#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; 12:04 GMT TreeBASE (cc) 1994-2008 Study reference: Walters-conte K.B., Johnson D.L., Johnson W.E., O'brien S., & Pecon-slattery J. 2014. The Dynamic Proliferation of CanSINEs Mirrors the Complex Evolution of Feliforms. BMC Evolutionary Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15822] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=89; TAXLABELS Caracal_aurata_105890 Caracal_caracal_133135 Caracal_serval_101187 Cryptoprocta_ferox_131713 Felidae_sp._122236 Felidae_sp._203464_ Felidae_sp._214534 Feliformia_sp._101187 Feliformia_sp._106256 Feliformia_sp._107176 Feliformia_sp._117885 Feliformia_sp._131713 Feliformia_sp._134929 Feliformia_sp._135256 Feliformia_sp._136949 Feliformia_sp._145617 Feliformia_sp._145754 Feliformia_sp._150913 Feliformia_sp._151787 Feliformia_sp._164336 Feliformia_sp._174511 Feliformia_sp._179189 Feliformia_sp._180515 Feliformia_sp._194731 Feliformia_sp._199572 Feliformia_sp._203536 Feliformia_sp._206155 Feliformia_sp._212906 Feliformia_sp._213652 Feliformia_sp._217179 Feliformia_sp._4743 Feliformia_sp._95036 Feliformia_sp._95892 Feliformia_sp._99463 Feliformia_sp._99534 Felis_nigripes_150951 Felis_nigripes_212075 Felis_nigripes_99643 Felis_silvestris_silvestris_203464 Felis_sp._105890 Leopardus_colocolo_122236 Leopardus_geoffroyi_chD4.80M Leopardus_pardalis_150951 Leopardus_sp._133135 Leopardus_tigrinus_213798 Lynx_canadensis_106256 Lynx_canadensis_73133 Lynx_lynx_204133 Lynx_pardinus_106256 Lynx_rufus_133135 Lynx_sp._139216_ Lynx_sp._154966 Neofelis_neofelis_199572 Neofelis_neofelis_212733 Otocolobus_manul_105890 Otocolobus_manul_139216 Otocolobus_manul_212331 Otocolobus_manul_213566 Otocolobus_manul_215122 Otocolobus_manul_73133 Panthera_onca_5313 Panthera_onca_chB1.32M Panthera_sp._782 Panthera_unica_134292 Pantherinae_sp._chA1.248M Pardofelis_badia_146417 Pardofelis_badia_150162 Pardofelis_marmorata_106256 Pardofelis_marmorata_133135 Pardofelis_marmorata_145617 Pardofelis_marmorata_150853 Pardofelis_marmorata_216162 Pardofelis_marmorata_216524 Pardofelis_sp._212075 Prionailurus_bengalensis_161275 Prionailurus_bengalensis_212075 Prionailurus_planiceps_212075 Prionailurus_sp._130416 Prionailurus_sp._134463 Prionailurus_sp._150853 Prionailurus_sp._150951 Prionailurus_sp._ch1.181M Prionailurus_sp._chA1.248M Prionailurus_viverrinus_125972 Prionailurus_viverrinus_164336 Priondontidae_115304 Puma_yagouaroundi_101187 SINEC_Fc_R SINEC_Fc2 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M22759] TITLE Subfamily_Tree_Short_Names; LINK TAXA = Taxa1; DIMENSIONS NCHAR=136; 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 ] [ . . . . . . . . . . . . . . ] Caracal_aurata_105890 GGGCGCCTAGGTGGCGCAGTTGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TTGAGCCCCGCGTCGGGCTC--TGTGCTGACTGCTCAGAGCCTGGAGCCTG-TTTCCG Caracal_caracal_133135 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TAGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Caracal_serval_101187 GGGCGCCTGGGTGGCCCCGTCGGTTAAGCGTCCGAC-------TTCAGC-CCGGTCACGATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCGGGCTT--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Cryptoprocta_ferox_131713 GGCCACCTGGGCGGCTCAGTCAGTTAAGCATCCGACTCCTGATTTTGGCTCAGGTCATGATCTCACT-TTTGTGAGA-TCAAGCCCCATGTTGGGCTC--TGTGCTGACAG-------TGCAGAGCCTG-CTT-GG Felidae_sp._122236 GGGCACCTGGGTGGCTCAGTCGGTTGAGCGTCCGAC-------TTCGGCTCAGGTCGTGATCTCGCA-TCCGTGAGT-TCGAGCCCCATGTCGGGCTC--TGTGCTGACCGCTCAGAGCCTGGAGCCTG-TTTCCG Felidae_sp._203464_ GGGCGCCTGTGTGGCTCAGTCAGTTAAGCTTCTGAC-------TTCAGTTCAAGTCATGATCTCGCA-TCTGTGAGT-TCAAACCCCATGTCGGGCTG--TATGCTAACAGCTTGGAGCCTGGAGCCTA-CTTCAG Felidae_sp._214534 GGGCGCCTGGGTGGCTCAGTCGGTTAAGCGTCCGAC-------TTTGGCTCAGGTCACGATCTCGCGGTATGTGAGT-TCGAGCCCTGCGTCGGGCTC--TGTGCTGACTGCTCAGAGCCTGGAGCCTG-TTTCAG Feliformia_sp._101187 GAGCACCTGGGTGGCTCAGTTGGTTGAGCATCTGATTCTTGATTT-GGCTCAGGTCATGATCCCAGG-TCATTGG-A-TCAAGCCCCACATT-GGCTC--TGAGCTGAGCG---------TGGAGCCTG-CTTATG Feliformia_sp._106256 GGGCACCTGGATGGCTTGGTTGGTTGAGCATCTGACTCTTGATTTCTGCTCAGGTCATGATCCCAGG-TT-GTGG-A-TCGAGCCCTGCGTCGGGCTC--CATGCTGAGTG---------TGGAACCTG-CTTAAG Feliformia_sp._107176 GGGCACCTGGGTGGCTCAGTCGGTTGAGCATCCCACTCTTGATTTCAGCTCAGGTCATGATCCCAGG-T-CATGGGA-TCAAGCCCTGTGTT-GGCTC--CATGCTGAGTG---------TGGAGCCTG-CTTAAG Feliformia_sp._117885 GAGTACCTAGGTGGCTCAGTCAGGTAAGCGTCAGGCTCTTGATTTTGGCTCAGGTCATGATCTCACA-TTCATGAAA-TAGAGCCCCATGTTGGGCTC--CGTGCTGGG---------CACGGAGCCTG-CTTAAG Feliformia_sp._131713 GGGCTCCTGGGTGGCTCAGTCAGTTAAGCGTCCAACTCCTGATTTCAGCTCAGATCATGATCTCATT-TTTGTGAGA-TCAAGCCCCACATTGGGCTC--TGTACTGACAG-------CCA-GAGCCTG-CTTGGG Feliformia_sp._134929 GGGGGCCTGAGTGACCCAGTTGGTTAAGCATCTGAATCTTGATTTCTGCTCAGATCATGATCTCCTG-TTCCTGAGA-TAGAGCCTTGAGTCAGGCTC--TGCACTGAGAG-------CATGGAGCTTA-CTTGGG Feliformia_sp._135256 GGGTACTTGGGTGGCTCGGTTGGTTAAGCACCTGACTCTTGATTTCTGCTCAGGTCATGATCTCTGG-TTCATGAGA-TCGAGCCCCACGTCAGGCTC--TGCACTGACAG-------CACAGAGTCTG-CTTGGG Feliformia_sp._136949 GGGCAC{CT}TGGGTGGCTCAGTCGGTTGAGCATC{CT}GACTCTTGATTTCAGCTCAGGTCATGATCCCAGG-T-CATGGGA-TTGAGCCCCGCATCGGACTC--CATGCTGAGTG---------TGGAGCCTG-CTTGAG Feliformia_sp._145617 GAGCACCTGGGTGGCTCAGTCAGTTGAGCACCTGACTCTTGATTTTGGCTCAGGTCATGATCCCAGG-TT-GTGGGA-TCGAGCCCCATGTTGGGCTC--TGCACTGAGTG---------TGGAGCCTG-CTTAAG Feliformia_sp._145754 GGGCACCTGGGTGACTTAGTTGGTTGAGCATCTGACTCTTGATTTCAGCTCAGGTTGTGATCCCAGG-TT-GTGGGA-TCGAGCCCCATATCGGGCTG--CTTACTGTGTG---------TGGAGGCTG-CTTAAG Feliformia_sp._150913 CGCCTCCTCGGTGGCTCAGTTGGTTGAGCCTCCACCTCTTGATTTCGGCTCAGGTCATGATCCCAGG-TT-GTGGGA-TCGAGCCCCATGTTGGGCTC--TGCGCTGAGTG---------TGGAACCTG-CTTAAG Feliformia_sp._151787 GGGCGCCTGGGTGGCTCAGCCGGTGAAGCGTCCAACTCTTGATTTCAGCTCAGGTCACGATCTCACC-TTCGTGAGA-TCGAGCCCCACGTCA-GCTC--TGTGCTGGTGG-------CTTGGAGCCTG-CTTGGG Feliformia_sp._164336 GGGCATCTGGGCAGCTCAGTCAGTTGAGCATCTGACT--TGATTTCAGCTCAGGTCATGATCCCAGA-T-CCTGAGA-TCGAGCCCCATGTCA-GCTC--TGTGCTGAGTG---------TGGAGGCTG-CTTGGG Feliformia_sp._174511 GGA?GTCTGGGTGGCTCATTTGGTTGAGCATCTGACTCTTGATTTCAGCTCAGGTCATGATCCCAGG-T-CATG-GA-TTGAGTCCCATGTTGGGCTC--CATGCTGGGTG---------TGGAGCCTG-CTTGAG Feliformia_sp._179189 GGGCGCCTGGGTGACTCAATCAATTGAGCATCCAACTCTTGATTTCTGCTCAGGTCATGATCCCAGG-T-CATGGGA-CCTAGCCCTGTGTCAGGCTT--CATGCTGAGTG---------TGGAGCCTG-CTTAAG Feliformia_sp._180515 GGGCACCTGGGTGGCTCAGTCAGTTAAGCGTCCAACTCTTGATTTCAGCTCAAGTCATGATCTCACA-TTCATGAAT-TCAAGCCCCACATTGGGCTC--TGTGCTGACAT-------CTCAGACCCTG-CTTGGG Feliformia_sp._194731 GGGCACCTGGGGGGCTCGGTGGGTTAAGCGTCCAACT--GGATTTCAGCTCAGGTCATGATCTCACG-TTCATGGGA-TCGAGCCCCACAGCGGGCTC--TGTGCTGACCA-------TGCAGAGCCTG-CTTGGG Feliformia_sp._199572 GAGTATCTGGGGGGCTCAGTCGGTTAAGCATCAGGCTCTTGATTTCAGCTCAGATCATGATCTCATG-TT-GTGGGA-TCGAGCCCCATGTCAGGCTC--TGCACTGACAG-------CACGGAGCCTG-CTTGGG Feliformia_sp._203536 GGGCACCTGGGTGGCTCAGTCGGTTGAGCATCTGACTCTTGATTTTGGCCCAGGTCATGATCCCAGG-TT-GTGGGA-TGGAGCCCCAT-GCCGGCTC--CATGCTGAG?--------TGTGGAGCCTG-CTTAAG Feliformia_sp._206155 GGGTGTGTGAGTGGCTCAGTTGGTTGAGCATCTGACTCTTGATTTCAGCTCAGGTCATGATCCCAGG-TT-GTGGGA-TTGAGCTGCACTTTGGGCTC--CATGCTGAGTG---------TGGAGCCTG-CTTAAG Feliformia_sp._212906 GGGCGCCTAGGTGGCTCAGTCAGTTGAGCATCTGACTCTTGATTTCGACTCAGGTCATGATCCCAGG-TC-CTGGGA-TCGAGCCCCATGTTGGGCTC--TGTGCTGAGTG---------TGAAGCCTA-CTTAAG Feliformia_sp._213652 GGGCACCTGGGTGGCTCAGTCAGTTAAGCATCTGACTCTTGGTTTTGGCTCAGGTCATGACCTCACGCTTTGTGGGA-TCGATCCCCATGTCAGGCTC--TGCGCTGGCCG-------TGCAGAGCCTG-CTTGGG Feliformia_sp._217179 GGGCGCCTGGGTGGCTCAGTCAGTTAAGCATCTGACTCTTGATTTTGGCTTAGGTCATGATCTCACG-AT-GTGAGA-TAGAGCCCTATGTTAGGCTC--TGTGCTGAG---------CATGGAGCCTG-CTTAAG Feliformia_sp._4743 GGGATCCAAGGTGTCTCAGTCAGTTAAGCGTCCAACTCTTGATTTCAGCTCAAGTCATGATCTCACG-TTCATGAGT-TTGGGCCCCGCATCA-GCTC--TGCGCTGACAG-------TGCAGAGCCTG-CTTGGG Feliformia_sp._95036 GGTTATCTGGGTGGCTCAGTTGGTTGAGCATCTGACTCTTGATTTCAGCTCAGGTCATGATCCCAGG-TT-ATGGGC-TCAAGCCTCACGTT-GGCTC--TGCACTGAG---------CATGGAGCCTG-CTTGTG Feliformia_sp._95892 GGGCACCTGGGGGGCTCAGTTGGTTAAACATAGGACTCTTGATTTCTGCTTAGGTCATGATCTCCTG-TTTGTGAGC-TAGAGCCCCAAGTCAGGCTC--TGCACTGACAG-------CAGGGAGCCTG-CTTGGG Feliformia_sp._99463 GGGCACCCGGGTGGCTCAATCAGTTAAGTATCTGACTCTTGGTTTCGGCTCAGGTCATGATCTCCCG-TTCGTGGGT-TCGAGCCCCATGTC-GGCTC--TGTGCTGATGG-------TGTGGAGCCTG-CTTGGG Feliformia_sp._99534 GGGCACCTGGGGGGCT--GTTGGTTAAGTGCCCAACTCTTGGTTTTGGCTCAGATCATGATCTCATG-TTCGTGAGT-TCGAGCCCCATGTCAGGCTC--CATGCTGATGG-------TATAGAGCCTG-CTTGGG Felis_nigripes_150951 GGGCGCCTGGGTGGCACAGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTGTTTTCCG Felis_nigripes_212075 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Felis_nigripes_99643 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCA Felis_silvestris_silvestris_203464 GGGCGCCTGGGTGGCGCAGTTGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCG- Felis_sp._105890 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCAGGGTCCGTGAGT-TCGAGCCCCGCGTCAGGCTCTGTGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Leopardus_colocolo_122236 GGGCGCCTGGGTGGCTCAGTCGGTTGAGCGTCCGAC-------TTCGGCTCAGGTCATGATCTCGCA-TCCGTGAGT-TCGAGCCCCGCGTTGGGCTC--TGTGCTGACCGCTCAGAGCCTGGAGCCTG-TTTCAG Leopardus_geoffroyi_chD4.80M GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCTG Leopardus_pardalis_150951 GGGCACCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGACCTCGTGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGACTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Leopardus_sp._133135 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Leopardus_tigrinus_213798 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Lynx_canadensis_106256 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCTGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAAAGCCTGGAGCCTG-TTTCCG Lynx_canadensis_73133 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-CTTCCG Lynx_lynx_204133 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCACG-TCCGGGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Lynx_pardinus_106256 GGGCGCCTGGGTGGC-CAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACTATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Lynx_rufus_133135 GGG--CCTGGGTGGGGCAGTCGGTTAAGTGTCCGAC-------TTCAGC-CAGGTCACGATTTCGCGGTCCGTGGAT-TCGAGCCCCGTGTCGGGCTT--TGGGGTGATGGGTCAGAGCCTGGAGCCTG-TTTCCT Lynx_sp._139216_ GGGCGCC-GGGTGGCTCAGTCGGTTAAGCATCCGAC------TTTCAGCTCAGGTCACGATCTCACGGTCCGTGAGT-TTGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-CTTCCG Lynx_sp._154966 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGCCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Neofelis_neofelis_199572 GGGCGCCTGGGTGGCTCAGTCGGTTGAGCGTCCGAC-------TTCAGCTCAGGTCACGATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-CTTCCG Neofelis_neofelis_212733 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Otocolobus_manul_105890 GGGCGCCTGGGTGGCGCAGTCGGTTAAGGGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCCGAGGGCTCGGAGTCGGGAGCCTG-TTTCGG Otocolobus_manul_139216 GGG--CCTGGGTGGCGCAGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCGCTCCGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Otocolobus_manul_212331 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGCTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Otocolobus_manul_213566 GGGCCCCTGGGTGGCGCGGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGGGT-TCGAGCCCCGCGTCAGGCTCT-GGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Otocolobus_manul_215122 GGGCACCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Otocolobus_manul_73133 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGCTCAGGTCACGATCTCGCGGCCTGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Panthera_onca_5313 GGGCGCCTGGGTGGCGTAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCGG Panthera_onca_chB1.32M GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTGACGATCTCACGGTCCATGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Panthera_sp._782 GGGCGCCTGGGTGGCTCAGTCGGTTGAGTGTCCGAC-------TTCAGCTCAGGTCATGATCTCACACTCTGTGAGT-TCGAGCCCCGCATCGGGCTC--TGTGCTGATGGCTCAGAGCCTGGAGCCCG-CTTCAG Panthera_unica_134292 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCTGTGAGT-TCGAGCTCCGCGTCAGGCTC--TGGACTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Pantherinae_sp._chA1.248M GGGCGCCTGGGTGGCTCAGTCGGTTAAGCGTCCGAC-------TTCGGCTCAGGTCATGATCTCGCGGTCCGTGAGT-TCGAGCCCTGCGTCGGGCTC--TGTGCTGACAGCTCAGAGCCTGGAGCCTG-TTTCAG Pardofelis_badia_146417 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCC Pardofelis_badia_150162 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Pardofelis_marmorata_106256 GGGCGCCTGGGTGGCACAGTCGATTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCCGTGAGT-TTGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCTG Pardofelis_marmorata_133135 GGGCGCCTGGGTGGCGCAGTCGGTTGGGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCAGTCCGTGAGT-TCGAGCCCTGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Pardofelis_marmorata_145617 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCTGGGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGC--------------CTGGAGCGTG-TTTCCG Pardofelis_marmorata_150853 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCTGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TTGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Pardofelis_marmorata_216162 GGGCGCCTGGGTGGCACAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Pardofelis_marmorata_216524 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCA Pardofelis_sp._212075 GGG--CCTGGGTGGGGCAGTCGGTTAAGGGTCCGAA-------TTCAGC-CAGGTCACGATTTCGTGATCCGGGAGT-TTGAGCCCCGGCTCAGGCTT--TGGGGTGATGGCTTAGCGCCTGGAGCCTG-TTTCCG Prionailurus_bengalensis_161275 GGGCGCCTGGGTGGCACAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTTGCGGTCCGTGAGT-TCGAGCCCCGCGTCGGGCCC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Prionailurus_bengalensis_212075 GGGCG-CTGGGTGGCGCAGTCGGTTAAGCATCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAACCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCCG-TTTCCG Prionailurus_planiceps_212075 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGGGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Prionailurus_sp._130416 GGGCACCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCAGTTTGGGAGT-TCGAGCCCCGCGTCAGGCTT--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Prionailurus_sp._134463 GGGCGCCTGGGTGGCGCAGTCCGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCATCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Prionailurus_sp._150853 GGGCGCCTGGGTGGTGCAGTCGGTTAAGCGTCC-AC-------TTCAAC-CCGGTCACGATCTCCCGGTCCCTGAGT-TCCAACCCCGCGTCGGGCTC--TGGGCTGATGGCTTAAAACCTGGAACCTG-GTTCCC Prionailurus_sp._150951 GGGCGCCTGGGTGGCACAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATTTCGCGGTCCATGAGT-TCGAGCCCCGCGTCGGGCTT--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG Prionailurus_sp._ch1.181M GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTTGCGGTCCGTGAGT-TCGAGCCCCACGTCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Prionailurus_sp._chA1.248M GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATGTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCGGAGCCTGGAGCCTG-TTTCCG Prionailurus_viverrinus_125972 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTTAGC-CAGGTCACGATCTCGCGGTCCGTGAGT-TCGAGCCCCGCGTCAGGCTT--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTTTG Prionailurus_viverrinus_164336 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCTTCCGAC-------TTCAGC-CAGGTCATGATCTCACG-TCCGTGAGT-TCGAGCCCCGCGTCAGGCTC--TGGGCTGATGGCTCGGAACCTGGAGCCTG-TTTCCG Priondontidae_115304 GGGCACCTGGGTGGCTCAGTCGGTTGAGCGTCCGAC-------TTGGGCTCAGGTCATGATCTCGCA-TCTGTGAGT-TCGAGCCCCATGTCGGGCTC--TGTGCTGACAGCTCAGAGCCTGGAGCCTG-TTTCGG Puma_yagouaroundi_101187 GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTTCCG SINEC_Fc_R GGGCGCCTGGGTGGCGCAGTCGGTTAAGCGTCCGAC-------TTCAGC-CAGGTCACGATCTCGCG-TCCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGGGCTGATGGCTCAGAGCCTGGAGCCTG-TTT??? SINEC_Fc2 GGGCGCCTGGGTGGCTCAGTCGGTTAAGCGTCCGAC-------TTCGGCTCAGGTCATGATCTCGCG-TTCGTGAGT-TCGAGCCCCGCGTCGGGCTC--TGTGCTGACAGCTCAGAGCCTGGAGCCTG-CTT??? ; END; BEGIN TREES; TITLE CanSINEs_and_Feliform_Evolution; LINK TAXA = Taxa1; TRANSLATE 1 Pardofelis_sp._212075, 2 Prionailurus_sp._150853, 3 Lynx_rufus_133135, 4 Prionailurus_sp._130416, 5 Otocolobus_manul_105890, 6 Caracal_aurata_105890, 7 Otocolobus_manul_213566, 8 Prionailurus_viverrinus_125972, 9 Pardofelis_marmorata_133135, 10 Prionailurus_sp._150951, 11 Leopardus_pardalis_150951, 12 Prionailurus_bengalensis_212075, 13 Panthera_onca_5313, 14 Prionailurus_bengalensis_161275, 15 Panthera_onca_chB1.32M, 16 Otocolobus_manul_139216, 17 Felis_silvestris_silvestris_203464, 18 Pardofelis_badia_146417, 19 Pardofelis_marmorata_216524, 20 Otocolobus_manul_215122, 21 Pardofelis_badia_150162, 22 Pardofelis_marmorata_216162, 23 Felis_sp._105890, 24 Prionailurus_sp._ch1.181M, 25 Pardofelis_marmorata_150853, 26 Prionailurus_sp._134463, 27 Felis_nigripes_150951, 28 Lynx_sp._154966, 29 Caracal_caracal_133135, 30 Neofelis_neofelis_212733, 31 Prionailurus_sp._chA1.248M, 32 Leopardus_geoffroyi_chD4.80M, 33 Prionailurus_planiceps_212075, 34 Lynx_canadensis_73133, 35 Otocolobus_manul_212331, 36 Felis_nigripes_212075, 37 Leopardus_sp._133135, 38 Leopardus_tigrinus_213798, 39 Lynx_canadensis_106256, 40 Caracal_serval_101187, 41 Puma_yagouaroundi_101187, 42 Lynx_lynx_204133, 43 Prionailurus_viverrinus_164336, 44 Felis_nigripes_99643, 45 Pardofelis_marmorata_106256, 46 Panthera_unica_134292, 47 Pardofelis_marmorata_145617, 48 Lynx_pardinus_106256, 49 SINEC_Fc_R, 50 Otocolobus_manul_73133, 51 Felidae_sp._203464_, 52 Lynx_sp._139216_, 53 Panthera_sp._782, 54 Pantherinae_sp._chA1.248M, 55 Felidae_sp._214534, 56 Leopardus_colocolo_122236, 57 Felidae_sp._122236, 58 Priondontidae_115304, 59 Neofelis_neofelis_199572, 60 SINEC_Fc2, 61 Feliformia_sp._99534, 62 Feliformia_sp._180515, 63 Feliformia_sp._131713, 64 Feliformia_sp._199572, 65 Cryptoprocta_ferox_131713, 66 Feliformia_sp._194731, 67 Feliformia_sp._135256, 68 Feliformia_sp._95036, 69 Feliformia_sp._117885, 70 Feliformia_sp._95892, 71 Feliformia_sp._217179, 72 Feliformia_sp._134929, 73 Feliformia_sp._151787, 74 Feliformia_sp._203536, 75 Feliformia_sp._4743, 76 Feliformia_sp._213652, 77 Feliformia_sp._99463, 78 Feliformia_sp._212906, 79 Feliformia_sp._206155, 80 Feliformia_sp._145754, 81 Feliformia_sp._145617, 82 Feliformia_sp._150913, 83 Feliformia_sp._106256, 84 Feliformia_sp._164336, 85 Feliformia_sp._174511, 86 Feliformia_sp._107176, 87 Feliformia_sp._101187, 88 Feliformia_sp._136949, 89 Feliformia_sp._179189; TREE tree_1 = [&R] ((2:0.097048,4:0.027509,6:0.031975,7:0.028833,8:0.022447,9:0.026839,10:0.013851,11:0.023809,12:0.014382,14:0.014415,16:0.002415,17:0.00561,18:0.002945,19:0.003438,20:0.003575,21:0.002288,22:0.002406,24:0.013325,25:0.010635,26:0.015631,27:0.001862,28:0.00832,29:0.004397,30:2.64E-4,31:0.007411,32:0.002055,33:6.88E-4,34:0.003197,35:0.00237,36:0.0,37:0.0,38:0.0,39:0.005923,40:0.023463,41:0.0,42:0.005238,43:0.020927,44:0.005154,45:0.021683,46:0.017809,47:0.010026,48:0.006282,49:0.0,50:0.00916,52:0.016417,59:0.008277,(1:0.081797,3:0.049038):0.027424,(5:0.040256,13:0.008316):0.001614,(15:0.016039,23:0.008101):0.002038):0.00947,(51:0.138478,53:0.04949,56:0.017222,60:0.008058,(57:0.01642,58:0.025121):0.019942,(54:0.007554,55:0.030253):0.014257,(73:0.066247,(61:0.099915,62:0.061633,63:0.061302,64:0.064457,66:0.080823,67:0.078919,68:0.060226,69:0.11521,70:0.071717,71:0.048446,72:0.127436,74:0.04975,75:0.095209,77:0.052941,78:0.056121,80:0.08988,81:0.037661,82:0.082332,83:0.050837,84:0.075661,87:0.062244,88:0.026085,(79:0.063816,85:0.045123):0.027507,(65:0.055743,76:0.070039):0.031437,(86:0.016394,89:0.081555):0.025593):0.022674):0.035064):0.009469); END;