCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGATTCGAGAAGAGTGAGGACTGACGCAGAGGGGCTT-?CGGC-TCTACTGTGATGGGAATCACTTTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTACCT Teratorhabditis_palmarum GATTAAGCCATGCA-???????TGTATTCGAACGGTCATTTTATGGCCCATCTGCGAA-CGG-???CTCATTACAACAGTTAAAATTCGCATGACGA-TTGTTTCTTGGATACTTTCAGTAATTCTGGAGCTAATACGT-?AAGCGTGCTTCGGCAC-??????????CACTTAT-TAG?-ATCGACCAACCGCTT-?AGGCGTTTTGTGTTGACTCTGAATATT-TTGCAGACCG-CATGCGAAAGCGGCGGCGTGTCATGCGATTAACTGCCCTATCAACTTTTGATGGTAGTTTAGTTGACTACCATGGTGATAACGGGTAACGGAGGATCAGGGTTTGACTCCGGAGAGTATCCT-GAGAGACGGCAAACACATCTAAGGAAGGCAGCAGGCGCGCAAATTACCCA-?CTCTCAATTC-?GAGGAG-?GTAGTGACAACAACTAACGAG-ACTGCTCCTACGGGAACAGTCATCG-AAATGGGTACAATTTAAACCCTTTAACGAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCAAAGTGTATGTCATTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTGAGCTCGTGAATCCAGT-??????CTGCC??????-TCTGTGTGGTACTGGCATTC-TGAGTTTGATTCGTCGGC-???????????????????????CTCGCCGGCGAG-?AGT-TACTCTTGAATAAATCGGAGTGCTCAAAACAAC-GTTTCGCTTGAACGTTTTTG-CATGGAATAATGGAAAAGGAATTCG-GTTCCTTACTGTTGGTTTCGGAATTGAATTAATGATTAAGAGGGACCAA-CGGGGGCATGCGTATCGCTGCGCGAGAGGTGAAATTCATGGACCGCAGCGAGACGGCCTACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCGTAGTTCTGACCGTAAACGATACCATCTAGC-??GATCCGGCGG-CGGTATT-TTCGCCTCGCCGGGGAGCT-TTCCGGAAACGAAAGACTTCAGGTTCCGGGGGTAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAATCGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCCGGCCCGGACACTGAAAGGACTGTCAGA-CT-GAAA-GCTCTTACTTGATTC-AGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTTATTCCGAT-AACGAGCGAGACGCACGCCTACTCAATACGACTCGAGT-?TCTTTC-??GCTCGATGCCGTTC-TTAGAGGAATGGGCGGTATAG-AACCGCATGAAAGTGCGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGGGTCTGCAGCG?GTTC-????CATAGCCGAAAGGTCATTGGT-??AAACCGTT?-GAAAGGACTCCGTGA-TCGGGATCGGGAATTGCA-????????ACTATTTC-???CCTTGAACGAGGAATTCCTAGTAAGTGTG-AATCATCATCTCGCTTTTAATACGTCCCTGCGATTTGTACACACCGCCCGTCGCTACCCGGGACT-?GAACCGTTTCGAGAAATCCAGGGAATCGCTCGCCGGGGTTCGC???????????????????????????????????????????????????????????????????????? ; END; BEGIN SETS; CHARSET MaleIndep (CHARACTERS = 18S_rDNA) = 1795; CHARSET MaleNonind (CHARACTERS = 18S_rDNA) = 1795; CHARSET Fusions (CHARACTERS = 18S_rDNA) = 1795; CHARSET MaleNonind (CHARACTERS = 18S_rDNA) = 1795; CHARSET MaleTail (CHARACTERS = 18S_rDNA) = 1795; CHARSET MaleIndep (CHARACTERS = 18S_rDNA) = 1795; CHARSET Fusions (CHARACTERS = 18S_rDNA) = 1795; CHARSET MaleMulti (CHARACTERS = 18S_rDNA) = 13-17 1795; CHARSET MaleTail (CHARACTERS = 18S_rDNA) = 1-35; CHARSET MaleMulti (CHARACTERS = 18S_rDNA) = 1795; END; BEGIN ASSUMPTIONS; WTSET * AllEqual = 1: 1-1795 ; WTSET AllEqual = 1: 1-1795 ; WTSET Lps5Stms4 = 5: 1795 , 4: 1 , 1: 2-1794 ; WTSET Lps2Stms1 = 1: 1-1794 , 2: 1795 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3979] TITLE Appendix_1; LINK TAXA = Taxa1; DIMENSIONS NCHAR=36; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5" MISSING=? GAP= -; CHARSTATELABELS 1 'Fan- anterior conformation' / 0 open closed, 2 'Fan- anterior position' / 0 near_base_of_spicules near_cloaca, 3 'Fan- extension' / 0 broad narrow, 4 'Body shape- overall shape' / 0 blunt elongate, 5 'Body shape- tail tip' / 0 peloderan leptoderan, 6 'Phasmid- position' / 0 posterior lateral, 7 'Rays- ray 8' / 0 present absent, 8 'Rays- tip position for 1,:2,4,' / 0 at_margin on_dorsal_or_ventral_surface, 9 'Rays- ray 6' / 0 'narrow, uniform, open' 'broad, tapered, closed', 10 'Rays- ray 3 position' / 0 separate tendency_to_fuse_with_ray_4, 11 Overall_retraction / 0 strong weak, 12 'Terminal cells- retraction' / 0 present absent, 13 'Terminal c:ells- fusion' / 0 do_not_fuse fuse, 14 'Ray cell associations- ray 1' / 0 R1.p 'R1.p+R2.p' 'R2.p+R3.p' 'R3.p+R4.p', 15 'Ray cell associati:ons- ray 2' / 0 R2.p 'R2.p+R3.p' R3.p 'R3.p+R4.p', 16 'Ray cell associations- ray 3' / 0 R3.p 'R2.p+R3.p' 'R3.p+R4.p' R6.p, 17 'Ray cell associations- ray 4' / 0 R4.p 'R4.p+R6.p' R6.p 'R6.p+R7.p', 18 'Ray cell associations- ray 5' / 0 R5.p 'R4.p+R6.p' 'R5.p+R6.p', 19 'Ray cell associations- ray 6' / 0 R6.p 'R6.p+R7.p', 20 'Ray cell associations- ray 7' / 0 R7.p 'R7.p+R9.p' migrates_into_R7.p, 21 'Ray cell associations- ray 8' / 0 R8.p R7.p '(No ray 8)', 22 'DV position of Rnst- ray 1' / 0 'seam-hyp 7 border' within_set, 23 'DV position of Rnst- ray 2' / 0 'seam-hyp 7 border' within_hyp_7, 24 'DV position of Rnst- ray 4' / 0 'seam-hyp 7 border' within_hyp_7, 25 'se-:set boundary position' / 0 near_base_of_spicules near_cloaca, 26 'Rn.p position- R1.p' / 0 within_seam ventral_of_seam, 27 'Rn.p position- R2.p' / 0 within_seam ventral_of_seam, 28 'Rn.p position:- R6.p' / 0 ventral_of_seam within_seam, 29 'Rn.p position- R9.p' / 0 strictly_lateral extends_to_dorsal_midline, 30 'Rn.p cell fusions- R1.p' / 0 remains_unfused 'fuses with R2.p+R3.p' fuses_with_set fuses_with_se, 31 'Rn.p cell fusions- R2.p' / 0 remains_unfused 'fuses with R2.p+R3.p' fuses_with_set fuses_with_se, 32 'Rn.p cell fusions- R3.p' / 0 remains_unfused 'fuses with R2.p+R3.p' fuses_with_set fuses_with_se, 33 'Rn.p :cell fusions- R4.p' / 0 remains_unfused fuses_with_set fuses_with_se, 34 'Rn.p cell fusions- R5.p' / 0 remains_unfused fuses_with_R7.p 'fuses with R6.p+R7.p' fuses_with_set fuses_with_hyp7_or_maybe_se, 35 'Rn.p cell fusions:- R6.p' / 0 remains_unfused 'fuses with R5.p+R7.p' fuses_with_se fuses_with_hyp7, 36 'Rn.p cell fusions- R7.p' / 0 remains_unfused fuses_with_R5.p 'fuses with R5.p+R6.p' fuses_with_hyp7, ; MATRIX [ 10 20 30 ] [ . . . ] Caenorhabditis_briggsae 221111122211222321211222211123332444 Caenorhabditis_elegans 221111122111222321211222211123332444 Caenorhabditis_remanei 221111122111222321211222211123332444 Caenorhabditis_sp._CB5161 221111122111222321211222211123332444 Pellioditis_typica 111111111111112232121111111214443242 Pelodera_strongyloides 111112111111133443211111111114443242 Rhabditella_axei 1122211111221122412111111111144435{34}4 Rhabditis_blumi 111121211112111112113111111111111144 Rhabditis_myriophila 111121111112111112112111111111111144 Teratorhabditis_palmarum 111112111111144441231111122212221323 ; END; BEGIN SETS; CHARSET MaleIndep (CHARACTERS = Appendix_1) = 1 6 9-36; CHARSET MaleMulti (CHARACTERS = Appendix_1) = 14-18 30-36; CHARSET Fusions (CHARACTERS = Appendix_1) = 31-34; CHARSET MaleNonind (CHARACTERS = Appendix_1) = 2-5 7-8; CHARSET MaleTail (CHARACTERS = Appendix_1) = 1-36; END; BEGIN ASSUMPTIONS; WTSET * AllEqual = 1: 1-36 ; WTSET AllEqual = 1: 1-36 ; WTSET Lps5Stms4 = 5: 1-36 ; WTSET Lps2Stms1 = 2: 1-36 ; END; BEGIN TREES; TITLE Tb5222; LINK TAXA = Taxa1; TRANSLATE 1 Pelodera_strongyloides, 2 Teratorhabditis_palmarum, 3 Pellioditis_typica, 4 Rhabditella_axei, 5 Rhabditis_blumi, 6 Rhabditis_myriophila, 7 Caenorhabditis_sp._CB5161, 8 Caenorhabditis_elegans, 9 Caenorhabditis_remanei, 10 Caenorhabditis_briggsae; TREE Fig._1.P = [&R] (((10,8),(6,5,4),3),(2,1)); TREE Fig._1.V = [&R] (((((((10,9),8),7),3),1),((6,5),4)),2); TREE Fig._1.IV = [&R] (((((10,9),8),7)Caenorhabditis,(((6,5)Rhabditis,4),3)Eurhabditis),(2,1))Rhabditidae; TREE Fig._1.III = [&R] (((((10,9),8),7),(((6,4),5),3)),(2,1)); TREE Fig._1.II = [&R] ((((((10,9),8),7),((6,5),4)),3),(2,1)); TREE Fig._1.I = [&R] ((((((10,9),8),7),((6,4),5)),3),(2,1)); END;