<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast namespace="beast.evolution.speciation:beast.evolution.alignment:beast.core:beast.math:beast.evolution:beast.evolution.tree:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" version="2.0">




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

    <data dataType="nucleotide" id="29" name="taxa">

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

	<taxonset spec='TaxonSet' id='lineagetaxa'>
		<taxon idref='Orthogeomys_heterodus'/>
		<taxon idref='Thomomys_bottae_albatus'/>
		<taxon idref='Thomomys_bottae_alpinus'/>
		<taxon idref='Thomomys_bottae_awahnee_a'/>
		<taxon idref='Thomomys_bottae_awahnee_b'/>
		<taxon idref='Thomomys_bottae_bottae'/>
		<taxon idref='Thomomys_bottae_cactophilus'/>
		<taxon idref='Thomomys_bottae_laticeps'/>
		<taxon idref='Thomomys_bottae_mewa'/>
		<taxon idref='Thomomys_bottae_riparius'/>
		<taxon idref='Thomomys_bottae_ruidosae'/>
		<taxon idref='Thomomys_bottae_saxatilis'/>
		<taxon idref='Thomomys_bottae_xerophilus'/>
		<taxon idref='Thomomys_idahoensis_pygmaeus_a'/>
		<taxon idref='Thomomys_idahoensis_pygmaeus_b'/>
		<taxon idref='Thomomys_mazama_mazama'/>
		<taxon idref='Thomomys_mazama_nasicus'/>
		<taxon idref='Thomomys_monticola_a'/>
		<taxon idref='Thomomys_monticola_b'/>
		<taxon idref='Thomomys_talpoides_bridgeri'/>
		<taxon idref='Thomomys_talpoides_ocius'/>
		<taxon idref='Thomomys_talpoides_yakimensis'/>
		<taxon idref='Thomomys_townsendii_relictus'/>
		<taxon idref='Thomomys_townsendii_townsendii'/>
		<taxon idref='Thomomys_umbrinus_atroavarius'/>
		<taxon idref='Thomomys_umbrinus_chihuahuae'/>        
    </taxonset>   
    
	<taxonset spec='TaxonSet' id='taxonsuperset'>
                <taxon spec='TaxonSet' id='Orthogeomys_heterodus_species'>
                    <taxon spec='Taxon' id='Orthogeomys_heterodus'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_bottae'>
                    <taxon spec='Taxon' id='Thomomys_bottae_awahnee_a'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_awahnee_b'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_xerophilus'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_cactophilus'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_albatus'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_ruidosae'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_bottae'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_alpinus'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_riparius'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_mewa'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_saxatilis'/>
                    <taxon spec='Taxon' id='Thomomys_bottae_laticeps'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_idahoensis'>
                    <taxon spec='Taxon' id='Thomomys_idahoensis_pygmaeus_a'/>
                    <taxon spec='Taxon' id='Thomomys_idahoensis_pygmaeus_b'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_mazama'>
                    <taxon spec='Taxon' id='Thomomys_mazama_mazama'/>
                    <taxon spec='Taxon' id='Thomomys_mazama_nasicus'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_monticola'>
                    <taxon spec='Taxon' id='Thomomys_monticola_a'/>
                    <taxon spec='Taxon' id='Thomomys_monticola_b'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_talpoides'>
                    <taxon spec='Taxon' id='Thomomys_talpoides_yakimensis'/>
                    <taxon spec='Taxon' id='Thomomys_talpoides_bridgeri'/>
                    <taxon spec='Taxon' id='Thomomys_talpoides_ocius'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_townsendii'>
                    <taxon spec='Taxon' id='Thomomys_townsendii_townsendii'/>
                    <taxon spec='Taxon' id='Thomomys_townsendii_relictus'/>
                </taxon>
                <taxon spec='TaxonSet' id='Thomomys_umbrinus'>
                    <taxon spec='Taxon' id='Thomomys_umbrinus_chihuahuae'/>
                    <taxon spec='Taxon' id='Thomomys_umbrinus_atroavarius'/>
                </taxon>
	</taxonset>

    <distribution id="posterior" spec="util.CompoundDistribution">
        <distribution id="prior" spec="util.CompoundDistribution">

		    <distribution id="speciesCoalescent" spec="util.CompoundDistribution">
		        <!-- gene tree priors -->
		        <distribution id='tree.prior.29' spec='GeneTreeForSpeciesTreeDistribution' tree='@tree29' speciesTree='@speciesTree' speciesTreePrior='@SpeciesTreePopSizePrior'/>
		        <distribution id='tree.prior.26' spec='GeneTreeForSpeciesTreeDistribution' tree='@tree26' speciesTree='@speciesTree' speciesTreePrior='@SpeciesTreePopSizePrior'/>

		        <!-- species tree priors -->
		        <distribution id='SpeciesTreePopSizePrior' spec='SpeciesTreePrior' tree='@speciesTree' 
		        		popFunction='constant' taxonset='@taxonsuperset'>
		            <bottomPopSize spec='parameter.RealParameter' id='popSize' value='1'/> 
		            <parameter name='gammaParameter' id='popMean' value='0.004'/>
		        </distribution>
		    </distribution>

            <distribution id="SpeciesTreeDivergenceTimesPrior" spec="speciation.YuleModel" tree='@speciesTree'>
                <birthDiffRate spec='parameter.RealParameter' id="birthRate" value='213.2021' lower='0' upper='10000' />
            </distribution>

            <!-- hyper priors for assorted parameters -->
            <distribution id='birthRatePrior' spec='distributions.Prior' x='@birthRate'>
                <distr id='OneOnX' spec='distributions.OneOnX'/>
            </distribution>

            <distribution id="popMean.prior26" spec="beast.math.distributions.Prior" x="@popMean" distr='@OneOnX'/>

            <distribution id="kappa.prior26" spec="beast.math.distributions.Prior" x="@hky.kappa26">
                <distr id='logNormal' spec='beast.math.distributions.LogNormalDistributionModel' M="1.0" S="1.25" offset="0.0" meanInRealSpace="false"/>
            </distribution>

            <distribution id="kappa.prior29" spec="beast.math.distributions.Prior" x="@hky.kappa29"  distr='@logNormal'/>

        </distribution>
        <distribution id="likelihood" spec="util.CompoundDistribution">
            <distribution data="@26" id="treelikelihood.26" spec="TreeLikelihood" tree="@tree26" useAmbiguities="false">
                <siteModel gammaCategoryCount="1" id="siteModel26" mutationRate="@mutationRate" proportionInvariant="@proportionInvariant" shape="@gammaShape" spec="SiteModel">
                    <substModel id="hky26" kappa="@hky.kappa26" spec="HKY">
                        <frequencies id="freqs26" spec="Frequencies" estimate='true' data='@26'/>
                    </substModel>
                </siteModel>
                <branchRateModel clock.rate="@clockRate" id="StrictClockModel26" spec="beast.evolution.branchratemodel.StrictClockModel"/>
            </distribution>
            <distribution data="@29" id="treelikelihood.29" spec="TreeLikelihood" tree="@tree29" useAmbiguities="false">
                <siteModel gammaCategoryCount="1" id="siteModel29" mutationRate="@mutationRate" proportionInvariant="@proportionInvariant" shape="@gammaShape" spec="SiteModel">
                    <substModel id="hky29" kappa="@hky.kappa29" spec="HKY">
                        <frequencies id="freqs29" spec="Frequencies" estimate='true' data='@29'/>
                    </substModel>
                </siteModel>
                <branchRateModel clock.rate="@clockRate" id="StrictClockModel29" spec="beast.evolution.branchratemodel.StrictClockModel"/>
            </distribution>
        </distribution>
    </distribution>

    <tree spec='RandomTree' id='randomSpeciesTree' initial='@speciesTree'
        taxonset='@taxonsuperset'>
        <populationModel spec='ConstantPopulation'>
		<popSize spec='parameter.RealParameter' value='1'/>
	</populationModel>
    </tree>


<tree spec='beast.util.TreeParser' id='newickSpeciesTree' IsLabelledNewick='true' newick='(Orthogeomys_heterodus_species:0.02065265792151943,(((Thomomys_talpoides:0.0013609706233106656,Thomomys_mazama:0.0013609706233106656):6.032405317365711E-4,(Thomomys_idahoensis:0.0019116640088644983,Thomomys_monticola:0.0019116640088644983):5.254714618273845E-5):0.01135560317788915,(Thomomys_umbrinus:0.001060205025110908,(Thomomys_townsendii:2.1835631905959876E-4,Thomomys_bottae:2.1835631905959876E-4):8.418487060513092E-4):0.01225960930782548):0.007332843588583044);'
initial='@speciesTree' threshold='1e-12' taxonset='@taxonsuperset'/>


<tree spec='beast.util.TreeParser' id='newickGeneTree1' IsLabelledNewick='true' newick='((((Thomomys_idahoensis_pygmaeus_a:4.790629004925939E-4,Thomomys_idahoensis_pygmaeus_b:4.790629004925939E-4):0.002807766516703272,(Thomomys_monticola_a:3.1053813362974055E-5,Thomomys_monticola_b:3.1053813362974055E-5):0.0032557756038328915):1.3936218139959985E-4,((Thomomys_talpoides_yakimensis:0.001392151582227928,(Thomomys_talpoides_bridgeri:4.271344427331326E-4,Thomomys_talpoides_ocius:4.271344427331326E-4):9.650171394947955E-4):2.3416363608392133E-4,(Thomomys_mazama_nasicus:5.938379928988402E-6,Thomomys_mazama_mazama:5.938379928988402E-6):0.001620376838382861):0.0017998763802836162):0.01709773249173348,(Orthogeomys_heterodus:0.009652282924590812,(((Thomomys_townsendii_townsendii:0.0026355773641040447,(Thomomys_townsendii_relictus:0.001886298607022084,(Thomomys_bottae_laticeps:0.0011492988922358863,Thomomys_umbrinus_atroavarius:0.0011492988922358863):7.369997147861978E-4):7.492787570819606E-4):0.002003647116192913,((Thomomys_bottae_awahnee_a:7.080639947397304E-4,((Thomomys_bottae_saxatilis:4.7332771620207383E-4,Thomomys_bottae_xerophilus:4.7332771620207383E-4):2.7590796315257195E-5,(Thomomys_bottae_riparius:2.2956067039993388E-4,Thomomys_bottae_awahnee_b:2.2956067039993388E-4):2.7135784211739715E-4):2.0714548222239932E-4):7.737704382886797E-4,(Thomomys_bottae_cactophilus:0.0014394832564564783,(Thomomys_bottae_alpinus:0.0013868072888249166,(Thomomys_umbrinus_chihuahuae:9.025787629100629E-4,(Thomomys_bottae_bottae:7.08841912043247E-4,Thomomys_bottae_ruidosae:7.08841912043247E-4):1.9373685086681593E-4):4.842285259148536E-4):5.267596763156176E-5):4.2351176571931706E-5):0.0031573900472685475):0.0015015284932928617,(Thomomys_bottae_mewa:8.285742263631879E-4,Thomomys_bottae_albatus:8.285742263631879E-4):0.005312178747226631):0.0035115299510009926):0.010871641165738136)' initial='@tree26' taxonset='@lineagetaxa' threshold='1e-12' />

<tree spec='beast.util.TreeParser' id='newickGeneTree2' IsLabelledNewick='true' newick='(Orthogeomys_heterodus:0.02555754747205849,((Thomomys_mazama_nasicus:0.001146519512253189,Thomomys_mazama_mazama:0.001146519512253189):0.01169723135080885,((Thomomys_talpoides_ocius:0.00703974619989265,(((Thomomys_talpoides_yakimensis:0.0014682135377831343,(Thomomys_monticola_a:3.1427207759506006E-5,Thomomys_monticola_b:3.1427207759506006E-5):0.0014367863300236282):3.5111237723683074E-4,(Thomomys_idahoensis_pygmaeus_a:2.52563963076903E-4,Thomomys_idahoensis_pygmaeus_b:2.52563963076903E-4):0.001566761951943062):0.0033770883069903614,Thomomys_talpoides_bridgeri:0.005196414222010327):0.001843331977882323):0.002676969649368072,((((Thomomys_umbrinus_chihuahuae:0.0017048445360954947,Thomomys_umbrinus_atroavarius:0.0017048445360954947):0.00109910693708295,(Thomomys_bottae_awahnee_a:0.0017104792362342403,Thomomys_bottae_awahnee_b:0.0017104792362342403):0.0010934722369442043):2.397726403374303E-4,(Thomomys_bottae_xerophilus:0.0028568232959683758,Thomomys_bottae_cactophilus:0.0028568232959683758):1.8690081754749914E-4):3.8269468803520503E-4,(Thomomys_bottae_mewa:0.0023122370757911325,((Thomomys_bottae_ruidosae:6.038316687617217E-4,Thomomys_bottae_bottae:6.038316687617217E-4):0.001291158181918091,(((Thomomys_bottae_albatus:0.0010882593426384808,Thomomys_bottae_saxatilis:0.0010882593426384808):7.144016389479342E-4,(Thomomys_bottae_riparius:0.0016565761010643102,Thomomys_bottae_laticeps:0.0016565761010643102):1.4608488052210477E-4):1.0681582125047617E-5,((Thomomys_townsendii_relictus:2.4739716804096176E-5,Thomomys_townsendii_townsendii:2.4739716804096176E-5):0.0017656857791623062,Thomomys_bottae_alpinus:0.0017904254959664023):2.2917067745060332E-5):8.164728696835014E-5):4.172472251113197E-4):0.0011141817257599475):0.006290297047709642):0.0031270350138013162):0.012713796608996452)'
initial='@tree29' taxonset='@lineagetaxa' threshold='1e-12' />

    <tree spec='RandomGeneTree' id='randomGeneTree1' 
	initial='@tree26' speciesTree='@speciesTree' taxa='@26'>
        <populationModel spec='ConstantPopulation'>
		<popSize spec='parameter.RealParameter' value='1'/>
	</populationModel>
    </tree>
    
    <tree spec='RandomGeneTree' id='randomGeneTree2' 
	initial='@tree29' speciesTree='@speciesTree' taxa='@29'>
        <populationModel spec='ConstantPopulation'>
		<popSize spec='parameter.RealParameter' value='1'/>
	</populationModel>
    </tree>

<run chainLength="10000000" id="mcmc" preBurnin="0" spec="MCMC">
    <!--init idref='randomSpeciesTree'/-->
    <init idref='newickSpeciesTree'/>
    <!--init idref='newickGeneTree1'/>
    <init idref='newickGeneTree2'/-->

    <init idref='randomGeneTree1'/>
    <init idref='randomGeneTree2'/>


    <distribution idref="posterior"/>

    <state id="State0" storeEvery="100000">
        <!--parameter dimension="1" estimate="false" id="popSize" name="stateNode" value="1.0"/-->
        <parameter dimension="1" estimate="false" id="mutationRate" name="stateNode" value="1.0"/>
        <parameter dimension="1" estimate="false" id="clockRate" name="stateNode" value="1.0"/>
        <parameter dimension="1" estimate="true" id="hky.kappa26" lower="0.0" name="stateNode" value="1.0"/>
        <parameter dimension="1" estimate="true" id="hky.kappa29" lower="0.0" name="stateNode" value="1.0"/>

        <stateNode idref='popSize'/> 
        <stateNode idref='popMean'/>

        <tree estimate="true" id="tree26" name="stateNode"/>
        <tree estimate="true" id="tree29" name="stateNode"/>
        <tree estimate="true" id="speciesTree" name="stateNode"/>

        <stateNode idref="birthRate"/>
       	<!--stateNode idref="relativeDeathRate"/-->
        <parameter dimension="1" estimate="false" id="gammaShape" name="stateNode" value="1.0"/>
        <parameter dimension="1" estimate="false" id="proportionInvariant" lower="0.0" name="stateNode" upper="1.0" value="0.0"/>
    </state>

    <operator degreesOfFreedom="1" id="popSizeScaler" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" parameter="@popSize" weight="5.0"/>
    <operator degreesOfFreedom="1" id="birthRateScaler" scaleFactor="0.5" spec="ScaleOperator" parameter="@birthRate" weight="3"/>
    <!--operator degreesOfFreedom="1" id="relDeathRateScaler" scaleFactor="0.5" spec="ScaleOperator" parameter="@relativeDeathRate" weight="1.0"/-->
    <operator degreesOfFreedom="1" id="psiScaler" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" parameter="@popMean" weight="94"/>
    <operator degreesOfFreedom="1" id="kappa26Scaler" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.35" spec="ScaleOperator" parameter="@hky.kappa26" weight="0.1"/>
    <operator degreesOfFreedom="1" id="kappa29Scaler" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.35" spec="ScaleOperator" parameter="@hky.kappa29" weight="0.1"/>

    <operator gaussian="true" id="SubtreeSlide26" size="0.003" spec="SubtreeSlide" tree="@tree26" weight="15.0"/>
    <operator degreesOfFreedom="1" id="treeScaler26" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.85" spec="ScaleOperator" tree="@tree26" weight="6.0"/>
    <operator id="wide26" isNarrow="false" spec="Exchange" tree="@tree26" weight="1.0"/>
    <operator id="narrow26" isNarrow="true" spec="Exchange" tree="@tree26" weight="15"/>
    <operator id="WilsonBalding26" spec="WilsonBalding" tree="@tree26" weight="3"/>
<!--
-->
    <operator id="Uniform26" spec="Uniform" tree="@tree26" weight="30.0"/>

    <operator gaussian="true" id="SubtreeSlide29" size="0.002" spec="SubtreeSlide" tree="@tree29" weight="15.0"/>
    <operator degreesOfFreedom="1" id="treeScaler29" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.85" spec="ScaleOperator" tree="@tree29" weight="6.0"/>
    <operator id="wide29" isNarrow="false" spec="Exchange" tree="@tree29" weight="1.0"/>
    <operator id="narrow29" isNarrow="true" spec="Exchange" tree="@tree29" weight="15"/>
    <operator id="WilsonBalding29" spec="WilsonBalding" tree="@tree29" weight="3"/>
<!--
-->
    <operator id="Uniform29" spec="Uniform" tree="@tree29" weight="30.0"/>

	<operator spec='UpDownOperator' scaleFactor="0.75" weight="30">
			<up idref="birthRate"/>
			<down idref="popSize"/>
			<down idref="popMean"/>
			<down idref="speciesTree"/>
			<down idref="tree26"/>
			<down idref="tree29"/>
	</operator>

<!--
    <operator id="wideSP" isNarrow="false" spec="Exchange" tree="@speciesTree" weight="1.0"/>
    <operator gaussian="true" id="SubtreeSlideSP" size="0.003" spec="SubtreeSlide" tree="@speciesTree" weight="15.0"/>
    <operator degreesOfFreedom="1" id="treeScalerSP" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.85" spec="ScaleOperator" tree="@speciesTree" weight="6.0"/>
    <operator id="UniformSP" spec="Uniform" tree="@speciesTree" weight="30.0"/>
-->

    <operator id="Reheight" spec="NodeReheight" tree="@speciesTree" weight="94" taxonset='@taxonsuperset'>
        <genetree idref='tree26'/>
        <genetree idref='tree29'/>
    </operator>

    <logger fileName="z$(seed).log" id="Logger0" logEvery="1000" mode="autodetect" model="@posterior">
        <log idref="posterior"/>
        <log idref="prior"/>
        <log idref="speciesCoalescent"/>
        <log idref="SpeciesTreePopSizePrior"/>
        <log idref="tree.prior.26"/>
        <log idref="tree.prior.29"/>
        <log idref="SpeciesTreeDivergenceTimesPrior"/>
        <log idref="likelihood"/>
        <log idref="popMean"/>
        <log idref="birthRate"/>
        <!--log idref="relativeDeathRate"/-->
        <log idref="hky.kappa26"/>
        <log idref="hky.kappa29"/>
        <log idref="popSize"/>
        <log id="TreeHeightSP" spec="beast.evolution.tree.TreeHeightLogger" tree="@speciesTree"/>
        <log id="TreeHeight26" spec="beast.evolution.tree.TreeHeightLogger" tree="@tree26"/>
        <log id="TreeHeight29" spec="beast.evolution.tree.TreeHeightLogger" tree="@tree29"/>
    </logger>

    <logger fileName="z$(seed).sp.trees" id="Logger4" logEvery="1000" mode="tree">
        <log spec='SpeciesTreeLogger' popSize='@popSize' tree="@speciesTree">
			<treetop spec='TreeTopFinder' id='treeTopFinder'>
				<tree idref='tree26'/>
				<tree idref='tree29'/>
			</treetop>
		</log>
    </logger>

    <logger fileName="z$(seed).26.trees" id="Logger2" logEvery="1000" mode="autodetect">
        <log idref="tree26"/>
    </logger>

    <logger fileName="z$(seed).29.trees" id="Logger3" logEvery="1000" mode="autodetect">
        <log idref="tree29"/>
    </logger>

    <logger id="Logger1" logEvery="100000" mode="autodetect">
        <log idref="posterior"/>
        <log spec='ESS' arg='@posterior'/>
        <log idref="prior"/>
        <log spec='ESS' arg='@prior'/>
    </logger>

</run>


</beast>
