<?xml version="1.0" standalone="yes"?>
<!-- Generated by BEAUTi v1.5.0                                              -->
<!--       by Alexei J. Drummond and Andrew Rambaut                          -->
<!--       Department of Computer Science, University of Auckland and        -->
<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
<!--       http://beast.bio.ed.ac.uk/                                        -->
<beast>
	
	<!-- The list of taxa analyse (can also include dates/ages).                 -->
	<!-- ntax=26                                                                 -->
	<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>
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=614                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=601                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=819                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=621                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=553                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=471                                                       -->
	<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>
	
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=26 nchar=706                                                       -->
	<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 prior assumption that the population size has remained constant       -->
	<!-- throughout the time spanned by the genealogy.                           -->
	<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                  -->
	<!-- trait = species trait_type = DISCRETE                                   -->
	<species id="species">
		<sp id="Orthogeomys_heterodus_species">
			<taxon idref="Orthogeomys_heterodus"/>
		</sp>
		<sp id="Thomomys_bottae">
			<taxon idref="Thomomys_bottae_awahnee_a"/>
			<taxon idref="Thomomys_bottae_awahnee_b"/>
			<taxon idref="Thomomys_bottae_xerophilus"/>
			<taxon idref="Thomomys_bottae_cactophilus"/>
			<taxon idref="Thomomys_bottae_albatus"/>
			<taxon idref="Thomomys_bottae_ruidosae"/>
			<taxon idref="Thomomys_bottae_bottae"/>
			<taxon idref="Thomomys_bottae_alpinus"/>
			<taxon idref="Thomomys_bottae_riparius"/>
			<taxon idref="Thomomys_bottae_mewa"/>
			<taxon idref="Thomomys_bottae_saxatilis"/>
			<taxon idref="Thomomys_bottae_laticeps"/>
		</sp>
		<sp id="Thomomys_talpoides">
			<taxon idref="Thomomys_talpoides_ocius"/>
			<taxon idref="Thomomys_talpoides_yakimensis"/>
			<taxon idref="Thomomys_talpoides_bridgeri"/>
		</sp>
		<sp id="Thomomys_idahoensis">
			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
		</sp>
		<sp id="Thomomys_mazama">
			<taxon idref="Thomomys_mazama_mazama"/>
			<taxon idref="Thomomys_mazama_nasicus"/>
		</sp>
		<sp id="Thomomys_monticola">
			<taxon idref="Thomomys_monticola_a"/>
			<taxon idref="Thomomys_monticola_b"/>
		</sp>
		<sp id="Thomomys_townsendii">
			<taxon idref="Thomomys_townsendii_townsendii"/>
			<taxon idref="Thomomys_townsendii_relictus"/>
		</sp>
		<sp id="Thomomys_umbrinus">
			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
			<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: tree prior                                                -->
	<!-- Species Tree: Birth Death Model                                         -->
	<birthDeathModel id="birthDeath" units="substitutions">
		<birthMinusDeathRate>
			<parameter id="species.birthDeath.meanGrowthRate" value="1.0" lower="0.0" upper="Infinity"/>
		</birthMinusDeathRate>
		<relativeDeathRate>
			<parameter id="species.birthDeath.relativeDeathRate" value="0.5" lower="0.0" upper="1.0"/>
		</relativeDeathRate>
	</birthDeathModel>
	<!-- Species Tree: Likelihood of species tree                                -->
	<!-- Species Tree: Birth Death Model                                         -->
	<speciationLikelihood id="speciation.likelihood">
		<model>
			<birthDeathModel idref="birthDeath"/>
		</model>
		<speciesTree>
			<speciesTree idref="sptree"/>
		</speciesTree>
	</speciationLikelihood>
	<!-- Species Tree: tmrcaStatistic                                            -->
	<tmrcaStatistic id="speciesTree.rootHeight" name="speciesTree.rootHeight">
		<speciesTree idref="sptree"/>
		<mrca>
			<taxa>
				<sp idref="Orthogeomys_heterodus_species"/>
				<sp idref="Thomomys_bottae"/>
				<sp idref="Thomomys_talpoides"/>
				<sp idref="Thomomys_idahoensis"/>
				<sp idref="Thomomys_mazama"/>
				<sp idref="Thomomys_monticola"/>
				<sp idref="Thomomys_townsendii"/>
				<sp idref="Thomomys_umbrinus"/>
			</taxa>
		</mrca>
	</tmrcaStatistic>
	<!-- Species Tree: Coalescent likelihood for gene trees under species tree   -->
	<speciesCoalescent id="species.coalescent">
		<species idref="species"/>
		<speciesTree idref="sptree"/>
	</speciesCoalescent>
	<!-- Species tree prior: gama2 + 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/>
		</indicators>
	</mixedDistributionLikelihood>
	<!-- 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.birthDeath.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>
		<scaleOperator scaleFactor="0.9" weight="5">
			<parameter idref="species.popMean"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="species.birthDeath.meanGrowthRate"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="species.birthDeath.relativeDeathRate"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.5" weight="94">
			<parameter idref="speciesTree.splitPopSize"/>
		</scaleOperator>
		<nodeReHeight weight="94">
			<species idref="species"/>
			<speciesTree idref="sptree"/>
		</nodeReHeight>
	</operators>
	
	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="10000000" autoOptimize="true">
		<posterior id="posterior">
			<prior id="prior">
				<speciesCoalescent idref="species.coalescent"/>
				<mixedDistributionLikelihood idref="species.popSize"/>
				<speciationLikelihood idref="speciation.likelihood"/>
				<oneOnXPrior>
					<parameter idref="26.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="29.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="47.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="53.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="59.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="64.kappa"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="72.kappa"/>
				</oneOnXPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="29.clock.rate"/>
				</gammaPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="47.clock.rate"/>
				</gammaPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="53.clock.rate"/>
				</gammaPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="59.clock.rate"/>
				</gammaPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="64.clock.rate"/>
				</gammaPrior>
				<gammaPrior shape="0.1" scale="10.0" offset="0.0">
					<parameter idref="72.clock.rate"/>
				</gammaPrior>
				<oneOnXPrior>
					<parameter idref="species.popMean"/>
				</oneOnXPrior>
				<oneOnXPrior>
					<parameter idref="species.birthDeath.meanGrowthRate"/>
				</oneOnXPrior>
				
				
				
				
				
				
				
			</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="1000000">
			<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>
			<column label="PopMean" dp="4" width="12">
				<parameter idref="species.popMean"/>
			</column>
			<column label="Root Height" sf="6" width="12">
				<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"/>
			</column>
			<column label="Rate" sf="6" width="12">
				<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"/>
			</column>
		</log>
		<!-- write log to file                                                       -->
		<log id="fileLog" logEvery="1000" fileName="g11.log">
			<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"/>
			<parameter idref="species.birthDeath.meanGrowthRate"/>
			<parameter idref="species.birthDeath.relativeDeathRate"/>
			<tmrcaStatistic idref="speciesTree.rootHeight"/>
			<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="1000" nexusFormat="true" fileName="g11.species.trees" sortTranslationTable="true">
			<speciesTree idref="sptree"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="26.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.26.trees" sortTranslationTable="true">
			<treeModel idref="26.treeModel"/>
			<strictClockBranchRates idref="26.26.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="29.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.29.trees" sortTranslationTable="true">
			<treeModel idref="29.treeModel"/>
			<strictClockBranchRates idref="29.29.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="47.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.47.trees" sortTranslationTable="true">
			<treeModel idref="47.treeModel"/>
			<strictClockBranchRates idref="47.47.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="53.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.53.trees" sortTranslationTable="true">
			<treeModel idref="53.treeModel"/>
			<strictClockBranchRates idref="53.53.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="59.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.59.trees" sortTranslationTable="true">
			<treeModel idref="59.treeModel"/>
			<strictClockBranchRates idref="59.59.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="64.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.64.trees" sortTranslationTable="true">
			<treeModel idref="64.treeModel"/>
			<strictClockBranchRates idref="64.64.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="72.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g11.72.trees" 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>
