<?xml version="1.0" standalone="yes"?>
<beast>                                                              -->
    <taxa id="taxa">
        <taxon id="Orthogeomys_heterodus"/>
        <taxon id="Thomomys_bottae_awahnee_a"/>
        <taxon id="Thomomys_bottae_awahnee_b"/>
        <taxon id="Thomomys_bottae_xerophilus"/>
        <taxon id="Thomomys_bottae_cactophilus"/>
        <taxon id="Thomomys_bottae_albatus"/>
        <taxon id="Thomomys_bottae_ruidosae"/>
        <taxon id="Thomomys_bottae_bottae"/>
        <taxon id="Thomomys_bottae_alpinus"/>
        <taxon id="Thomomys_bottae_riparius"/>
        <taxon id="Thomomys_bottae_mewa"/>
        <taxon id="Thomomys_bottae_saxatilis"/>
        <taxon id="Thomomys_bottae_laticeps"/>
        <taxon id="Thomomys_talpoides_ocius"/>
        <taxon id="Thomomys_idahoensis_pygmaeus_a"/>
        <taxon id="Thomomys_idahoensis_pygmaeus_b"/>
        <taxon id="Thomomys_mazama_mazama"/>
        <taxon id="Thomomys_mazama_nasicus"/>
        <taxon id="Thomomys_monticola_a"/>
        <taxon id="Thomomys_monticola_b"/>
        <taxon id="Thomomys_talpoides_yakimensis"/>
        <taxon id="Thomomys_talpoides_bridgeri"/>
        <taxon id="Thomomys_townsendii_townsendii"/>
        <taxon id="Thomomys_townsendii_relictus"/>
        <taxon id="Thomomys_umbrinus_chihuahuae"/>
        <taxon id="Thomomys_umbrinus_atroavarius"/>
    </taxa>

    <!-- Sequence alignment 1. Gene 26        -->                                               -->
    <alignment id="alignment1" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGAGGTATTACAATACCAGACTTCAAACTTTACTATAGAGCCATAATAACAAAAACCGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAATGGAAYAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCACCATGCACAGGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCAGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGGGAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATAGGAGAAAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAATAATACATCTGACAAATGCTTGAT--ATCCAGT-ATCTACAGGGAACTCAAGAAATTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACMCAGTCTATTCAATTATTGGKGCTGGCAAAACTGGGCAGCCMCATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCM-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGT????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAAYTGTTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGATCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGATAAAGGAGCTAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCT-------------------------------------CATAGGCACTCATAGGCACAGGCAAAAGATTCCTATACAGGAACCCAGGGTCAACAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAA-GTTTCTGCAC?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAAATTCCTGAACAGAATCCCAGGGTCA-CAACAGATKGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATA?????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCTATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            ????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACA???????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            ????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATAT????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            ???CTAGGCAAAA-G-AGC-ATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CKCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            ????????CAAAA-G-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            ????GGCGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGCTATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ATTCTAGGCAAAAAGAAGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCSCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTA-TC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            ??????????????G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAWATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACRAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATATATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            ATTCTAGGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTKTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATCCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTYGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTCTGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACAGG-AACTCAAG?????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            ??????????????G-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTAYTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCACTATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAATGTTTCTGTACAGATAAAAACATAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            ?????????????AG-AGC-ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCTTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACA????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGCATTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGKCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAATTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTT-ATATATCCAGT-ATCTACAGAGAACTCAAG?????????
        </sequence>
    </alignment>


    <!-- Sequence alignment 2. Gene 29        -->
    <alignment id="alignment2" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCACAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCGTTTCTGGAAAACTGAGATCTTGTTTTGACCAACAGAAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGATGTCTCTGTCAGGATCTAGTCCCATCCTG-AATCCATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTCAGAACTGACTGAATCAGGCCAGTGAAAGTTA-CAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATTGTGCATGGCTTCATTAGCAGGTTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCATCAGATTGTCAGGGTCTTGGATTCTGATAAGTTCTGTGTTCCTGATGAGAGACTGGTTATTCAGTAAGTTGTAGGACAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAGAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAKAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTAAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTRTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            C-AGCTTGCTG-TCACACTACCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCASTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGTGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            ?????????????????????????????C-AGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            C-AGCTTGCTG-TCACACYGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTAKGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCRTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCC-AGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGTTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCYACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAATTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCATATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAAWGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGACAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTTTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGTCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATKGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            CAAGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCACCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            C-AGCTTGCTG-TCACAATGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCKTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTYCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGAMTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAAGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTGGAATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGAGGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
        </sequence>
    </alignment>


    <!-- Sequence alignment 3. Gene 47        -->
    <alignment id="alignment3" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTAYCTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACARAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAMGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTARGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            ???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA?????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            ?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            ??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT?????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAAYGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTTSAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTKTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGAYCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCYAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            ?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC???????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCYCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTRCCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            CATGATTTTGTCATGYTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTYGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTTYATATCATCTTTGTGAAACT-A
        </sequence>
    </alignment>


    <!-- Sequence alignment 4. Gene 53        -->
    <alignment id="alignment4" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            ?????????????????????????????AAAAAACCAAAAACCAAAACC-TAAACAAAACCCTGGCATTTGAGTTCTAAGGGTT-TCTAAGAGAACTCAGACACAAGGGAAAAAAATGG-CTGTTTGAAAATGGGCTGCTACCCCTAGTAGGTAGGTACTACCTACTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATACAAATAAAAATTAACCGTAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTT-GGGAAAAA--CATCAGGAATTAGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGTTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATATAACTTTGTCCCTTAATAAGCTCCATGCTTAAGAACTATTTCTACTGACCTCCTTGTTGCTTCCTTGGAGTAAAGTGGCTTTTTG----GACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTAA-TGGTTAATTGAAATACAAATGAAAATTAAATGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGTT?????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTAA-TGGTTAATTGAAATACAAATGAAAATTAAATGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGTTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATACAGACAGCARAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            CCCCAGGACTGGAAAAAAAAAATTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAAATGG-CTGTTTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCARAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            CCCCAGGCCKGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAAATGG-CTGTTTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            CCCTAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACA-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGTTTTAAAATGGGCTGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGCCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            CCCTAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACA-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGTTTTAAAATGGGCTGC-----CTTG-AGG-AC-TAGTACCTAGTACTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            ?????????TGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAARAGAACTCARACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTM-TGGTTAACTGAAATACAAATGAAAATTAAAYGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGARAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAARATTCCTGTGAGACTCTCATCTCTATATAGACAGCASAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAATGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATAGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            CCGTAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACCCAAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGTTTTAAAATGGGCTGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            CCCTAGGRCTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGTTTTAAAATGGGCCGC-----CTTG-AGACAC-TAGTACATAGTGCTTCAARGTTTCTAA-TGGTTAATTGAAATACAAATGAAAATTAAACRTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAAACCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            CCCCAGGACTAGAAAAAAAAA-TTAAAGTT-------AAAAACCCAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCAC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGTAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGTTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            CCCCAGGACTGGAAAAAAAA--TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTTAAAAACCAAAAACCAGAACC-AAAACAAAACCCTGTCATTTGATTTCTAARGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGRAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCCAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            CCCCAGGACTGGAAAAAAAA--TTAAAGTTAAAAWCCAAAAACCAAAACC-AAAACAAGACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGTGC-----TTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTTCCCTATATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTATAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            CCCCAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGTGC-----TTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTTCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTATAAAGACTCATTGGTCTGAAAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ??????????GGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGTGTTGTTTAAGAGAACTCAGACTCAAGGGAAAATA-TGGGCTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----G-GCCTCAAGCTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTKGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACGGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCC?????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            CCCCAGGACTGGAAAAAAA---TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTAT?????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            CCCGAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACCAAACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGA---------AAATA-TGG-CTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTRGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            CCCGAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTC-----TATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            CCCCAGGACTGGAAAAAAA---TTAAAGTTAAAAACCAAAAACCAA------------AACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGTGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTAAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCGAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTGCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACGGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAG-CTCTC--G??????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            ?????????????????????????????????????AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TTTAAGAGAACTCAGACTCAAGGGAAAATA-TGG-CTGTTTGAAAAAGGGGCGC-----CTTG-AGGCAA-TAATA----GTGCCTCAAGGTTTCTAA-TGGTTAATTGAAATTCAAATGAAAATTAAACATAAAATGCTAGGGGAAAGGTCATTTAAAAGGTTTTGGGAAAAA-CCATCAGGAATTGGTTCCTGGAATTAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAGAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCGAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATGGACAGCAGAATA--CTGG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CTATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAG----------------ATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATAGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            CCCCAGGACTGGAAAAAAAAA-TTAAAGTT-------AAAAACCAAAACC-AAAACAAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTTA-TGGTTAACTGAAATACAAATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGGAAA-CTATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGCCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGAGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATAGACAGCAGAATA--CTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            CCCTAGGACTGGAAAAAAAA--TTAAAGTTAAAAACCAAAAACCAAAACC-AAAACCAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGACTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGCTTCAAGGTTTCTAA-TGGTTAATTGAAATACAMATGAAAATTAAACGTAAAATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGTCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGGCTTTTTGTAAAGACTCATTGGTCTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATACAGACAGCAGAATAACCTGA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            CCCTAGGACTGGAAAAAAAA--TTAAAGTTCAAAACCAAAAACCAAAACC-AAAATCAAACCCTGTCATTTGATTTCTAAGGGTT-TCTAAGAGAACTCAGAYTCAAGGGAAAAAA-TGG-CTGATTTAAAATGGGCCGC-----CTTG-AGGCAC-TAGTACCTAGTGTTTCAAGGTTTCTAA-TGGTTAATTGAAATACAAATGAAAATTAAACGTAAMATGCTAGGGGAAAGGTTATTAAAAAGGTTTTGGGGAAAA-CCATCAGGAATTGGTTCCTGGAAATAGAATTTGGAAGTAAAAATTGTCCTAAATGTTTATTTCAAAGTAGAGAAAGGACTACCAAAATGATTGCTTAATTGCTATTCCAGTTTGTCTGTAGCAATTACAGGCAGGCCCACAGAGGGACAGATGATTCTTATAAGTTTGTCAGATGTTACTTTGTCCCTTAATAAGCTCCATGCTTAGGAACTATTTCTACTGACCTCCTTGTTGCTTCATTGGAGTAAAGTGACTTTTTGTAAAGACTCATTGGACTGAGAACTGCTGTTCAAAGCCAGCCTGGGAAGAAAAAGATTCCTGTGAGACTCTCATCTCTATATAGACAGCAGAATA--CTGA
        </sequence>
    </alignment>


    <!-- Sequence alignment 5. Gene 59        -->
    <alignment id="alignment5" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTCTTTCTCTC-----------------------GATATRCTTTTGCTCATGAACCATCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGGAGGGTTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTTTTTTCCTCTGAGGGCTTAAGTGTGTATAA-CTATTTTGTGCATGATATTGCAACAAACAAAAATGCCACATACTCGCACTGGGTACAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGACAAACAGTTTATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTCTCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTAAGACAAAAATCAT-GG----AAGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGRG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGYGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAACCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGRG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTRGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGYGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAACCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCYSTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTRCACTGGGTGYAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAACAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACRTACTTRCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAAYAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCTGTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGTAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTYTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACRTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGKTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGAAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            AATGCAATGGACCCACACCCACCACCTGTGAATACATATGTGATAGGTRTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCG---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAAGAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACKGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCTSTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGYAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATSTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCYTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAACCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCYCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATKTTCCTATCATCCCGRTGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACKGAAGCAAAAACCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            ????????G-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCT------------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCACTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCGGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCACTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCGTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGATTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTCGATATACTTTTGCTCATGAAACGGATATACTTTTGCTCATGAAACGTCTTGTTATCACTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGATTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ??TGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACAYTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGACATCTGGGCGAACAGTTCATGAAATCTCTTCTTAACCAATACAGACTGGGTATGGTACCATGTTCCTATCGTCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCGGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ATGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATGTACTTTTGCTCATGAAACATCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGATGCAGTGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACACA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTGTTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGATGCAGTGGAATCCTAGCTACTCTGGAAGCTGAAACTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCACTGG----ACACA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCACTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGRAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTTTGAGGGCTTAAGTGTGTRGAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCACGAAATCTCTTTTCAACCAATAAAGACTGGGTACAGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATATACTTTTGCTCATGAAACGTCTTGTTATCACTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCGTCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTTCCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGATGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGATTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTTTCAACCAATGAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTTAAAAGTAACTGAAGAAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCCCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTGCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATAAATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ACGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTTGCACTGGGTKCAATGGAATCCT---------GGAAGCTGAAATTGAGAGGATTGTGGTTTGAGATCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATACATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCGCTGG----ATGCA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            AATGCAATG-ACCCACACCCACCACCTGTGAATACATATGTGATAGGTTTGCAAATGAATCTATTTCTCTC-----------------------GATACACTTTTGCTCATGAAACGTCTTGTTATCGCTTTACCTGAACATTGCTAAGCAGGG----TTTGCTGCCATCATCACTCTTCCTCTCTTTGAACTGGGAAGATTTCTGATAGGAAATCTTTCCTGTCTTTACCTCTGAGGGCTTAAGTGTGTATAAACTATTTTGTACGTGATATTGCACCAAACAAAAATGCCACATACTCGCACTGGGTGCAATGGAATCCTAGCTACTCTGGAAGCTGAAATTGAGAGGATTGTGGTTTGAGGTCATCTGGGCAAACAGTTCATGAAATCTCTTCTCAACCAATAAAGACTGGGTATGGTACCATGTTCCTATCATCCCGATGGTTCAGGAAGCATACATAGCTGATCTCATAGATGGTTCAAGCCTGTCTGGACAAAAA-TCAGGTCCTATTTTAAAAAGTAACTGAAGCAAAAATCACTGG----ATGCA
        </sequence>
    </alignment>


    <!-- Sequence alignment 6. Gene 64        -->
    <alignment id="alignment6" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            ???????????????????????????C-TCATAGGACTTATCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTC-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGTTAACATTGATTTTTC--TGTTTTGTTTTGCCC-TTGGTGATTTTCCT-AGGGTTTTAAATCAGGGCC????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            ??GGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTA-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTT--TGTTTTGTTTTGCCCCTTGGTGATTTTCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTAAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATYTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTGGTTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTA-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTC--TGTTTTGTTTTGCCCCTTGGTGATTTTCCT-AGGGTTTTAAATCAGGGCCTTGTATACTCTCACTGAAAGTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTAAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATTTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTGGTTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGYC-TAGCCTCTGGCTTT?
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            ???GACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTT-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTCCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACKGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWARATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTSTTTATTTTCTT--AAGTCTACTRGKTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            CAGGACTGGCATACAATGCACAGAAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTC-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTGGGGGATTTCCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACGGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTSTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTT?
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            CAGGACTGGCATACAATGCACA-AGGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTG-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTC--TGTTTTGTTTTGCCCTT-GGTGATTTCCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWARATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTSTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCWGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGYC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            CAGGACTGGCATACAATGCAGA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTW-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTC--TGTTTTGTTTTGCCCTTTGGTGATTTWCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWARATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTAGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCWGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTY-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTY--TGTTTTGTTTTGCCCTTGGGGGATTTWCCT-AGGGTTTTAAATCAGGGCCTWGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWARATTTGGGT-GCTGGTACTATGCCTTWAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTRTTTATTTTCTT--AAGTCTACTRGKTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGC????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTT-AGATTTCAGYGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTY--TGTTTTGTTTTGCCC-TTGGTGATTTACCT-AGGGTTTTAAATCAGGGCCTWGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTAAGATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTAGTTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGCCTT-TCCTGTCCAGGC-TGGCTTA-GAACTATGATCCCC-AGATTTCAGCGAGCTAGGCTGCTAGAATTCTTTAGCTACAATTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAAGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGCTAGAAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTTATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTTAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTGTTTATTTTCTT--AAGTCTCCTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGA-CTTTGGTTTTGTTTTG-C-TTTTC-TGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGACTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            ???????GGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTA-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTC--TGTTTTGTTTTGCCCCTTGGTGATTTTCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTA-AGATTTCAGTGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTT--TGTTTTGTTTTGCCCCTTGGTGATTTACCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCAYTGAAAGTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTAAGATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTCTTTATTTTCTT--AAGTCTACTGGTTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGTC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCTC-AGATTTCAGYGAGCTAGGCAGCTAGAATTCTTTAGGTACAAGGTAACATTGATTTTTC--TGTTTTGTTTTGCCCCTTGGTGATTTWCCT-AGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAARTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTWARATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-MTCTGAA-GTTTTTSTTTATTTTCTT--AAGTCTACTGGKTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGYC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            ??????????????????????????????????????????????????????????????GAACTGTGATC-TC-AGATTTCAGCRAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGAGTGTAGAAATTGAGACAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACAWATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            CAGGACTGGTATACAGTGCACG-AAGTC-TCAT-GGCCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAAATTGAGCCAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            ???????????????????????????????????GCCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAAATTGAGCCAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ??????????????????CACG-AAGTCATCAT-GGCCTT-TCCTGTCCAGAGCTGGCTTATAAAGAGTGATCCCC-AGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGCTACAAGWTAACATTGATTT--YTTTGTTTTGTTTTGCCCGTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAATTTGATCCAAACCTTRATTACTCATGTTTATTTTTGAAATTTGGGTTGCAGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-CTTTTTCCTGGGCTGGTCCCTACTCCCAT-GAAACTCAGGGCC-TA?????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            ??????TGGTATACAGTGCACG-AAGTC-TCAT-GGYCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCKTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTARAAATTGAGCCAAACCTTAACTACTCATGTTTATTTTTGAAAWTTGGG-GGCTGGTACTATGCCTTAAACCCAAGGGCTGGGGCTTTT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CCATTG-AACTCAGGGCC-TAGCCTCTGGC????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            CAGGACTGGTATACAGTGCACG-AAGTC-TCAT-GGCCTT-TCCTGTCCAGGC-TGGCTTA-AAACCTTGATCCCC-AGATATCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCTCTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAAATTGAGCCAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            CAGGACTGATATACAGTGCATG-AAGTC-TCTT-GGCCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATAGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTT-CTTCAGAGGAAGCAGGCTGTAGAAATTGAGCCAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            CAGGACTGGTATACAGTGCACG-AAGTC-TCAT-GGCCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCAAGCTAGGCAGCTAGAATTCTTTAGCTACAAGTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTARGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAAATTGAGCCAAACCTTGATTACTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTGTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCY-TACT-CC-TTG-AACTCAGGGCC-TAGCCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            ?????????????????????G-AAGTM-TCAT-GGCCTT-TCCTGTCCAGGCATG---TACAGACTGTGATCATCCAGATTTCAGCGAGCTAGGCAGCTAGAATTCTTTAGCTACAAGATAACATTGATTT--YTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAGGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGGAAGCAGGCTGTAGAAWTTGAGCCAAACCTTGATTACTCATGTTTATTTTTKAAATTTGGGTTGCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCTCATCTGAA-GTTTGTGTTTATTTTCTTCTAAGTCTACTGGGTGCTATTACTTGCAACATATGTCCAAGTTTGGTCTTTGGCTTTTTTTTAACTTTTTCCTGGGCTGGTCC-TTCTTCCAT??????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCGAGCTAGGCTGCTAGAATTCTTTAGCTACAATTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTGGGTGATTTTCCT-AGGGTTTTAAATCAGGGCCTTGTATACTCTCACTGAAAATTTTTCCTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTAAACCCAAGGGCTGGTGCTTCT-ATTTGAA-GTTTTTGTTTATTTTCTT--AAGTCTACTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGG-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGYC-TAGCCTCTGGCTTTA
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGACTT-TCCTGTCCAGGC-TGGCTTA-GAACTRTGATCCYC-AGATTTCAGCGAGCTAGGCTGCTAGAATTCTTTAGCTACAATTTAACATTGATTT--CTTTGTTTTGTTTTGCCCTTTGGTGATTTTCCTTAGGGTTTTAAATCAAGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGCTAGMAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTTATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTTAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTGTTTATTTTCTT--AAGTCTCCTGGGTGCTATTACTTGCAACATATGTC-AAGTTTGA-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CY-TTG-AACTCAGGGYC-TAGMCTCTGGCATTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGMCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCCC-AGATTTCAGCGAGCTAGGCTGCTAGAATTCTTTAGCTACAATTTAACATTGATTT--YTTTGTTTTGTTTTGCCCYTTGGTGATTTTCCTTAGGGTTTTAAATCAAGGCCTAGTATACTCTCACTGAAAGTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTATGCCTTTAACCCAAGGGCTGGTGCTTCT-ATYTGAA-GTTTATCTTTATTTTCTT--AAGTCTCCTGGGTGCTATTACYTGCAACATAWGTC-AAGTTTGR-CTTTGGTTTTGKTTTG-C-TTTYC-TGGGCTGGTCC-TACT-CY-TTG-AACTCAGGGYC-TAGYCTCTGGCTTTT
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            CAGGACTGGCATACAATGCACA-AAGTC-TCAT-GGMCTT-TCCTGTCCAGGC-TGGCTTA-GAACTGTGATCCYC-AGATTTCAGCGAGCTAGGCTGCTAGAATTCTTTAGCTACAATTTAACATTGATTT--CTTTGTTTTGTTTTGCCCYTTGGTGATTTTCCTTAGGGTTTTAAATCARGGCCTAGTATACTCTCCCTGAAAGTTTTTCTTCAGAGCTAGCAGGCTGTAGAATTTGAGCCAAACCTTGATTGCTCATGTTTATTTTTTAAATTTGGGT-GCTGGTACTAAGCCTTTAACCCAAGGGCTGGTGCTTCT-ATCTGAA-GTTTTTGTTTATTTTYTY--AAGTYTMCTGGGTGSTATTMCYTSCMACMTATGTC-AAGTTTGA-CTTTGGTTTTGTTTTG-C-TTTTCCTGGGCTGGTCC-TACT-CC-TTG-AACTCAGGGCC-TAGMCTCTGGCTTTT
        </sequence>
    </alignment>


    <!-- Sequence alignment 7. Gene 72        -->
    <alignment id="alignment7" dataType="nucleotide">
        <sequence>
            <taxon idref="Orthogeomys_heterodus"/>
            ?????????????????????????????????????????????????????????????GGAGCCCCTGGCAGCCCATAGACCTGGCCTAGCAGAAGCTCGTCCATTTGCTTCGAGTTGTGGTCCAGAAGATCCAACGTCTCACAGTGCATGGCCAGCTCCGAGGCCAAAGTGCCCACCCGTGGGCGTTTCCGGAAGCCCTCCTCTGCAACCTTCTC-CTTTCATTGCTCCC--C-CTCCTG---------------CT-------------------------CCTCTTCCTCCTCCCCTCTGG-GCTC---------TGGAGCC-CCT---GGTTCCC-------------------------------------CAGGGA-TCT----------GCCCCAGC---AGAAGCTCAGCCA-TT--------TGCTTCGA---GTTGCGCCC-CA--GGAGAAC--CAAAGTCTCC---CAG---------------------CGC--------------------AT---GG-------------------------CCAGCTCCT---------GGGCCAAAG-------TGCCCA--------CCCACGGGTGTTCCC--G-GAAGCCCTC--CACTGTCCTGCT---------------GAA??????????????????????????????????????
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_a"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_awahnee_b"/>
            ???????????????????????CCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_xerophilus"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_cactophilus"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_albatus"/>
            ???????????????????????CCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCATCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_ruidosae"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_bottae"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGKGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCKTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTYTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGAATCTTGCTCGAAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_alpinus"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAG-GCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_riparius"/>
            ???????????????????????CCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAAAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCATCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTYTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_mewa"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_saxatilis"/>
            ???????????????????????CCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGYGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_bottae_laticeps"/>
            ??????????????????????CCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGYGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCRGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_ocius"/>
            ?????CTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGAAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
            GCAACCTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACGCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTTGTATCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATATGAGGCCCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
            ?CAACCTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCARAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGARAGCAGCCGCAAGGACTGTCGCACRCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTTGTATCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATATGAGGCCCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_mazama"/>
            ??CACCTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTYGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_mazama_nasicus"/>
            GCAACCTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTTGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTYGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCYTGCTCAGGGACCTTGCTCGGAACCTCTGATATGAGGCYCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_a"/>
            ?????????????TTCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTGTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_monticola_b"/>
            GCAACCTTCTCCTTCCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTGTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_yakimensis"/>
            ??????????????????????????????????????????????????????GGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGC-AGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCGCACCCCCTCCCCRTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGAYTCTCGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCYGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCAGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_talpoides_bridgeri"/>
            GCAACCTTCTCCTTTCATTGCTCCCCCTCCTGCTCCTCTTCCTCCTC-CGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGACTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAGTTGCGGCCCAGGAGAACCAACGTCTGCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATGGGCAGCACTGAGAGCAGCCGCAAGGACTGTCRCACCYCCTCCCYGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGACACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTCAGCTCCAGGATCC-AGCGGGTTACCCGCGGTGCTCTGGCACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCCGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTGCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGAGTCCTGAGCGCCGTCCTGCTCAGGGACCTTGCTCGGAACCTCTGATTTGAGGCTCAGGGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_townsendii"/>
            GCAACCTTCTCCTTCCATTGCTCCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGYTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGMTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_townsendii_relictus"/>
            GCAACCTTCTCCTTTCATTGCTCCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGTTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGATGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
            GCAACCTTCTCCTTCCATTGCTCCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAARCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
        <sequence>
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
            GCCACCTTCTCCTTCCATTGCTCCCCCCCCTGCTCCTCTTCCTCCTC-TGCTCTGGCCTCTGGATTCCCTGGCTGTCCAGGGGCTTGGCCCAGCAGAAGCTCGGCCATTTGCTTCGAATTGCGGCCCAGGAGAACCAACGTCTCCCAGCGCATGGCCAGCTCCTGGGCCAAAGTGCCCACCAGCGGGTGTTTGCAGAAGCCCTCCACTGTG--CTTCTCACACCCGTGGCTGCCAGCATTTCTGGGGTGATAGGCAGCACTGACAGCAGCCTCAAGGACTGTCGCACTCCCTCCCCGTCTTTTCTAGAGCTCAGGTGCTGCTGGAGCTGCCTCAAGGCTCCCGAAACCCACTCCGTCTGCGTCCCACTCACCACCTCCTCAGGGACTCTCGTGTCACTCACCTTAGCTCCAGGATCC-AGTGGATTACCCCCGGTGCTCTGACACATCACGTCCTCACTGGATGACTCCAAAATCTCCTCCCGGTTCTGCTCTGCCTCCTGCTCCTGCTCCTCCTCCTGGTCCTCCTCATCTTGGTACTCTTCCTTCTGGTCTTCGTCCTCCTGCTCCTCTTCCCCCTGGACC--GGCTCCCCCTTCCCATCTCTCTGCC-CCAGACCCTCCCTCGTGGGGTCCTGAGCGCCGTCCTGCTCAGGGATCTTGCTCGGAACCTCTGATTTGAGGCTCAGTGCAGCCAAGGTCTCCCAG
        </sequence>
    </alignment>

    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=144                                                           -->
    <patterns id="26.patterns" from="1">
        <alignment idref="alignment1"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=71                                                            -->
    <patterns id="29.patterns" from="1">
        <alignment idref="alignment2"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=153                                                           -->
    <patterns id="47.patterns" from="1">
        <alignment idref="alignment3"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=140                                                           -->
    <patterns id="53.patterns" from="1">
        <alignment idref="alignment4"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=92                                                            -->
    <patterns id="59.patterns" from="1">
        <alignment idref="alignment5"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=157                                                           -->
    <patterns id="64.patterns" from="1">
        <alignment idref="alignment6"/>
    </patterns>
    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=85                                                            -->
    <patterns id="72.patterns" from="1">
        <alignment idref="alignment7"/>
    </patterns>

    <!-- A constant population size generating starting trees -->
    <constantSize id="constant" units="substitutions">
        <populationSize>
            <parameter id="constant.popSize" value="0.02" lower="0.0" upper="Infinity"/>
        </populationSize>
    </constantSize>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="26.startingTree" rootHeight="0.017">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="29.startingTree" rootHeight="0.016">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="47.startingTree" rootHeight="0.017">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="53.startingTree" rootHeight="0.026">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="59.startingTree" rootHeight="0.015">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="64.startingTree" rootHeight="0.028">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a random starting tree under the coalescent process            -->
    <!-- No calibration                                                          -->
    <coalescentTree id="72.startingTree" rootHeight="0.025">
        <taxa idref="taxa"/>
        <constantSize idref="constant"/>
    </coalescentTree>

    <!-- Generate a tree model                                                   -->
    <treeModel id="26.treeModel">
        <coalescentTree idref="26.startingTree"/>
        <rootHeight>
            <parameter id="26.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="26.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="26.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="29.treeModel">
        <coalescentTree idref="29.startingTree"/>
        <rootHeight>
            <parameter id="29.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="29.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="29.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="47.treeModel">
        <coalescentTree idref="47.startingTree"/>
        <rootHeight>
            <parameter id="47.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="47.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="47.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="53.treeModel">
        <coalescentTree idref="53.startingTree"/>
        <rootHeight>
            <parameter id="53.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="53.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="53.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="59.treeModel">
        <coalescentTree idref="59.startingTree"/>
        <rootHeight>
            <parameter id="59.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="59.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="59.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="64.treeModel">
        <coalescentTree idref="64.startingTree"/>
        <rootHeight>
            <parameter id="64.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="64.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="64.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Generate a tree model                                                   -->
    <treeModel id="72.treeModel">
        <coalescentTree idref="72.startingTree"/>
        <rootHeight>
            <parameter id="72.treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="72.treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="72.treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>


    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="26.26.branchRates">
        <rate>
            <parameter id="26.clock.rate" value="1.0"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="29.29.branchRates">
        <rate>
            <parameter id="29.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="47.47.branchRates">
        <rate>
            <parameter id="47.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="53.53.branchRates">
        <rate>
            <parameter id="53.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="59.59.branchRates">
        <rate>
            <parameter id="59.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="64.64.branchRates">
        <rate>
            <parameter id="64.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The strict clock (Uniform rates across branches)                        -->
    <strictClockBranchRates id="72.72.branchRates">
        <rate>
            <parameter id="72.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
        </rate>
    </strictClockBranchRates>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="26.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="26.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="26.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="29.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="29.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="29.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="47.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="47.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="47.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="53.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="53.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="53.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="59.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="59.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="59.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="64.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="64.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="64.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
    <HKYModel id="72.hky">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <frequencies>
                    <parameter id="72.frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="72.kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
        </kappa>
    </HKYModel>

    <!-- site model                                                              -->
    <siteModel id="26.siteModel">
        <substitutionModel>
            <HKYModel idref="26.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="29.siteModel">
        <substitutionModel>
            <HKYModel idref="29.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="47.siteModel">
        <substitutionModel>
            <HKYModel idref="47.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="53.siteModel">
        <substitutionModel>
            <HKYModel idref="53.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="59.siteModel">
        <substitutionModel>
            <HKYModel idref="59.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="64.siteModel">
        <substitutionModel>
            <HKYModel idref="64.hky"/>
        </substitutionModel>
    </siteModel>

    <!-- site model                                                              -->
    <siteModel id="72.siteModel">
        <substitutionModel>
            <HKYModel idref="72.hky"/>
        </substitutionModel>
    </siteModel>

    <treeLikelihood id="26.26.treeLikelihood" useAmbiguities="false">
        <patterns idref="26.patterns"/>
        <treeModel idref="26.treeModel"/>
        <siteModel idref="26.siteModel"/>
        <strictClockBranchRates idref="26.26.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="29.29.treeLikelihood" useAmbiguities="false">
        <patterns idref="29.patterns"/>
        <treeModel idref="29.treeModel"/>
        <siteModel idref="29.siteModel"/>
        <strictClockBranchRates idref="29.29.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="47.47.treeLikelihood" useAmbiguities="false">
        <patterns idref="47.patterns"/>
        <treeModel idref="47.treeModel"/>
        <siteModel idref="47.siteModel"/>
        <strictClockBranchRates idref="47.47.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="53.53.treeLikelihood" useAmbiguities="false">
        <patterns idref="53.patterns"/>
        <treeModel idref="53.treeModel"/>
        <siteModel idref="53.siteModel"/>
        <strictClockBranchRates idref="53.53.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="59.59.treeLikelihood" useAmbiguities="false">
        <patterns idref="59.patterns"/>
        <treeModel idref="59.treeModel"/>
        <siteModel idref="59.siteModel"/>
        <strictClockBranchRates idref="59.59.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="64.64.treeLikelihood" useAmbiguities="false">
        <patterns idref="64.patterns"/>
        <treeModel idref="64.treeModel"/>
        <siteModel idref="64.siteModel"/>
        <strictClockBranchRates idref="64.64.branchRates"/>
    </treeLikelihood>

    <treeLikelihood id="72.72.treeLikelihood" useAmbiguities="false">
        <patterns idref="72.patterns"/>
        <treeModel idref="72.treeModel"/>
        <siteModel idref="72.siteModel"/>
        <strictClockBranchRates idref="72.72.branchRates"/>
    </treeLikelihood>


    <!-- Species definition: binds taxa, species and gene trees                  -->
    <!-- DISSECT One individual in each species                                      -->
    <species id="species">
        <sp id="Orthogeomys_heterodus1">
            <taxon idref="Orthogeomys_heterodus"/>
        </sp>

        <sp id="Thomomys_bottae1">
            <taxon idref="Thomomys_bottae_awahnee_a"/>
        </sp>
        <sp id="Thomomys_bottae2">
            <taxon idref="Thomomys_bottae_awahnee_b"/>
        </sp>
        <sp id="Thomomys_bottae3">
            <taxon idref="Thomomys_bottae_xerophilus"/>
        </sp>
        <sp id="Thomomys_bottae4">
            <taxon idref="Thomomys_bottae_cactophilus"/>
        </sp>
        <sp id="Thomomys_bottae5">
            <taxon idref="Thomomys_bottae_albatus"/>
        </sp>
        <sp id="Thomomys_bottae6">
            <taxon idref="Thomomys_bottae_ruidosae"/>
        </sp>
        <sp id="Thomomys_bottae7">
            <taxon idref="Thomomys_bottae_bottae"/>
        </sp>
        <sp id="Thomomys_bottae8">
            <taxon idref="Thomomys_bottae_alpinus"/>
        </sp>
        <sp id="Thomomys_bottae9">
            <taxon idref="Thomomys_bottae_riparius"/>
        </sp>
        <sp id="Thomomys_bottae10">
            <taxon idref="Thomomys_bottae_mewa"/>
        </sp>
        <sp id="Thomomys_bottae11">
            <taxon idref="Thomomys_bottae_saxatilis"/>
        </sp>
        <sp id="Thomomys_bottae12">
            <taxon idref="Thomomys_bottae_laticeps"/>
        </sp>

        <sp id="Thomomys_talpoides1">
            <taxon idref="Thomomys_talpoides_ocius"/>
        </sp>
        <sp id="Thomomys_talpoides2">
            <taxon idref="Thomomys_talpoides_yakimensis"/>
        </sp>
        <sp id="Thomomys_talpoides3">
            <taxon idref="Thomomys_talpoides_bridgeri"/>
        </sp>

        <sp id="Thomomys_idahoensis1">
            <taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
        </sp>
        <sp id="Thomomys_idahoensis2">
            <taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
        </sp>

        <sp id="Thomomys_mazama1">
            <taxon idref="Thomomys_mazama_mazama"/>
        </sp>
        <sp id="Thomomys_mazama2">
            <taxon idref="Thomomys_mazama_nasicus"/>
        </sp>

        <sp id="Thomomys_monticola1">
            <taxon idref="Thomomys_monticola_a"/>
        </sp>
        <sp id="Thomomys_monticola2">
            <taxon idref="Thomomys_monticola_b"/>
        </sp>

        <sp id="Thomomys_townsendii1">
            <taxon idref="Thomomys_townsendii_townsendii"/>
        </sp>
        <sp id="Thomomys_townsendii2">
            <taxon idref="Thomomys_townsendii_relictus"/>
        </sp>

        <sp id="Thomomys_umbrinus1">
            <taxon idref="Thomomys_umbrinus_chihuahuae"/>
        </sp>
        <sp id="Thomomys_umbrinus2">
            <taxon idref="Thomomys_umbrinus_atroavarius"/>
        </sp>

        <!-- Collection of Gene Trees                                                -->
        <geneTrees id="geneTrees">
            <treeModel idref="26.treeModel"/>
            <treeModel idref="29.treeModel"/>
            <treeModel idref="47.treeModel"/>
            <treeModel idref="53.treeModel"/>
            <treeModel idref="59.treeModel"/>
            <treeModel idref="64.treeModel"/>
            <treeModel idref="72.treeModel"/>
        </geneTrees>
    </species>

    <!-- Species Tree: Provides Per branch demographic function                  -->
    <speciesTree id="sptree" constantRoot="true">
        <species idref="species"/>
        <sppSplitPopulations value="0.02">
            <parameter id="speciesTree.splitPopSize"/>
        </sppSplitPopulations>
    </speciesTree>

    <!-- Species Tree prior: Birth Death Collapse Model                            -->
    <!-- DISSECT Similar to birthDeathModel, but has an extra fixed value collapseHeight           -->
    <!--  and two extra parameters originHeight and collapseWeight.  -->
    <!-- DISSECT (implementation)  sampleProbability is not yet implemented.                                 -->
    <!-- DISSECT (implementation)  The ref to speciesTree is to set initial originHeight.                    -->
    <birthDeathCollapseModel id="birthDeathCollapse" units="substitutions" collapseHeight="0.0001">
        <speciesTree>
            <speciesTree idref="sptree"/>
        </speciesTree>
        <birthMinusDeathRate>
            <parameter id="species.birthDeathCollapse.meanGrowthRate" value="100" lower="0.0" upper="Infinity"/>
        </birthMinusDeathRate>
        <relativeDeathRate>
            <parameter id="species.birthDeathCollapse.relativeDeathRate" value="0.5" lower="0.0" upper="1.0"/>
        </relativeDeathRate>
        <originHeight>
            <parameter id="species.birthDeathCollapse.originHeight" value="0.2" lower="0.0" upper="Infinity"/>
        </originHeight>
        <collapseWeight>
            <parameter id="species.birthDeathCollapse.collapseWeight" value="0.5" lower="0.0" upper="1.0"/>
        </collapseWeight>
    </birthDeathCollapseModel>

    <!-- Species Tree: Likelihood of species tree                                -->
    <!-- DISSECT refers to birthDeathCollapseModel -->
    <speciationLikelihood id="speciation.likelihood">
        <model>
            <birthDeathCollapseModel idref="birthDeathCollapse"/>
        </model>
        <speciesTree>
            <speciesTree idref="sptree"/>
        </speciesTree>
    </speciationLikelihood>

    <!-- Species Tree: Coalescent likelihood for gene trees under species tree   -->
    <speciesCoalescent id="species.coalescent">
        <species idref="species"/>
        <speciesTree idref="sptree"/>
    </speciesCoalescent>

    <!-- Species tree prior: gamma2 + gamma4                                      -->
    <mixedDistributionLikelihood id="species.popSize">
        <distribution0>
            <gammaDistributionModel>
                <shape>
                    2
                </shape>
                <scale>
                    <parameter id="species.popMean" value="0.02"/>
                </scale>
            </gammaDistributionModel>
        </distribution0>
        <distribution1>
            <gammaDistributionModel>
                <shape>
                    4
                </shape>
                <scale>
                    <parameter idref="species.popMean"/>
                </scale>
            </gammaDistributionModel>
        </distribution1>
        <data>
            <parameter idref="speciesTree.splitPopSize"/>
        </data>
        <indicators>
            <parameter
                    value="1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/>
        </indicators>
    </mixedDistributionLikelihood>


    <!-- Statistics -->

    <!-- DISSECT a statistic to count clusters -->
    <bdcNClustersStatistic id="nClusters" name="nClusters">
        <collapseModel>
            <birthDeathCollapseModel idref="birthDeathCollapse"/>
        </collapseModel>
        <speciesTree>
            <speciesTree idref="sptree"/>
        </speciesTree>
    </bdcNClustersStatistic>

    <!-- Species Tree: tmrcaStatistic                                            -->
    <tmrcaStatistic id="speciesTree.rootHeight" name="speciesTree.rootHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Orthogeomys_heterodus1"/>
                <sp idref="Thomomys_bottae1"/>
                <sp idref="Thomomys_bottae2"/>
                <sp idref="Thomomys_bottae3"/>
                <sp idref="Thomomys_bottae4"/>
                <sp idref="Thomomys_bottae5"/>
                <sp idref="Thomomys_bottae6"/>
                <sp idref="Thomomys_bottae7"/>
                <sp idref="Thomomys_bottae8"/>
                <sp idref="Thomomys_bottae9"/>
                <sp idref="Thomomys_bottae10"/>
                <sp idref="Thomomys_bottae11"/>
                <sp idref="Thomomys_bottae12"/>
                <sp idref="Thomomys_talpoides1"/>
                <sp idref="Thomomys_talpoides2"/>
                <sp idref="Thomomys_talpoides3"/>
                <sp idref="Thomomys_idahoensis1"/>
                <sp idref="Thomomys_idahoensis2"/>
                <sp idref="Thomomys_mazama1"/>
                <sp idref="Thomomys_mazama2"/>
                <sp idref="Thomomys_monticola1"/>
                <sp idref="Thomomys_monticola2"/>
                <sp idref="Thomomys_townsendii1"/>
                <sp idref="Thomomys_townsendii2"/>
                <sp idref="Thomomys_umbrinus1"/>
                <sp idref="Thomomys_umbrinus2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>

    <!-- DISSECT You can add any of these tmrcaStatistics that seem of particular interest         -->
    <tmrcaStatistic id="speciesTree.bottaeHeight" name="speciesTree.bottaeHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_bottae1"/>
                <sp idref="Thomomys_bottae2"/>
                <sp idref="Thomomys_bottae3"/>
                <sp idref="Thomomys_bottae4"/>
                <sp idref="Thomomys_bottae5"/>
                <sp idref="Thomomys_bottae6"/>
                <sp idref="Thomomys_bottae7"/>
                <sp idref="Thomomys_bottae8"/>
                <sp idref="Thomomys_bottae9"/>
                <sp idref="Thomomys_bottae10"/>
                <sp idref="Thomomys_bottae11"/>
                <sp idref="Thomomys_bottae12"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.talpoidesHeight" name="speciesTree.talpoidesHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_talpoides1"/>
                <sp idref="Thomomys_talpoides2"/>
                <sp idref="Thomomys_talpoides3"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.idahoensisHeight" name="speciesTree.idahoensisHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_idahoensis1"/>
                <sp idref="Thomomys_idahoensis2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.mazamaHeight" name="speciesTree.mazamaHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_mazama1"/>
                <sp idref="Thomomys_mazama2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.monticolaHeight" name="speciesTree.monticolaHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_monticola1"/>
                <sp idref="Thomomys_monticola2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.townsendiiHeight" name="speciesTree.townsendiiHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_townsendii1"/>
                <sp idref="Thomomys_townsendii2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>
    <tmrcaStatistic id="speciesTree.umbrinusHeight" name="speciesTree.umbrinusHeight">
        <speciesTree idref="sptree"/>
        <mrca>
            <taxa>
                <sp idref="Thomomys_umbrinus1"/>
                <sp idref="Thomomys_umbrinus2"/>
            </taxa>
        </mrca>
    </tmrcaStatistic>


    <!-- Define operators                                                        -->
    <operators id="operators">
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="26.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="26.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="29.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="29.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="47.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="47.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="53.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="53.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="59.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="59.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="64.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="64.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="1">
            <parameter idref="72.kappa"/>
        </scaleOperator>
        <deltaExchange delta="0.01" weight="1">
            <parameter idref="72.frequencies"/>
        </deltaExchange>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="29.clock.rate"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="47.clock.rate"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="53.clock.rate"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="59.clock.rate"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="64.clock.rate"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="72.clock.rate"/>
        </scaleOperator>
        <upDownOperator scaleFactor="0.75" weight="30">
            <up>
                <parameter idref="29.clock.rate"/>
                <parameter idref="47.clock.rate"/>
                <parameter idref="53.clock.rate"/>
                <parameter idref="59.clock.rate"/>
                <parameter idref="64.clock.rate"/>
                <parameter idref="72.clock.rate"/>
                <parameter idref="species.birthDeathCollapse.meanGrowthRate"/>
            </up>
            <down>
                <speciesTree idref="sptree"/>
                <parameter idref="species.popMean"/>
                <parameter idref="speciesTree.splitPopSize"/>
                <parameter idref="26.treeModel.allInternalNodeHeights"/>
                <parameter idref="29.treeModel.allInternalNodeHeights"/>
                <parameter idref="47.treeModel.allInternalNodeHeights"/>
                <parameter idref="53.treeModel.allInternalNodeHeights"/>
                <parameter idref="59.treeModel.allInternalNodeHeights"/>
                <parameter idref="64.treeModel.allInternalNodeHeights"/>
                <parameter idref="72.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <subtreeSlide size="0.0017000000000000001" gaussian="true" weight="15">
            <treeModel idref="26.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="26.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="26.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="26.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="26.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="26.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0016" gaussian="true" weight="15">
            <treeModel idref="29.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="29.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="29.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="29.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="29.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="29.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0017000000000000001" gaussian="true" weight="15">
            <treeModel idref="47.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="47.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="47.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="47.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="47.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="47.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0026" gaussian="true" weight="15">
            <treeModel idref="53.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="53.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="53.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="53.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="53.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="53.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0015" gaussian="true" weight="15">
            <treeModel idref="59.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="59.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="59.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="59.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="59.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="59.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0028" gaussian="true" weight="15">
            <treeModel idref="64.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="64.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="64.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="64.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="64.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="64.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <subtreeSlide size="0.0025" gaussian="true" weight="15">
            <treeModel idref="72.treeModel"/>
        </subtreeSlide>
        <narrowExchange weight="15">
            <treeModel idref="72.treeModel"/>
        </narrowExchange>
        <wideExchange weight="3">
            <treeModel idref="72.treeModel"/>
        </wideExchange>
        <wilsonBalding weight="3">
            <treeModel idref="72.treeModel"/>
        </wilsonBalding>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="72.treeModel.rootHeight"/>
        </scaleOperator>
        <uniformOperator weight="30">
            <parameter idref="72.treeModel.internalNodeHeights"/>
        </uniformOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
            </up>
            <down>
                <parameter idref="26.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="29.clock.rate"/>
            </up>
            <down>
                <parameter idref="29.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="47.clock.rate"/>
            </up>
            <down>
                <parameter idref="47.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="53.clock.rate"/>
            </up>
            <down>
                <parameter idref="53.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="59.clock.rate"/>
            </up>
            <down>
                <parameter idref="59.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="64.clock.rate"/>
            </up>
            <down>
                <parameter idref="64.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="72.clock.rate"/>
            </up>
            <down>
                <parameter idref="72.treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>

        <!-- Species trees operators -->
        <scaleOperator scaleFactor="0.9" weight="5">
            <parameter idref="species.popMean"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="species.birthDeathCollapse.meanGrowthRate"/>
        </scaleOperator>
        <!-- GRJ randomWalkOperator more appropriate here?       -->
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="species.birthDeathCollapse.relativeDeathRate"/>
        </scaleOperator>
        <!-- DISSECT Add operator for originHeight                  -->
        <!-- DISSECT (implementation)  this can make origin more recent than root, which has  -->
        <!-- DISSECT  zero likelihood. Could be improved.  -->
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="species.birthDeathCollapse.originHeight"/>
        </scaleOperator>
        <!-- DISSECT Optionally add operator for collapseWeight                  -->
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="species.birthDeathCollapse.collapseWeight"/>
        </scaleOperator>
        <scaleOperator scaleFactor="0.5" weight="94">
            <parameter idref="speciesTree.splitPopSize"/>
        </scaleOperator>
        <!-- DISSECT (implementation)  new operators might help here too     -->
        <nodeReHeight weight="94">
            <species idref="species"/>
            <speciesTree idref="sptree"/>
        </nodeReHeight>
    </operators>

    <!-- Define MCMC                                                             -->
    <mcmc id="mcmc" chainLength="5000000" autoOptimize="true">
        <posterior id="posterior">
            <prior id="prior">
                <speciesCoalescent idref="species.coalescent"/>
                <mixedDistributionLikelihood idref="species.popSize"/>
                <speciationLikelihood idref="speciation.likelihood"/>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="26.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="29.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="47.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="53.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="59.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="64.kappa"/>
                </logNormalPrior>
                <logNormalPrior mean="1" stdev="1.25" offset="0" meanInRealSpace="false">
                    <parameter idref="72.kappa"/>
                </logNormalPrior>

                <!-- GRJ these priors are quite diffuse but is not appropriate for all genes   -->
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="29.clock.rate"/>
                </logNormalPrior>
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="47.clock.rate"/>
                </logNormalPrior>
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="53.clock.rate"/>
                </logNormalPrior>
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="59.clock.rate"/>
                </logNormalPrior>
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="64.clock.rate"/>
                </logNormalPrior>
                <logNormalPrior meanInRealSpace="false" offset="0" stdev="1" mean="0">
                    <parameter idref="72.clock.rate"/>
                </logNormalPrior>

                <!-- GRJ this prior is quite diffuse but is not appropriate for all species   -->
                <logNormalPrior mean="-9" stdev="1" offset="0" meanInRealSpace="false">
                    <parameter idref="species.popMean"/>
                </logNormalPrior>

                <!-- GRJ Very loosely, this prior says P(0.0002 < branch length < 0.5) ~= .95    -->
                <logNormalPrior mean="4.6" stdev="2" offset="0" meanInRealSpace="false">
                    <parameter idref="species.birthDeathCollapse.meanGrowthRate"/>
                </logNormalPrior>

                <!-- DISSECT Uniform prior for mu/lambda.     -->
                <betaPrior shape="1.0" shapeB="1.0">
                    <parameter idref="species.birthDeathCollapse.relativeDeathRate"/>
                </betaPrior>

                <!-- DISSECT Example hyperprior for w  -->
                <betaPrior shape="5" shapeB="2">
                    <parameter idref="species.birthDeathCollapse.collapseWeight"/>
                </betaPrior>

            </prior>
            <likelihood id="likelihood">
                <treeLikelihood idref="26.26.treeLikelihood"/>
                <treeLikelihood idref="29.29.treeLikelihood"/>
                <treeLikelihood idref="47.47.treeLikelihood"/>
                <treeLikelihood idref="53.53.treeLikelihood"/>
                <treeLikelihood idref="59.59.treeLikelihood"/>
                <treeLikelihood idref="64.64.treeLikelihood"/>
                <treeLikelihood idref="72.72.treeLikelihood"/>
            </likelihood>
        </posterior>
        <operators idref="operators"/>
        <!-- write log to screen                                                     -->
        <log id="screenLog" logEvery="100000">
            <column label="Posterior" dp="4" width="12">
                <posterior idref="posterior"/>
            </column>
            <column label="Prior" dp="4" width="12">
                <prior idref="prior"/>
            </column>
            <column label="Likelihood" dp="4" width="12">
                <likelihood idref="likelihood"/>
            </column>
        <!-- DISSECT new things you might want to see on screen -->
            <column label="nClusters" dp="0" width="8">
            <bdcNClustersStatistic idref="nClusters"/>
        </column>
            <column label="cllpsWt" dp="4" width="8">
                <parameter idref="species.birthDeathCollapse.collapseWeight"/>
            </column>
            <column label="PopMean" dp="4" width="12">
                <parameter idref="species.popMean"/>
            </column>
            <column label="Spp mrca" sf="6" width="12">
                <tmrcaStatistic idref="speciesTree.rootHeight"/>
            </column>
            <column label="Spp origin" sf="6" width="12">
                <parameter idref="species.birthDeathCollapse.originHeight"/>
            </column>
            <column label="29.clock.rate" sf="6" width="12">
                <parameter idref="29.clock.rate"/>
            </column>
            <column label="Growth" sf="6" width="12">
                <parameter idref="species.birthDeathCollapse.meanGrowthRate"/>
            </column>
        </log>

        <!-- write log to file                                                       -->
        <log id="fileLog" logEvery="5000" fileName="g11params.txt">
            <posterior idref="posterior"/>
            <prior idref="prior"/>
            <likelihood idref="likelihood"/>
            <speciesCoalescent idref="species.coalescent"/>
            <mixedDistributionLikelihood idref="species.popSize"/>
            <speciationLikelihood idref="speciation.likelihood"/>
            <parameter idref="species.popMean"/>
            <parameter idref="speciesTree.splitPopSize"/>

            <!-- DISSECT parameters and statistics -->
            <parameter idref="species.birthDeathCollapse.meanGrowthRate"/>
            <parameter idref="species.birthDeathCollapse.relativeDeathRate"/>
            <parameter idref="species.birthDeathCollapse.originHeight"/>

            <bdcNClustersStatistic idref="nClusters"/>

            <parameter idref="species.birthDeathCollapse.collapseWeight"/>

            <tmrcaStatistic idref="speciesTree.rootHeight"/>
            <tmrcaStatistic idref="speciesTree.bottaeHeight"/>
            <tmrcaStatistic idref="speciesTree.talpoidesHeight"/>
            <tmrcaStatistic idref="speciesTree.idahoensisHeight"/>
            <tmrcaStatistic idref="speciesTree.mazamaHeight"/>
            <tmrcaStatistic idref="speciesTree.monticolaHeight"/>
            <tmrcaStatistic idref="speciesTree.townsendiiHeight"/>
            <tmrcaStatistic idref="speciesTree.umbrinusHeight"/>

            <parameter idref="26.treeModel.rootHeight"/>
            <parameter idref="29.treeModel.rootHeight"/>
            <parameter idref="47.treeModel.rootHeight"/>
            <parameter idref="53.treeModel.rootHeight"/>
            <parameter idref="59.treeModel.rootHeight"/>
            <parameter idref="64.treeModel.rootHeight"/>
            <parameter idref="72.treeModel.rootHeight"/>

            <parameter idref="26.kappa"/>
            <parameter idref="26.frequencies"/>
            <parameter idref="29.kappa"/>
            <parameter idref="29.frequencies"/>
            <parameter idref="47.kappa"/>
            <parameter idref="47.frequencies"/>
            <parameter idref="53.kappa"/>
            <parameter idref="53.frequencies"/>
            <parameter idref="59.kappa"/>
            <parameter idref="59.frequencies"/>
            <parameter idref="64.kappa"/>
            <parameter idref="64.frequencies"/>
            <parameter idref="72.kappa"/>
            <parameter idref="72.frequencies"/>

            <parameter idref="26.clock.rate"/>
            <parameter idref="29.clock.rate"/>
            <parameter idref="47.clock.rate"/>
            <parameter idref="53.clock.rate"/>
            <parameter idref="59.clock.rate"/>
            <parameter idref="64.clock.rate"/>
            <parameter idref="72.clock.rate"/>

            <treeLikelihood idref="26.26.treeLikelihood"/>
            <treeLikelihood idref="29.29.treeLikelihood"/>
            <treeLikelihood idref="47.47.treeLikelihood"/>
            <treeLikelihood idref="53.53.treeLikelihood"/>
            <treeLikelihood idref="59.59.treeLikelihood"/>
            <treeLikelihood idref="64.64.treeLikelihood"/>
            <treeLikelihood idref="72.72.treeLikelihood"/>
        </log>
        <!-- write tree log to file                                                  -->
        <logTree id="species.treeFileLog" logEvery="5000" nexusFormat="true" fileName="g11speciestreesamples.txt"
                 sortTranslationTable="true">
            <speciesTree idref="sptree"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="26.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene26trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="26.treeModel"/>
            <strictClockBranchRates idref="26.26.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="29.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene29trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="29.treeModel"/>
            <strictClockBranchRates idref="29.29.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="47.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene47trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="47.treeModel"/>
            <strictClockBranchRates idref="47.47.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="53.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene53trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="53.treeModel"/>
            <strictClockBranchRates idref="53.53.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="59.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene59trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="59.treeModel"/>
            <strictClockBranchRates idref="59.59.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="64.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene64trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="64.treeModel"/>
            <strictClockBranchRates idref="64.64.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
        <logTree id="72.treeFileLog" logEvery="10000" nexusFormat="true" fileName="g11gene72trees.txt"
                 sortTranslationTable="true">
            <treeModel idref="72.treeModel"/>
            <strictClockBranchRates idref="72.72.branchRates"/>
            <posterior idref="posterior"/>
        </logTree>
    </mcmc>

    <report>
        <property name="timer">
            <mcmc idref="mcmc"/>
        </property>
    </report>

</beast>
