<?xml version="1.0" standalone="yes"?>
<!-- Generated by BEAUTi v1.5.3                                              -->
<!--       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 unique patterns for codon positions 1                               -->
	<mergePatterns id="26.CP1.26.patterns">
		<!-- The unique patterns from 1 to end every 3                               -->
		<!-- npatterns=78                                                            -->
		<patterns from="1" every="3">
			<alignment idref="alignment1"/>
		</patterns>
	</mergePatterns>
	<!-- The unique patterns for codon positions 2                               -->
	<mergePatterns id="26.CP2.26.patterns">
		<!-- The unique patterns from 2 to end every 3                               -->
		<!-- npatterns=67                                                            -->
		<patterns from="2" every="3">
			<alignment idref="alignment1"/>
		</patterns>
	</mergePatterns>
	<!-- The unique patterns for codon positions 3                               -->
	<mergePatterns id="26.CP3.26.patterns">
		<!-- The unique patterns from 3 to end every 3                               -->
		<!-- npatterns=69                                                            -->
		<patterns from="3" every="3">
			<alignment idref="alignment1"/>
		</patterns>
	</mergePatterns>
	
	
	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=71                                                            -->
	<patterns id="29.patterns" from="1">
		<alignment idref="alignment2"/>
	</patterns>
	
	
	<!-- The unique patterns for codon positions 1 & 2                           -->
	<mergePatterns id="47.CP1+2.47.patterns">
		<!-- The unique patterns from 1 to end every 3                               -->
		<!-- npatterns=64                                                            -->
		<patterns from="1" every="3">
			<alignment idref="alignment3"/>
		</patterns>
		<!-- The unique patterns from 2 to end every 3                               -->
		<!-- npatterns=77                                                            -->
		<patterns from="2" every="3">
			<alignment idref="alignment3"/>
		</patterns>
	</mergePatterns>
	<!-- The unique patterns for codon positions 3                               -->
	<mergePatterns id="47.CP3.47.patterns">
		<!-- The unique patterns from 3 to end every 3                               -->
		<!-- npatterns=80                                                            -->
		<patterns from="3" every="3">
			<alignment idref="alignment3"/>
		</patterns>
	</mergePatterns>
	
	
	<!-- The unique patterns for codon positions 1 & 2                           -->
	<mergePatterns id="53.CP1+2.53.patterns">
		<!-- The unique patterns from 1 to end every 3                               -->
		<!-- npatterns=71                                                            -->
		<patterns from="1" every="3">
			<alignment idref="alignment4"/>
		</patterns>
		<!-- The unique patterns from 2 to end every 3                               -->
		<!-- npatterns=70                                                            -->
		<patterns from="2" every="3">
			<alignment idref="alignment4"/>
		</patterns>
	</mergePatterns>
	<!-- The unique patterns for codon positions 3                               -->
	<mergePatterns id="53.CP3.53.patterns">
		<!-- The unique patterns from 3 to end every 3                               -->
		<!-- npatterns=59                                                            -->
		<patterns from="3" every="3">
			<alignment idref="alignment4"/>
		</patterns>
	</mergePatterns>
	
	
	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=92                                                            -->
	<patterns id="59.patterns" from="1">
		<alignment idref="alignment5"/>
	</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="0.018" 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 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 coalescent likelihood                                        -->
	<coalescentLikelihood id="26.coalescent">
		<model>
			<constantSize idref="constant"/>
		</model>
		<populationTree>
			<treeModel idref="26.treeModel"/>
		</populationTree>
	</coalescentLikelihood>
	
	<!-- Generate a coalescent likelihood                                        -->
	<coalescentLikelihood id="29.coalescent">
		<model>
			<constantSize idref="constant"/>
		</model>
		<populationTree>
			<treeModel idref="29.treeModel"/>
		</populationTree>
	</coalescentLikelihood>
	
	<!-- Generate a coalescent likelihood                                        -->
	<coalescentLikelihood id="47.coalescent">
		<model>
			<constantSize idref="constant"/>
		</model>
		<populationTree>
			<treeModel idref="47.treeModel"/>
		</populationTree>
	</coalescentLikelihood>
	
	<!-- Generate a coalescent likelihood                                        -->
	<coalescentLikelihood id="53.coalescent">
		<model>
			<constantSize idref="constant"/>
		</model>
		<populationTree>
			<treeModel idref="53.treeModel"/>
		</populationTree>
	</coalescentLikelihood>
	
	<!-- Generate a coalescent likelihood                                        -->
	<coalescentLikelihood id="59.coalescent">
		<model>
			<constantSize idref="constant"/>
		</model>
		<populationTree>
			<treeModel idref="59.treeModel"/>
		</populationTree>
	</coalescentLikelihood>
	
	<!-- The strict clock (Uniform rates across branches)                        -->
	<strictClockBranchRates id="26.branchRates">
		<rate>
			<parameter id="26.clock.rate" value="1.0"/>
		</rate>
	</strictClockBranchRates>
	
	<!-- The strict clock (Uniform rates across branches)                        -->
	<strictClockBranchRates id="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.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.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.branchRates">
		<rate>
			<parameter id="59.clock.rate" value="1.0" lower="0.0" upper="Infinity"/>
		</rate>
	</strictClockBranchRates>
	
	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="26.CP1.hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="26.CP1.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="26.CP1.kappa" value="1.0" lower="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="26.CP2.hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="26.CP2.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="26.CP2.kappa" value="1.0" lower="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="26.CP3.hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="26.CP3.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="26.CP3.kappa" value="1.0" lower="0.0" 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="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	
	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="47.CP1+2.hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<mergePatterns idref="47.CP1+2.47.patterns"/>
				<frequencies>
					<parameter id="47.CP1+2.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="47.CP1+2.kappa" value="1.0" lower="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="47.CP3.hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<mergePatterns idref="47.CP3.47.patterns"/>
				<frequencies>
					<parameter id="47.CP3.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="47.CP3.kappa" value="1.0" lower="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	
	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="53.CP1+2.gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="53.CP1+2.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="53.CP1+2.ac" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="53.CP1+2.ag" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="53.CP1+2.at" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="53.CP1+2.cg" value="1.0" lower="0.0" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="53.CP1+2.gt" value="1.0" lower="0.0" upper="Infinity"/>
		</rateGT>
	</gtrModel>
	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="53.CP3.gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="53.CP3.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="53.CP3.ac" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="53.CP3.ag" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="53.CP3.at" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="53.CP3.cg" value="1.0" lower="0.0" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="53.CP3.gt" value="1.0" lower="0.0" upper="Infinity"/>
		</rateGT>
	</gtrModel>
	
	<!-- 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="0.0" upper="Infinity"/>
		</kappa>
	</HKYModel>
	
	<!-- site model                                                              -->
	<siteModel id="26.CP1.siteModel">
		<substitutionModel>
			<HKYModel idref="26.CP1.hky"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="26.CP1.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
	</siteModel>
	<!-- site model                                                              -->
	<siteModel id="26.CP2.siteModel">
		<substitutionModel>
			<HKYModel idref="26.CP2.hky"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="26.CP2.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
	</siteModel>
	<!-- site model                                                              -->
	<siteModel id="26.CP3.siteModel">
		<substitutionModel>
			<HKYModel idref="26.CP3.hky"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="26.CP3.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
	</siteModel>

	<compoundParameter id="26.allMus">
		<parameter idref="26.CP1.mu"/>
		<parameter idref="26.CP2.mu"/>
		<parameter idref="26.CP3.mu"/>
	</compoundParameter>
	
	<!-- site model                                                              -->
	<siteModel id="29.siteModel">
		<substitutionModel>
			<HKYModel idref="29.hky"/>
		</substitutionModel>
	</siteModel>
	
	<!-- site model                                                              -->
	<siteModel id="47.CP1+2.siteModel">
		<substitutionModel>
			<HKYModel idref="47.CP1+2.hky"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="47.CP1+2.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
		<gammaShape gammaCategories="4">
			<parameter id="47.CP1+2.alpha" value="0.5" lower="0.0" upper="1000.0"/>
		</gammaShape>
	</siteModel>
	<!-- site model                                                              -->
	<siteModel id="47.CP3.siteModel">
		<substitutionModel>
			<HKYModel idref="47.CP3.hky"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="47.CP3.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
		<gammaShape gammaCategories="4">
			<parameter id="47.CP3.alpha" value="0.5" lower="0.0" upper="1000.0"/>
		</gammaShape>
	</siteModel>

	<compoundParameter id="47.allMus">
		<parameter idref="47.CP1+2.mu"/>
		<parameter idref="47.CP3.mu"/>
	</compoundParameter>
	
	<!-- site model                                                              -->
	<siteModel id="53.CP1+2.siteModel">
		<substitutionModel>
			<gtrModel idref="53.CP1+2.gtr"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="53.CP1+2.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
	</siteModel>
	<!-- site model                                                              -->
	<siteModel id="53.CP3.siteModel">
		<substitutionModel>
			<gtrModel idref="53.CP3.gtr"/>
		</substitutionModel>
		<relativeRate>
			<parameter id="53.CP3.mu" value="1.0" lower="0.0" upper="Infinity"/>
		</relativeRate>
	</siteModel>

	<compoundParameter id="53.allMus">
		<parameter idref="53.CP1+2.mu"/>
		<parameter idref="53.CP3.mu"/>
	</compoundParameter>
	
	<!-- site model                                                              -->
	<siteModel id="59.siteModel">
		<substitutionModel>
			<HKYModel idref="59.hky"/>
		</substitutionModel>
	</siteModel>
	
	<treeLikelihood id="26.CP1.26.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="26.CP1.26.patterns"/>
		<treeModel idref="26.treeModel"/>
		<siteModel idref="26.CP1.siteModel"/>
		<strictClockBranchRates idref="26.branchRates"/>
	</treeLikelihood>
	<treeLikelihood id="26.CP2.26.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="26.CP2.26.patterns"/>
		<treeModel idref="26.treeModel"/>
		<siteModel idref="26.CP2.siteModel"/>
		<strictClockBranchRates idref="26.branchRates"/>
	</treeLikelihood>
	<treeLikelihood id="26.CP3.26.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="26.CP3.26.patterns"/>
		<treeModel idref="26.treeModel"/>
		<siteModel idref="26.CP3.siteModel"/>
		<strictClockBranchRates idref="26.branchRates"/>
	</treeLikelihood>
	
	<treeLikelihood id="29.treeLikelihood" useAmbiguities="false">
		<patterns idref="29.patterns"/>
		<treeModel idref="29.treeModel"/>
		<siteModel idref="29.siteModel"/>
		<strictClockBranchRates idref="29.branchRates"/>
	</treeLikelihood>
	
	<treeLikelihood id="47.CP1+2.47.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="47.CP1+2.47.patterns"/>
		<treeModel idref="47.treeModel"/>
		<siteModel idref="47.CP1+2.siteModel"/>
		<strictClockBranchRates idref="47.branchRates"/>
	</treeLikelihood>
	<treeLikelihood id="47.CP3.47.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="47.CP3.47.patterns"/>
		<treeModel idref="47.treeModel"/>
		<siteModel idref="47.CP3.siteModel"/>
		<strictClockBranchRates idref="47.branchRates"/>
	</treeLikelihood>
	
	<treeLikelihood id="53.CP1+2.53.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="53.CP1+2.53.patterns"/>
		<treeModel idref="53.treeModel"/>
		<siteModel idref="53.CP1+2.siteModel"/>
		<strictClockBranchRates idref="53.branchRates"/>
	</treeLikelihood>
	<treeLikelihood id="53.CP3.53.treeLikelihood" useAmbiguities="false">
		<mergePatterns idref="53.CP3.53.patterns"/>
		<treeModel idref="53.treeModel"/>
		<siteModel idref="53.CP3.siteModel"/>
		<strictClockBranchRates idref="53.branchRates"/>
	</treeLikelihood>
	
	<treeLikelihood id="59.treeLikelihood" useAmbiguities="false">
		<patterns idref="59.patterns"/>
		<treeModel idref="59.treeModel"/>
		<siteModel idref="59.siteModel"/>
		<strictClockBranchRates idref="59.branchRates"/>
	</treeLikelihood>
	
	<!-- Define operators                                                        -->
	<operators id="operators">
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="26.CP1.kappa"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="26.CP2.kappa"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="26.CP3.kappa"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="26.CP1.frequencies"/>
		</deltaExchange>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="26.CP2.frequencies"/>
		</deltaExchange>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="26.CP3.frequencies"/>
		</deltaExchange>
		<deltaExchange delta="0.75" parameterWeights="205 205 204" weight="9">
			<parameter idref="26.allMus"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="29.kappa"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="29.frequencies"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="47.CP1+2.kappa"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="47.CP3.kappa"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="47.CP1+2.alpha"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="47.CP3.alpha"/>
		</scaleOperator>
		<deltaExchange delta="0.75" parameterWeights="546 273" weight="9">
			<parameter idref="47.allMus"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP1+2.ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP1+2.ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP1+2.at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP1+2.cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP1+2.gt"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP3.ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP3.ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP3.at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP3.cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="53.CP3.gt"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="53.CP1+2.frequencies"/>
		</deltaExchange>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="53.CP3.frequencies"/>
		</deltaExchange>
		<deltaExchange delta="0.75" parameterWeights="414 207" weight="9">
			<parameter idref="53.allMus"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="59.kappa"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="59.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>
		<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>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="constant.popSize"/>
		</scaleOperator>
		<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>
	</operators>
	
	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="10000" autoOptimize="true">
		<posterior id="posterior">
			<prior id="prior">
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="26.CP1.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="26.CP2.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="26.CP3.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="29.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="47.CP1+2.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="47.CP3.kappa"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP1+2.ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="53.CP1+2.ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP1+2.at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP1+2.cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP1+2.gt"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP3.ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="53.CP3.ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP3.at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP3.cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="53.CP3.gt"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="40.0" offset="0.0">
					<parameter idref="59.kappa"/>
				</gammaPrior>
				<oneOnXPrior>
					<parameter idref="constant.popSize"/>
				</oneOnXPrior>
				<coalescentLikelihood idref="26.coalescent"/>
				
				<coalescentLikelihood idref="29.coalescent"/>
				
				<coalescentLikelihood idref="47.coalescent"/>
				
				<coalescentLikelihood idref="53.coalescent"/>
				
				<coalescentLikelihood idref="59.coalescent"/>
				
			</prior>
			<likelihood id="likelihood">
				<treeLikelihood idref="26.CP1.26.treeLikelihood"/>
				<treeLikelihood idref="26.CP2.26.treeLikelihood"/>
				<treeLikelihood idref="26.CP3.26.treeLikelihood"/>
				<treeLikelihood idref="29.treeLikelihood"/>
				<treeLikelihood idref="47.CP1+2.47.treeLikelihood"/>
				<treeLikelihood idref="47.CP3.47.treeLikelihood"/>
				<treeLikelihood idref="53.CP1+2.53.treeLikelihood"/>
				<treeLikelihood idref="53.CP3.53.treeLikelihood"/>
				<treeLikelihood idref="59.treeLikelihood"/>
			</likelihood>
		</posterior>
		<operators idref="operators"/>
		<!-- write log to screen                                                     -->
		<log id="screenLog" logEvery="1000">
			<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="26.rootHeight" sf="6" width="12">
				<parameter idref="26.treeModel.rootHeight"/>
			</column>
			<column label="29.rootHeight" sf="6" width="12">
				<parameter idref="29.treeModel.rootHeight"/>
			</column>
			<column label="47.rootHeight" sf="6" width="12">
				<parameter idref="47.treeModel.rootHeight"/>
			</column>
			<column label="53.rootHeight" sf="6" width="12">
				<parameter idref="53.treeModel.rootHeight"/>
			</column>
			<column label="59.rootHeight" sf="6" width="12">
				<parameter idref="59.treeModel.rootHeight"/>
			</column>
			<column label="26.clock.rate" sf="6" width="12">
				<parameter idref="26.clock.rate"/>
			</column>
			<column label="29.clock.rate" sf="6" width="12">
				<parameter idref="29.clock.rate"/>
			</column>
			<column label="47.clock.rate" sf="6" width="12">
				<parameter idref="47.clock.rate"/>
			</column>
			<column label="53.clock.rate" sf="6" width="12">
				<parameter idref="53.clock.rate"/>
			</column>
			<column label="59.clock.rate" sf="6" width="12">
				<parameter idref="59.clock.rate"/>
			</column>
		</log>
		<!-- write log to file                                                       -->
		<log id="fileLog" logEvery="1000" fileName="g10.log">
			<posterior idref="posterior"/>
			<prior idref="prior"/>
			<likelihood idref="likelihood"/>
			<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="constant.popSize"/>
			<parameter idref="26.CP1.kappa"/>
			<parameter idref="26.CP2.kappa"/>
			<parameter idref="26.CP3.kappa"/>
			<parameter idref="26.CP1.frequencies"/>
			<parameter idref="26.CP2.frequencies"/>
			<parameter idref="26.CP3.frequencies"/>
			<compoundParameter idref="26.allMus"/>
			<parameter idref="29.kappa"/>
			<parameter idref="29.frequencies"/>
			<parameter idref="47.CP1+2.kappa"/>
			<parameter idref="47.CP3.kappa"/>
			<parameter idref="47.CP1+2.alpha"/>
			<parameter idref="47.CP3.alpha"/>
			<compoundParameter idref="47.allMus"/>
			<parameter idref="53.CP1+2.ac"/>
			<parameter idref="53.CP1+2.ag"/>
			<parameter idref="53.CP1+2.at"/>
			<parameter idref="53.CP1+2.cg"/>
			<parameter idref="53.CP1+2.gt"/>
			<parameter idref="53.CP3.ac"/>
			<parameter idref="53.CP3.ag"/>
			<parameter idref="53.CP3.at"/>
			<parameter idref="53.CP3.cg"/>
			<parameter idref="53.CP3.gt"/>
			<parameter idref="53.CP1+2.frequencies"/>
			<parameter idref="53.CP3.frequencies"/>
			<compoundParameter idref="53.allMus"/>
			<parameter idref="59.kappa"/>
			<parameter idref="59.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"/>
			<treeLikelihood idref="26.CP1.26.treeLikelihood"/>
			<treeLikelihood idref="26.CP2.26.treeLikelihood"/>
			<treeLikelihood idref="26.CP3.26.treeLikelihood"/>
			<treeLikelihood idref="29.treeLikelihood"/>
			<treeLikelihood idref="47.CP1+2.47.treeLikelihood"/>
			<treeLikelihood idref="47.CP3.47.treeLikelihood"/>
			<treeLikelihood idref="53.CP1+2.53.treeLikelihood"/>
			<treeLikelihood idref="53.CP3.53.treeLikelihood"/>
			<treeLikelihood idref="59.treeLikelihood"/>
			<coalescentLikelihood idref="26.coalescent"/>
			
			<coalescentLikelihood idref="29.coalescent"/>
			
			<coalescentLikelihood idref="47.coalescent"/>
			
			<coalescentLikelihood idref="53.coalescent"/>
			
			<coalescentLikelihood idref="59.coalescent"/>
			
		</log>
		<!-- write tree log to file                                                  -->
		<logTree id="26.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g10.26.trees" sortTranslationTable="true">
			<treeModel idref="26.treeModel"/>
			<strictClockBranchRates idref="26.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="29.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g10.29.trees" sortTranslationTable="true">
			<treeModel idref="29.treeModel"/>
			<strictClockBranchRates idref="29.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="47.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g10.47.trees" sortTranslationTable="true">
			<treeModel idref="47.treeModel"/>
			<strictClockBranchRates idref="47.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="53.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g10.53.trees" sortTranslationTable="true">
			<treeModel idref="53.treeModel"/>
			<strictClockBranchRates idref="53.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		<logTree id="59.treeFileLog" logEvery="1000" nexusFormat="true" fileName="g10.59.trees" sortTranslationTable="true">
			<treeModel idref="59.treeModel"/>
			<strictClockBranchRates idref="59.branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
	</mcmc>
	
	<report>
		<property name="timer">
			<mcmc idref="mcmc"/>
		</property>
	</report>
	
</beast>
