#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 May 15, 2024; 19:46 GMT TreeBASE (cc) 1994-2008 Study reference: Belfiore N., Liu L., & Moritz C. 2008. Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae). Systematic Biology, 57(2): 294-310. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2005] BEGIN TAXA; TITLE Importance_sampled_tree_9_taxa; DIMENSIONS NTAX=28; TAXLABELS Geomys_breviceps Orthogeomys_heterodus Thomomys_bottae_albatus Thomomys_bottae_alpinus Thomomys_bottae_awahnee_a Thomomys_bottae_awahnee_b Thomomys_bottae_bottae Thomomys_bottae_cactophilus Thomomys_bottae_laticeps Thomomys_bottae_mewa Thomomys_bottae_riparius Thomomys_bottae_ruidosae Thomomys_bottae_saxatilis Thomomys_bottae_xerophilus Thomomys_bulbivorus Thomomys_idahoensis_pygmaeus_a Thomomys_idahoensis_pygmaeus_b Thomomys_mazama_mazama Thomomys_mazama_nasicus Thomomys_monticola_a Thomomys_monticola_b Thomomys_talpoides_bridgeri Thomomys_talpoides_ocius Thomomys_talpoides_yakimensis Thomomys_townsendii_relictus Thomomys_townsendii_townsendii Thomomys_umbrinus_atroavarius Thomomys_umbrinus_chihuahuae ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3083] TITLE TBO47; LINK TAXA = Importance_sampled_tree_9_taxa; DIMENSIONS NCHAR=819; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Geomys_breviceps CATGATTTTGTCAGGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTACTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGATTAGGCCATCTGTGAATTGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGGGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCGAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A Orthogeomys_heterodus CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTA{CT}CTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A Thomomys_bottae_albatus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_alpinus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCC{CT}GCCATTCTGAGTTCTGATTTCATGATACCTTTTCCA{AC}CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGG{CG}TCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGA{CT}GGTGACCTCG{AT}TTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTC{CG}ACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_awahnee_a CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACA{AG}AAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATC{CT}TCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_awahnee_b CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACA{CG}AAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATC{CT}TCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCA{AC}CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGG{CG}TCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGA{AC}GGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_bottae CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGT{CT}GTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCC{CT}GCCATTCTGAGTTCTGATTTCATGATACCTTTTCCA{AC}CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGA{CT}GGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_cactophilus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTT{AG}TGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_laticeps CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACA{CG}AAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATC{CT}TCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_mewa CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_riparius CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTT{AG}TGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCG{AT}TTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTC{CG}ACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_ruidosae CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGT{CT}GTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACA{CG}AAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGG{CG}TCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_saxatilis CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGG{CG}TCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTA{AG}GCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bottae_xerophilus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTC{CG}ACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_bulbivorus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_idahoensis_pygmaeus_a ???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA????????????????????????????????????????????????????? Thomomys_idahoensis_pygmaeus_b ?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA???? Thomomys_mazama_mazama ??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Thomomys_mazama_nasicus ??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT????????????????????????????? Thomomys_monticola_a CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A Thomomys_monticola_b CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAA{CT}GGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTT{CG}AGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCT{GT}TACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGA{CT}CTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGC{CT}AGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A Thomomys_talpoides_bridgeri CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCC{CT}CAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A Thomomys_talpoides_ocius CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A Thomomys_talpoides_yakimensis ?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC??????????????????????????????????????????????????????? Thomomys_townsendii_relictus CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCG{AT}TTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A Thomomys_townsendii_townsendii CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A Thomomys_umbrinus_atroavarius CATGATTTTGTCATG{CT}TTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGT{CT}GATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTT{AG}TGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT{CT}ATATCATCTTTGTGAAACT-A Thomomys_umbrinus_chihuahuae CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCT{AG}CCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = TBO47) = N: 1-819; CODONPOSSET CodonPositions (CHARACTERS = TBO47) = N: 1-819; END;