<?xml version="1.0" standalone="yes"?>

<!-- Generated by BEAUTi v1.8.1                                              -->
<!--       by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard         -->
<!--       Department of Computer Science, University of Auckland and        -->
<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
<!--       David Geffen School of Medicine, University of California, Los Angeles-->
<!--       http://beast.bio.ed.ac.uk/                                        -->
<beast>

	<!-- The list of taxa to be analysed (can also include dates/ages).          -->
	<!-- ntax=33                                                                 -->
	<taxa id="taxa">
		<taxon id="Phymaturus_palluma_RAG1_JF806209"/>
		<taxon id="Chalarodon_madagascariensis_RAG1_JF806204"/>
		<taxon id="Gambelia_wislizenii_RAG1_HQ876434"/>
		<taxon id="Basiliscus_plumifrons_RAG1_HM161150"/>
		<taxon id="Phymaturus_somuncurensis_RAG1_AY662594"/>
		<taxon id="Corytophanes_cristatus_RAG1_JF806205"/>
		<taxon id="Uta_stansburiana_RAG1_JF806216"/>
		<taxon id="Hoplocercus_spinosus_RAG1_AY662592"/>
		<taxon id="Dipsosaurus_dorsalis_RAG1_FJ356747"/>
		<taxon id="Anolis_cupreus_RAG1_JN112651"/>
		<taxon id="Stenocercus_guentheri_RAG1_HQ876440"/>
		<taxon id="Pristidactylus_torquatus_RAG1_JF806210"/>
		<taxon id="Enyalioides_laticeps_RAG1_GU457971"/>
		<taxon id="Urostrophus_gallardoi_RAG1_JN112661"/>
		<taxon id="Liolaemus_lineomaculatus_RAG1_FJ356740"/>
		<taxon id="Polychrus_marmoratus_RAG1_FJ356748"/>
		<taxon id="Crotaphytus_collaris_RAG1_FJ356749"/>
		<taxon id="Sauromalus_ater_RAG1_AY662591"/>
		<taxon id="Oplurus_cuvieri_RAG1_JQ073188"/>
		<taxon id="Anolis_equestris_RAG1_JN112653"/>
		<taxon id="Phrynosoma_mcallii_RAG1_AY662590"/>
		<taxon id="Chalarodon_madagascariensis_RAG1_JQ073189"/>
		<taxon id="Uranoscodon_superciliosus_RAG1_JF806215"/>
		<taxon id="Leiosaurus_catamarcensis_RAG1_JF806207"/>
		<taxon id="Uma_scoparia_RAG1_JF806214"/>
		<taxon id="Basiliscus_basiliscus_RAG1_JF806202"/>
		<taxon id="Leiocephalus_carinatus_RAG1_AY662598"/>
		<taxon id="Leiocephalus_raviceps_RAG1_FJ356744"/>
		<taxon id="Basiliscus_galeritus_RAG1_FJ356743"/>
		<taxon id="Pristidactylus_scapulatus_RAG1_JN112660"/>
		<taxon id="Diplolaemus_darwinii_RAG1_JQ073190"/>
		<taxon id="Morunasaurus_annularis_RAG1_FJ356741"/>
		<taxon id="Petrosaurus_mearnsi_RAG1_HQ876437"/>
	</taxa>
	<taxa id="Corytophanidae">
		<taxon idref="Basiliscus_basiliscus_RAG1_JF806202"/>
		<taxon idref="Basiliscus_galeritus_RAG1_FJ356743"/>
		<taxon idref="Basiliscus_plumifrons_RAG1_HM161150"/>
		<taxon idref="Corytophanes_cristatus_RAG1_JF806205"/>
	</taxa>
	<taxa id="Chalo_Uros">
		<taxon idref="Chalarodon_madagascariensis_RAG1_JF806204"/>
		<taxon idref="Urostrophus_gallardoi_RAG1_JN112661"/>
	</taxa>

	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=33 nchar=975                                                       -->
	<alignment id="alignment1" dataType="nucleotide">
		<sequence>
			<taxon idref="Phymaturus_palluma_RAG1_JF806209"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGTCTTGTACCTAAGTAAAGGGAAGGCTGACCCGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGAAGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGGACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACAGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JF806204"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACTCGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGATTTACAAATGACAAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAACACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACAGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Gambelia_wislizenii_RAG1_HQ876434"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCAGGAGCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_plumifrons_RAG1_HM161150"/>
			------------------AAGAGGGTCGAGAGGAAGAGGGATCCCTGAGACTAATACAAGAGGTCAACAGGGACCGACCCCTCATGGTTCAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGTGAACCAATTCCTTAGGCAATAATCTGCTTCAAGCGGTCCCTTATGGTGATCCGGAAAACGCACCCAAATAAG-GGTGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAATACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAACCAATCGAGTCGGGTTGATTTCCTACAGGGGAGGTGTGAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGAAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGGGGTCAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGAGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCACACCTAAAACGGATGATGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTGCGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAA-----------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phymaturus_somuncurensis_RAG1_AY662594"/>
			AGATCGACCTGGACCGAAAAGAGGGTCGAGAGGAAGAGGCACCTCAGAGAGTAAGACGGGAGGTCAACAGAGACCGATCACTCATGGTTAAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTCGGGCAATAATCTGATTCACGCGGTCCCTTATGGTGATTCGGAAAACGCACCAAAACAAG-GGCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCATGGCGGAATACTTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAGCCGATCGAGTCGGGTTGATTCCCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGTAGAAGCACGGGCGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGAAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCCGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGAAGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGGACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGCTAGGAAATCTGCGACCAAAAATACGGAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCGAGTCGCGTCTATATCCTGGTCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTC----------------------------
		</sequence>
		<sequence>
			<taxon idref="Corytophanes_cristatus_RAG1_JF806205"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTCAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGAGAGGAAGGGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGATGATGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCCGAGGGTAACAGTAGGAAATCTGCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uta_stansburiana_RAG1_JF806216"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACATGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTATACCCGAGGGCCGAGAGGTGACTCGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Hoplocercus_spinosus_RAG1_AY662592"/>
			AGATCGACCCGGACCGAAAAGAGGGTCGAGAGGAAGAGAGATCTCTGAGAGTAAGACAAGAGTTCAACAGGGACCGACCCCTCATGGTTAAGCTAAACCGCGCGGAGACGCCAAAGAAGATTCGCCGAGTAAGGAAGAGAACCAATTCCTTAGGCAATAATCTGATTTAATCGGTCCCTTATGGTGATTCGGAAAACGCACCTAAATAAG-GGCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACCTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAATAACCGATCGAGTCGGGTTGATTCCCTACAGGGGAGGTGTAAAGGCCACCTCTCACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCGGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAGTGGAACATGCTTACTTCACGGGTGCGACAGACACCGAGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCACACCTAAAACGGACCCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTACGACCAAAAATACAAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTACCTCTATACT-
		</sequence>
		<sequence>
			<taxon idref="Dipsosaurus_dorsalis_RAG1_FJ356747"/>
			AGATCGACCCGGACCGAAAAGAGTATCGAGAGGAAGAGGCATCCCTGAGAGTAAGGCAAGGAGTCAACAGGGGCCGACCCCTCATGGTTAAGCTAAACCGCGCAGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGGCAATAATCTGCTTCAAGCGGTCSCGTATGGTGATTCGGAAAACAAACCTAAACACG-GACGAAAACGAACACGACAATAAATGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCTGAATACTTTAGTACATCAGAGATTCGTCTCTTCAGTGACGATTCAACAACCGATCGAGTCGGATTGATTCCATACAGGGAAGGTGTGAAGGCCACCTCTTAAAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTCGAAGAATCATACTCAATAAGAGGAGCCATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGATAGACACCGGGAGGAAGAGTACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTCTACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTACGACCCAAAATACGAAAAGATGAACAAAGAGGGGTGTAAGGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Anolis_cupreus_RAG1_JN112651"/>
			----CGACCCGGACCGAAAAGAGGGTCGCGAGGAAGAGGCACCTCTGAGAGTAAAACAAGAGGTCGACAGGGACCGACCCCTCATGGTTAAGCTAAACCGCGCAGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGGCAATAATCTGATTCAAACGGTACCTTATGGTGATCCGGAAAACGCACCCAAATAAG-GGCAAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCTATGATATTCATGCACGGCGGAATACCTTAGTATATCAGAGATTCGTCTCTTCAGCGACGATTCAAAAATCGATCAAGTCGGGTTGATACCCTACAGAAGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTTCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGAGCTCGTCCTGTACCTAAGTAAAGGGAAGGTTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGATTTACAAATGACTAAAAAGTGGTACATGCTTACTTCACGGGTGCGACAGATACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACTGGTCATACCTAAAACGGACGCTGTTAAACTCGAAGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAAAGGTAGGAAATCTACGACCAAAAATACAAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATTGAAAATTCAACGC----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Stenocercus_guentheri_RAG1_HQ876440"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGGAGACATCCCCGCCAGGATCTCGTCGTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGACTCTGGGTGTGCAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATTACGAGAAAATGGAACATGCTTACTTCATGGGTGCGACAGACACCGGGAGGAAAAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCCGTCATACCTAAAACAGACGCTGGTCTACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACGACCAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_torquatus_RAG1_JF806210"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGAACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACGACCAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Enyalioides_laticeps_RAG1_GU457971"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAAAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAGTGGAACATGCTTACTTCACGGGTGCGACAGACACCGAGAGGAAGAGTACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCACACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTACGACCAAAAATACAAAAAG-----------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Urostrophus_gallardoi_RAG1_JN112661"/>
			AGATTGATCCGGACCGAAAAGAGAGTTGAGAGGAAGAGGCATCTCTGAGAGTAAGACAAGAAGTCAACAGAGACCGACCCCTCATGGTTAAGCTAAACCGCGCGGTGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAGTTCCTTAGGCAATAATCTGATTCAAGCGGTCCCTCATGGTGATTCGGAAAACACACCTAAATAAG-GGTGAAAACAACCACAACAATAAAAAATGAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAACCGATCGAGTCGGGTTGATTACCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTCAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGAAGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGATAGACACCGGGAGGAAGAGAACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGAACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCTGAATCTATGGAAAATTCAACGC----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Liolaemus_lineomaculatus_RAG1_FJ356740"/>
			AGATCGACCCGGATCGAAAAGAGGATCGAAGGGCAGAGGCATCTCTGAGAGTAA-----------AACAGAGACCTACCACTCATGATTAGGCAAATCCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGGCAATAATCTGATTCACGCGGTCCCTTATGGTGATTCGGAAAACGCACCGAAATATG-GGCGAAAACAAACAAGACAATAAAAGATAAACCAAAACGGGTCGTTGATATTCATGCATGGCGGAATACTTTAGTACATCAGAGATTCATCTCTTCAGCGACGATTTAACAGCCGATCGAGTCGGGTTGATTCCCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTTTGTAGAAGCACGGGTGGAACGAGAGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAMCGTGGTTAGCTAGGAAGGTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCATGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATATTGGACCGGTCAAACCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGCTAGGAAATCTGCGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGCCAGCAGCTCAAACGTCTTTCGAGTCGCGTCTATATCCTGGTCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGG-------------
		</sequence>
		<sequence>
			<taxon idref="Polychrus_marmoratus_RAG1_FJ356748"/>
			AGATCGATCCGGACCGGAAAGAGGGCCGAGAGCAAGAGGCATCTCTCAGAGTAATACAAGAGGTCGACAGGGACCGACCCCTCATGGTTAAGCTAAACCGCGCAGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGGCAATAATCTGATTCAAGCAGTCCCTTATRGTGATGCGGAAAACGCACCTAAACMAGAGGCGACAACAAACACGACAATAAAAGATAATCCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAACCGATCGAGTCGGGTTGATTCCCTACAGGAGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTCGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGAAGGCAACGCGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACAAGAAAATGGAACATGCTTACCTCACGGGTGCGACAGACACCGGGAGGAAAAGCACGAAGACAATATATAGAGTGGACGCGGGGCGGTGTATATATTGGACCGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATGGTAGGAAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGARGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Crotaphytus_collaris_RAG1_FJ356749"/>
			AGATCGACCTGGACCGAAAAGAGAGTCGAGAGGACGAGGCATCTCTGAGAGCAAGACAAGAAGTCATCAGGGACCGACCTCTCATGGTTAAGCTAAACCGCGCGGGGACGCCCAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTGGGCAATAATCTGATTTAAGCGGTCCCTTATGGTGATTCGGAAAAAGCACCTAAATATG-GGCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAATACATCAGAGATTCGTTTCTTCAGCGACGATTCAACAACCGATCGAGTCGGGTTGATTCCCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTTATTCTGCAGAAGCACGAGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGAGCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTGCGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATATATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Sauromalus_ater_RAG1_AY662591"/>
			---------------GAAAAGAGGTTCGAGAGGAAGGGGCATCCCTGAGAGTAAGGCAAGAAGTCAACAGGGACCGACCCCTCATGGTTAAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGCGAACCAATTCCTTAGGCAATAATCTGGTTCAAGCGGTCCCGTATGGTGATTCGAAAAACGCACCTAAACACG-GGCGAAAACGAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACCTTAGTACATCAGAGATTCGTCTCTTCAGTGACGATTCAACAACCGATCGAGTCGGATTGATTCCCTACAGGGAAGGTGTGAAGGCCACCTCTTAAAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGTAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGCCATCCCCGCCAGGATCTCGTCTTGTACCTAAGTAAAGGGAAGGCTGACTTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGCGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTCTACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTA--------------------
		</sequence>
		<sequence>
			<taxon idref="Oplurus_cuvieri_RAG1_JQ073188"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACTCGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACAAGAGAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAACACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACAGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTA-----------
		</sequence>
		<sequence>
			<taxon idref="Anolis_equestris_RAG1_JN112653"/>
			AGATCGACCCGG-----AAAGAGGGTCGCGAGAAAGAGGCACCTTTGGGAGTAAAACAAGAGGTCGACAGGGACCGACCCCTCATGGTTAAGCTAAACCGCGCAGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAATCAATTCCTTAAGCAATAATCTGATTCAAACGGTCCCTTATGGTGATCCGGAAAACGCACCTAAATAAG-GGTGAAAACAAACACGACATTAAAAGATAAACCAAAACGGGTCTGTGATATTCATGCACGGCGGAATACCTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAAAAATCGGTCGAGTCGGGTTGATTCCCTACAGAAGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGAGCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAGTGGTACATGCTTACTTCACGGGTGCGACAGACACCGAGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACTGGTCACACCTAAAACAGACGCTGTTAAACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAAGGGTAGGAAATCTACGACCAAAAATACAAAAAGATGAACAAAGAGGGGT-------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phrynosoma_mcallii_RAG1_AY662590"/>
			AGATCGACCCGGACCGAAAAGAG----GAGAGAGAGAGTCATAACTGAGAGTAAGACAAGAAGTTAACAGGGACCGACCCCTCCTGGTTAAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGCACCAATTCCTTAGGCAATAATCTGATTCAAACGGTCCCTCATGGTGGTTCGGAAAAAGCACCCAAATAAG-AAAGAAAAGGAACACGACAATGAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAGTACATCAAAGATTCGTCTCTTCAGCGGCGATTCAATAATCGATCGAGTCGGGTTGATTTCCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCATCGAGTGGAGGGGGGATGTCATTTCGCAGAAGCACGGGCGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACATGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGATAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCAGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCGGCGACCAAAAACACGGAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTC----------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JQ073189"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAMGGCTGACCTGGGTCGGAAGAATATGGGTGTGTAGAGGGACGGCAACTCGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGATTTACAAATGACAAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAACACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATATTGGACCGGTCATATCTAAAACAGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGCAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTAT-------------------
		</sequence>
		<sequence>
			<taxon idref="Uranoscodon_superciliosus_RAG1_JF806215"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCAGGATCCCGTCGTGTACCTAAGTAAAGGGAAGGCTGAGCTGGGTCGGAAGACTCTGGGTGTGTAGAGGGACGGCAACGTGGTCAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCATGGGTGCGACAGATACCGGGAGGAATAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATATTGGACTGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAACCTGAGGGTAATAGTAGGAAATCTACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiosaurus_catamarcensis_RAG1_JF806207"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGAACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uma_scoparia_RAG1_JF806214"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGACTCTGGGTGTGTAGAGGGACGGCAACATGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCAGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTGCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_basiliscus_RAG1_JF806202"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGAGGTCAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCACACCTAAAACGGATGATGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_carinatus_RAG1_AY662598"/>
			AGATCGACCTGGACCGAAAAGAGGCTCGAGGGAAAGAGGCATCTCTGAGAGTAAGACAAGAATTCGACAGGGACCGATCACTCATGGTTAAGCTAAATCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGCCAATAATCTGATTCAAGTGGTCCCTTATGGTGATTCGGAAAACGCATCTAAAAAAG-GGCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAATACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAGCCGATCGAGTCGGTTTGATCCCCTACAGGGGCGGTGTGAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGAGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGAAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAATAATCTGGGTGTGTAGAGGGACGGCAACGTGGTAAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGATCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTTACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAAGGGTAGGAAATCTGCGACCAAAAACACAAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATGCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTC----------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_raviceps_RAG1_FJ356744"/>
			AGATCGACCTGGACCGGAAAGAGGCTCGAGAGAAAGAGGCATCTCTGAGAGTAAGACAAGAAGTCGACAGGGACCGATCACTCATGGTTAAGCTAAATCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGCCAATAATCTGATTCAAGCGGTCCCTTATGGTGATTCGGAAAACGCATCGAAATAAG-GCCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAATACATCAGAGATTCGTCTCTTCAGTGACGATTCAACAGCCGATCGAGTCGGTTTGATCCCCTACAGGGGCGGTGTGAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGAGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGAAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAATAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGATCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTTACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAAGGGTAGGAAATCTGCGACCAAAAATACAAAAAGATGAACAAAGAGGGGTGTAAAGGACAGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_galeritus_RAG1_FJ356743"/>
			AGATCGACCTGGACCGAAAAGAGGGTCGAAAGGAAGAGGGATCTCTGAGAGTAAAACAAGAGGTCAACAGGGACCGACCCCTCATGGTTCAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAATTCCTTAGGCAATAATCTGCTTCAAGCGGTCCCTTATGGTGATCCGGAAAACGCACCCAAATAAG-GGTAAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACTTTAATACATCAGAGATTCGTCTCTTCAGCGACGATTCAACAACCGATCGAGTCGGGTTGATTACCTACAGGGGAGGTGTGAAGGCCACCTCTCACAGCACCTAGCACCGAGTGGAGGGGGGATGTCATTCCGCCGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGAAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGCGGTCAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATACCTAAAACGGATGATGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACAGTAGGAAATCTGCGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCGGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCTGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_scapulatus_RAG1_JN112660"/>
			AGATTGATCCGGACCGAAAAGAGAGTCGATAGGAAGAGGCATTTCTGAGAGTAAGACAAGAAGTCAACAGAGACCGATCCCTCATGGTTAAGCTAAACCGCGCGGGGACGGCAAAGAAGATTCGCCGAGTAAGGAGGAGAACCAGTTCCTTAGGCAATAATCTGATTCAAGCGGTCCCTTATGGTGATTCGGAAAACGCACCTAAATACG-AGCGAAAACAAACACGACAATAAAAGATGAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACGTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAATAACCGATCGAGTCGGGTTGATTCCCTACAGGGAAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAAGAAGAGAACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAATAGTAGGAAATCTACGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGAACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGC----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Diplolaemus_darwinii_RAG1_JQ073190"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGTTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGAACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCATATCTAAAACGGACGCTGATATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACAGTAGGAAATCTGCGACCAAAAATACGAAAAGATGAACAAAGAGGGGTGTAAAGGACGGCAGCGGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCTGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Morunasaurus_annularis_RAG1_FJ356741"/>
			AGATCGACCCGGACCGAAAAGAGGGTCGAGAGGAAGAGAGATCTCTGAGAGTAAGACAAGAGTTCAACAGGGACCAACCCCTCATGGTTAAGCTAAACCGCGCGGGGACGCCAAAGAAGATTCGCCGAGTAAGGAAGAGAACCAATTCCTTAGGCAATAATCTGATTTGATCGGTCCCTTATGGTGATTCGGAAAACGCACCTAAATAAG-GGCGAAAACAAACACGACAATAAAAGATAAACCAAAACGGGTCGGTGATATTCATGCACGGCGGAATACCTTAGTACATCAGAGATTCGTCTCTTCAGCGACGATTCAATAACCGATCGAGTCGGGTTGATTCCCTACAGGGGAGGTGTAAAGGCCACCTCTTACAGCACCCAGCACCGAGTGGAGGGGGGATGTCATTCCGCAGAAGCACGGGTGGAACGAGTGCCCGGTTGAAGAATCATACTCAATAAGAGGAGACATCCCCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACGTGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAGTGGAACATGCTTACTTCACGGGTGCGATAGACACCGAGAGGAAGAGTACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCGGTCACACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTAGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTACGACCAAAAATACAAAAAGATGAACAAAGAGGGGTGCAAAGGACGGCAGCAGCTCAAACGTCTTTCAAGTCGCGTCTATATCCTGGCCGAATCTATGGAAAATTCAACGCGCGAAGAGGTAGGTGAGGAGTGAACTACTCAAAGACTATTGAGGGTAC----------
		</sequence>
		<sequence>
			<taxon idref="Petrosaurus_mearnsi_RAG1_HQ876437"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGCCAGGATCTCGTCCTGTACCTAAGTAAAGGGAAGGCTGACCTGGGTCGGAAGAATCTGGGTGTGTAGAGGGACGGCAACATGGTTAGCTAGGAAGTTGGAGGGAGACGTGCGGCGAGGCTTTACAAATGACGAGAAAATGGAACATGCTTACTTCACGGGTGCGACAGACACCGGGAGGAAGAGCACGAGGACAATATATAGAGTGGACGCGGGGCGGTGTATATACTGGACCRGTCACACCTAAAACGGACGCTGGTATACTCGAGGGCCGAGAGGTGACTCGAGCTAGGTCTGAGAGGGTTAATCTGAGGGTAACGGTAGGAAATCTGCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
	</alignment>

	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=33 nchar=976                                                       -->
	<alignment id="alignment2" dataType="nucleotide">
		<sequence>
			<taxon idref="Phymaturus_palluma_RAG1_JF806209"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCGAACCTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JF806204"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTATCTCAAACCTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTTAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Gambelia_wislizenii_RAG1_HQ876434"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTCTCTCAAACATGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCATCAAAGAGGACCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_plumifrons_RAG1_HM161150"/>
			------------------AAGATCCCTAATGAAACACTCTACACCTACATATAAGTAATAAGCTATGACACACAATATAATGGTGGGCTACACAAGAACTAGCTAAACACTTGAAAAACCCGCATTGATTACATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCTAGTAGAAATTACATGAATGT-TCGGCGATGATGACAATAAAGTTAATCGGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTCAGTAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAGACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTGCCAATTTACTCAAATAATAGAATGGCACAGACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAAGACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATT------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phymaturus_somuncurensis_RAG1_AY662594"/>
			ATGCTAACTCCAGATCAAAAGATCCCTAATTAAACACTCTTCATCTACACATAAGTACTAAGCTATGAGACACAACATAATGGTGGGCTACACGAGGACTAGCTAAACAATTGAAAAACCCGCATTCGTTGTATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACTGGATGGCCCAGTAGCAATTACATAAATGT-TCGGCGATGATAACAATAAAGTTAATCAGGATATGCATTCTAACCGTTACTCGATGAATTCACTACCGGATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTAAGAAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTGGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGT------------------------------
		</sequence>
		<sequence>
			<taxon idref="Corytophanes_cristatus_RAG1_JF806205"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAAYCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAGACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAATAATAGAATGGCACAGACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCACCAAAGAGGACCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uta_stansburiana_RAG1_JF806216"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACTTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGATCTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Hoplocercus_spinosus_RAG1_AY662592"/>
			ATGCTAACTCAAGATCAAAAGATCTCTAATTAAACATTCTTCACCTACACATAAGTACTAAGCTATAAGACACAATATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTATATATATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATGATGACAATGAAGTTAATCGGAATATGCATTCTAACTATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTAAGAAATGTGAAGAATCGAAATAAAAGATTTAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCTTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAGACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGATTTATCGTCGCTGTTTAGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAATACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAATTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTAAAGTACCAAT--
		</sequence>
		<sequence>
			<taxon idref="Dipsosaurus_dorsalis_RAG1_FJ356747"/>
			ATGCTAACTCAAGATCAAAAGATCCCTAATTAAACATTCTCCCCTTAGACATAAGTACTAAGCTATGAGACACARCATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTACATACATACTACCATGAAGGCTTAAATGACTGACTTCGACCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGRCGATGATAACAATAAAGTTAATCAGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTTGCTAAGAAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAACTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAGACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGAACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCATCGAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Anolis_cupreus_RAG1_JN112651"/>
			---CTAACTCAAGATCAAAAGAACCCTAATTAAACATTCTTCACCTACACATAAATACCAAGTTATGAGACACAAAATAATGGTGGGCTACACAAGGACTAGCTAAATATTTGAAAAACCCGCATTCATTATATAGATACTACCATGAAGGCTTAAATGACCAATGTCGAGCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATGATGACAATAAAGTTAATCGGAATATGCATTCTAACCATTACTCGATGAATTCACTACTGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTTGCTAAGAAATGTGAAGAATCGAAATAAAAGATGTAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAAATAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTCTCTCAGACGTGTTAAGACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACCAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGACGATCAATAACTCA-----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Stenocercus_guentheri_RAG1_HQ876440"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTCGGATTACTACTGGCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAAGTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATCAATAGCTTTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCGCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGCTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACGCCAAAGAGGACCTAAATGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_torquatus_RAG1_JF806210"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAATCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTGTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACATCAAAGAGGACCTAAATGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Enyalioides_laticeps_RAG1_GU457971"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTGTTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACTACCAAAGAGGACCTAAATGAATATACTCGTA-------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Urostrophus_gallardoi_RAG1_JN112661"/>
			ATGCTAACTCAAGATCAAAAAATCCCTAATTAAACACTCTTCCCCTACACATAAGTACTAAGTTATGAGACACAACATAATGGTGGGTTACACTAGGACTAGCTAAACACTTGAAAAACCCGCATTCGTTATATAGATACTACCATGAAGGCTTAAATGACCGGTTTCGAGCTAGACACTGGATGGGCCGGTAGAAATTACGTGAATGT-TCGGCGATGACGACAATAAAATTAATCGGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTAGTTAGTCTGGCTAAGAAATGTGAAGAATCGAAATAGAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACATCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTAATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCA-----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Liolaemus_lineomaculatus_RAG1_FJ356740"/>
			ATGCTAACTCCAGATCAAAAGATCCCTAACTAAACATTCTTCACCTACACATA-----------ATGAGATGTAACTTACTGGTGGGCTATACAAGGACTAGCTAAACACTTGAAAARCCCGCATTCGTTGTATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCCAGACACCGGATGGCCCGGTAGAAATTATATAAATGT-TCGACGGTGATAACAATCAAGTTAATCAGAATATGCATTCTAACCGTTACTCGATGAATTCACTACCGGATTGGCGTTAGTACTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTAAGTAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGTTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCGAAAATATTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAGGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAAAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATAAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAA---------------
		</sequence>
		<sequence>
			<taxon idref="Polychrus_marmoratus_RAG1_FJ356748"/>
			ATGCTAACTCAAGATCAAAAGATCCCTAATTAAACACTCTTCACTTACACATAAGTACTAAGTTATGAGACACAACATAATGGTGGGTTAAACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTACATACATACCACCATGAAGGCTTAAATGACCGATTTCGAACTAGACACTGGATGGCCCAGTAGAAATTACATGAATGTTTCGGCGATGATGACAATAAAGTTAATCGGACTATRCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTAAGAAATGTGAAAAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGGGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAGGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGATAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTAA-----------
		</sequence>
		<sequence>
			<taxon idref="Crotaphytus_collaris_RAG1_FJ356749"/>
			ATGCTAACTCAAGATCAAAAGATCCCTAATTAAACACCCTTCACCTACACATAAGTACTAAGCTATGAGACACAACATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTACATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCGGTAGAAAGTACATGAATGT-TCGACGATGATGACAATAAAGTTAATCGGAACATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATAGCTACTTGTTAGTCTGGCTAAGAAATGTCAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCCCAAACATGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCATCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACARTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTAA-----------
		</sequence>
		<sequence>
			<taxon idref="Sauromalus_ater_RAG1_AY662591"/>
			---------------CAAAAGATCCCTAATTAAACGTTCTTCACCTACACATAAGTACTAAGCTATGAGACACAACATAATGGTGGGCTACACGAGGACTAGCTAAACACTTGAAAAACCCGCATTCGTTATATACATACTACCATGAAGGCTTAAATGACCGACTTCGGCCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATGATATCAATAAAGTTAATCAGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTATTAGTCTTGCTAAGAAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAACTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGAACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCGAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACA---------------------
		</sequence>
		<sequence>
			<taxon idref="Oplurus_cuvieri_RAG1_JQ073188"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACCTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTTAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACTAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAAAAGAACTAATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATAAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Anolis_equestris_RAG1_JN112653"/>
			ATGCTAACTCA-----AAAAGATCCCTAAGTAAACATTCTTCACCTACACATAAGTACTAAGCTATGAGACACAAAATAATGGTGGGCTACACAAGGACTAGCTAAATACTTGAAAAACCCGCATTCATTATATAGATACTGCCATGAAGGCTTAAATGACCAATTTCGATCTAGACACTGGATGGCCCAGTAGAAATTACATGAATGT-TCGGCGATGATGACAATAAAGTTAATCGGAATATGCATTCTAACCATTACTCGATGAATTTACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTTGCTAAGAAATGTGAAGAATCGAAATAAAAGATGTAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTCCCTTATAAATTAGTAGAATAAATGGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTCTCTCAGACGTGTTAAGACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGGGGACCTAAATGAATATACTCGTAGATCGATTCAACTACT---------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phrynosoma_mcallii_RAG1_AY662590"/>
			GTGCTAATTCAAGATCAAAAGA----TAATTAAATACTCTACACCTACACATAAGTACTAAGCTATGAGATACAACATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTACATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGTTAGACACCGGATGGCCTAGTAGAAATTACATAAATGT-TCGGCGAAGACGACAATAAAGTTATTCGGAATATCCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGTGTTACTATTGGAGCCGGACGTCCATTGCTACTTATTAGTCTGGCTAAGAAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTCTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGATCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAAAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATAAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGT------------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JQ073189"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACCTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTTAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTGCCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTAATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATAAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACA---------------------
		</sequence>
		<sequence>
			<taxon idref="Uranoscodon_superciliosus_RAG1_JF806215"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAAGTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGAGCCTCAACTGTCTCTTGTCTTAAAAGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGATTTATCGTCGATATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAGACACCAAAGAGGACCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiosaurus_catamarcensis_RAG1_JF806207"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAATCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACATCAAAGAGGACC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uma_scoparia_RAG1_JF806214"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTCTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_basiliscus_RAG1_JF806202"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAGACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAATAATAGAATGGCACAGACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAAGACCAAAGAGGACC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_carinatus_RAG1_AY662598"/>
			ATGCTAACTCAAGATCAAAAGATCCCAAATTAAACACTCTTCACCTACACATAAGTACTAAGCTATGAGACACAACATAATGGTGGGCTACATAAGAACTAGCTAAACACTTGAAAAGCCCGCATTGGTTATATGGATACTACCATGAAGGTTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCAGTAGAAATTACATGAATGT-TCGACGATGATGACAATAAAGTTAATCAGAATATGCATTCTAACTATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTTAGAAATGTGAAAAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAAGGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCAATGCTGACCGAACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAAAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGAACAGTCATTCCATAAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGT------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_raviceps_RAG1_FJ356744"/>
			ATGCTAACTCAAGATCAAAAGATCCCCAATTAAACACTCTTCACCTACACATAAGTACTAAGCTATGAGACACAACATAATGGTGGGCTACATAAGAACTAGCTAAACACTTGAAAAGCCCGCATTGGTTATATGGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATGATGACAATAAAGTTAATCAGAATATGCATTCTAACTATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTTAGAAATGTGAAAAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGYTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAAGGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCAATGCTGACCGAACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAAAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGAACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_galeritus_RAG1_FJ356743"/>
			ATGCTAACTCAAGATCCAGAGATCCCTAAAGAAACACTCTACACCTACATATAAGTAATAAGCTATGACACACAATATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAATCCGCATTGATTACATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCTGGTAGAAATTACATGAATGT-TCGGCGATGATGACAATAAAGTTAATCGGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTCAGTAATGTGAAGAATCGAAATAAAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATGCTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAGACGGGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGTTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGATAATAGAATGGCACAGACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_scapulatus_RAG1_JN112660"/>
			ATGCTAACTCAAGATCATAAAATTCCTAATTAAACACTCTTCCCCTACACATAAGTACTAAGTTATGAGACACAACATAATGGTGGGTTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCGTTATATAGATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATAACGACAATAAAATTAATCGGAATATGCATTCTAACCATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGTACGTCCATTGCTACTAGTTAGTCTGGCTAAGAAATGTAAAGAATCGAAATAGAAGATATAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAATCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACATCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAACTAATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCA-----------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Diplolaemus_darwinii_RAG1_JQ073190"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAATCTCCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTTTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGAAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACCACCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTCAACTACTGATTAGAAGAACTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Morunasaurus_annularis_RAG1_FJ356741"/>
			ATACTAACTCAAGATCAAAAGATCTCTAATTAAACACTCTTCACCTACACATAAGTACTAAGCTATAAGACACAATATAATGGTGGGCTACACAAGGACTAGCTAAACACTTGAAAAACCCGCATTCATTATATATATACTACCATGAAGGCTTAAATGACCGATTTCGAGCTAGACACCGGATGGCCCGGTAGAAATTACATGAATGT-TCGGCGATGATGTCAATGAAGTTAATCGGAATATGCATTCTAACTATTACTCGATGAATTCACTACCGAATTGGCGTTAGTATTGGAGCCGGACGTCCATTGCTACTTGTTAGTCTGGCTAAGAAATGTGAAGAATCGAAATAAAAGATTTAAGGGCGAATTCTCGGCAAAGTGATATATACTCAAAAGGATACTGTCTTTTCTGCGAAAGACAATACTTAGAGCGTACCTGTCTGTACTTGGGAAAATAGCTACTCGGATTACTACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTCTCAAACGTGTTAAGACACATGGACTGTTTCAACAAACTCCTTGCTTCAGATTAAGTTTTATCGTCGCTGTTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGAAAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAACTGCCAAAGAGGACCTAAATGAATATACTCGTAGATCGATTGAACTACTGATTAGAAGAATTGATTATATATACTGGCCGCCAAGCATTGAAGTACAGTCATTCCATGAGAAGATCAATAACTCATCATTAGAGCTGCGCGAGAACGAATTGGTGATACGACAGAATAATTA------------
		</sequence>
		<sequence>
			<taxon idref="Petrosaurus_mearnsi_RAG1_HQ876437"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTGCCAACTTCGAACTAGACCTAATCGACATGTTAGTCGTAATTAAACTACTCAGTGAACCTTCCTTATAAATTAGTAGAATAAATAGCTCTTTAACGAGTGATGAAAGGGCCTCAACTGTCTCTTGTGTCAAACGTGTTAAAACACATGGACTGTTTCAACAAACTCCTTGCTTCAGACTAAGTTCTATCGTCGCTATTTGGCGAAAATTGATAGTACCGCCATGCTGACCGTACCAATTTACTCGGACAATAGAATGGCACAAACTAATGAGTAGTCCACTTACTCCTACTAGATGACCATAATTATATGATAAACACCAAAGAGGACCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
	</alignment>

	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=33 nchar=975                                                       -->
	<alignment id="alignment3" dataType="nucleotide">
		<sequence>
			<taxon idref="Phymaturus_palluma_RAG1_JF806209"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCTATGGAACGATCTTCAAAATTTGTACAATGTTTCAACATAGATATTATGTTCGGTGAACCAACGATGCGTCCCACTCTGGTAGCTTAGATTTGATCTCATTTGAACACTCACGCCTCAACTACAGTTAACGCTAGGTTATGCTGGTTAATCGACACCGTTTGAAAGCGACTAGATTGTACAAACACCTGCTATTAGTCTAAGCTAGACTTCTCTGTTAACGACCGCGCTTCCAGTTGACAAGTGGGGCCCCTGTTTAGTCAAGGTGAGTTTGCTTGATCGCTCTCTATATCGACGTGTTAGCACTTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JF806204"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATATAAACCGAACTATGGAACGATCCCCAAACTTTGTACAATATTCCAACATAGATATTATGTTCGGTGAACCAACGATCCGTCCCATTCTGGTAGCTTAGATTTGATCTTATTTGAATACTCACGCCTCTTCTATAGTTAACGCCAGGTTATGCTGGTTAACTGACACCGTTTGAAAGCAACTAGATTGTACAAACACCTGCTATTAGTCTAAACTATACCTCTTCATTAACGACCGCGCTCCCAGTTGACGAATGGGGGTCCTGTTTAGTCAGAGTTAGTTTGTTTAATCGCTCTCTATATTAACGTGTTAGCACCAAAAAGAGAGGATTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Gambelia_wislizenii_RAG1_HQ876434"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTATTAGCCGATCTATGGAACGATCCTCAAATCTTGTACAATGTTCCAACATGGATATTATGTTCGGTGAACCAACGATGCGTCCCACTCGGGTAGCTTAGATGTGATCTCATCTGAATACTCGTGCTTTTTCTATAGTTAACGCTAGGTTATGCTGGTTAATTGCCACCGTTTGAAAGCGACTAGATTGTACAAACACTTGCTGTTAAACTAAGYTATACCTCACTGTTAACGGATGCGCTTCCAGTTTACAAGCGGGGCCCCTGGTTAATCAGGATTAGTTTGTTTAATCACTCTCTTTATCGACGTGTTACCACTTAGAAGAGAGGAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_plumifrons_RAG1_HM161150"/>
			-------------------TAAAGATTGCACTGAGTGTGTAGACACTAACCGGCATTGAATGTCTTGCAAGTAACGACGGACCCCTACATATCTTGACCATTAATTTGTGCTCAGAGAGAATGATCTCATTGTTGAGCTCACTAAGTTCGTGTGTAAAACTCATAATTAGACAGAGTCTCACTTTTCTCCTAGGAGGACTTAGGCAGGGG-GTATTAAAAGAGTAAACCAGTGGAATCCCGGTCTTCGCTAACTCCCTAGACCCGCTGCCCTCAAAGACACATCACCCTACCAAGACTCATTCTTCTTTTGGCTGACCGCCGCTATGATAGATTGGGCTGAACTCTTGACAGAACAGCTGTACATCAAAACATAGAGATAGCCAAACGAAGATTTGAAAGATCGTGTATGCAGTGACATACAATTGGATAGAGGGACTTATTCGACACTTTCCTCGCTAGCGTAATACGAGACGACTCCATTAGCCGATCTATGGAACGATCCTCAAACTTTGTACAATGTTTCATCACAGATATTCTGTTCGGTGAACCAACGATGCGTCTCGCTCTGGTAGCTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAGTTAATGCTAAGTTATGCTGGTTAACTGACACCGTTTGAAAGCGACTAGATTGTACAAGCACATACTATTAGTCTAAGCTATACTTCCCGGTTAACGACAGCGCTTCCAGTTGACAAGCGGGGCCCTTGTTTAGTCAGGGTTAGTTTGTGTGATCGCTCTCTATATCGATGTGTTACCACCTAAAAGAGAGGATTCACCAGGGCGGTCCAGTGTTCAGCGCGCTGAATTAAAGTGGACACCAACGCTCTGGAAGGGTATCCGACAAAACGTTTTTATTGGGGTAACTCATGCGTCTCTCACTTTTAATT----------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phymaturus_somuncurensis_RAG1_AY662594"/>
			CAAAATGGATTTCCTGTCCTAAAGATTGCACTGAGTGGATAGACACTATCTAGCATTGAATATCTTGCAAATAACGACGATCCCCTACATATCTTCRCCATTAAATTGTGTTCAGAAAGTATGACGTCATTGTTGAACTTACTTAGTTCATGTGTAGAACTCATAATTAGACAAGGTCTCGTTTTTCTCCTATGAGGACTTAGGCAAGGG-GTATTAAAGGAGTAAACCAGTAGAGTCCCTGTCCTCGTTATCTTATTAGACTCGCTGCCGTTAAAGACTCACCACCCTACCAAGATTTATTCTTCTTTTGGCTGACCGCCGTTATCATAGATTGGGCTGAACCCTTCACAGAACAGCTGCACATTCAAACGTCGAGATAGCCAAACGGAAATTTGAAGGATCGTGTATGCAGTGACATACAAATGGATAGAGGGACTTATTCGACACTTTCCTCACTAGCGTAATACGAGACGATTATATTAGTCGATCTATGGAACGATTTTCAAAATTTGTACAATGTTTCAACACAGATATTATGTGCGGTGAACCAACGACGCGTCYCACTCTGGTAGCTTAGATTTGATCTCATTTGAATACTCACGCCTCAACTACAGTTAACGCTAGGTTATGCTGGTTAATCGACACCGTTTGAAAGCGACTAGATTGTATAAACACCTGCTATTAGTTTAAGCTAGACTTCTCTGTTAACGATCGCGCTTCCAGTTGACAAGTGGGGCCCCTATTTAGTCAAGGTGAGTTTGCTTGATCGCTCTCTATATCAACGTGTTAGCACTTAAAAGAGAGGATTCACCAGGGTGGTAAGGTGCTCAACGCGGTGAATTAAAGTGGATACCAACGTTCTGGAAGGATATTCAACAAAACATTCTTAATAGGGTAACTCATGCGTCTCTCGCTTTTAATTAATATTTTGATGATGTGCATCACT----------------------------
		</sequence>
		<sequence>
			<taxon idref="Corytophanes_cristatus_RAG1_JF806205"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACTCCATTAGCCGATCTRTGGAACGATCCCCAAACTTTGTACAATGTTTCACCATAGATATTCTGTTCGGTGAACCAARGATGCGTCTCACTCTGGTAGCTTAGATTTGATCTCATCTGAATACTCATGCCTCTTCTACAGTTAACGCTAAGTTATGCTGGTTAACCGACACTGTTTGAAAGCGATTAGATTGTGCAGGCACATACTATTAGTCTAAGCTATACTTCTCGGTTAACGGCAGCGCTCGCAGTTGACAAGCGGGGCCCCTGTCTAGTCAGGGTTAGTTTGTGTGATCGCTTTCTATATCGATGTGTTACTACCTACAAGAGAGGATTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uta_stansburiana_RAG1_JF806216"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACATTAGCCGATCTATGGAACGATCCTCAAACTTTGTACAAAGTTCCAATATAGATACCATGTTCGGTGAACCAACGACGCGTTCCACTCTGGTAGCTTAGATTTGATTTCATCTGAAGACCCACGCCTCTTATACAGTTAACGCTAGATCAAGTTGGCTGACTGACACCGTTTGAAAGCGACTAGATTGTACCAACATCTACTCTTAGATTAAGCTACATTTCTCGGTTAACGACCGTGCTCCCTGTTAACAAGCGAGGCTTCAGTTTAGCCAAGGTTAGTTTGTTTGATCGCTCTCTATATCGACGTGTTAGCATCTAAAAGAGAGGAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Hoplocercus_spinosus_RAG1_AY662592"/>
			CAGAATGGATTTCCTGTCCTAAAGATTGGACTGAGTGGGTAGACACTAACTGGCATCGAATATTTTGCAAGTAACGACTGTCCCCTACATATTTTGACCATTAAATTGTGTTCAGAGAGAGTGATCTCATTGTTGAACTCACTTAGTTCATGTGTAGAACTCATAATTAGACAGGGTCTCGCTTTTCTTCTAGGAGGAGTTAGGCAAGGG-GTATCAAGGGAGTAGACCAGTGGAGTCCCGGTCCTCGCTAACTTGCTAGACTCGCTACCGTCAAAAGCGCACCACCCGACCAAGACTCATTCTTCTTTTGGCTGACCGCCGCCATGATATATCGGGCTGAACTCTTCACGGAACGGCTGCACATCAAAACATAGAGATAGCTAAACGAAAATTTGAAAGATCGTGTATGCAGTGACATACAATTGGATAGGGGAACTTATTCGACACCTTCCTCGCTAGCGTAATATGAGACGACTGTATTAGTCGATCTATAGAGCGATCCTTAAACTTTGTATAATGTTTCAGCACAGATATTATGTTCGGTGAATCAACGATACGTCCCACTCTGGTAGCTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAATTAACGCTAGGTTATGCCGGTTAACCGACACCGTTTGAAAACGACTAGATTGTACAAACACCTGCTATTAGTCTAAGCTACACTTCTCTGTTAACGACCGCGCTCCCAGTTAACAACTGGGGCCCCCGTTTAGTCAGAGTTAGCTTGTTTGATTGCTCTCTATATCGACGTGTTACTACTTAGAAGAGAGGATTCACCAGGGCGGTAAGGTGTTCAGCGCGATGAACTAAAATGGATACCAACGCTCTGGAAGGGTATCCAACAAAACGTCCTTATTAGAGTAACTCATGCGTCTCTCATTTTTAATTAATGTTATGATGACGTGCATCACTAAGTCGAAACTAGATCAGCTGATCAATG
		</sequence>
		<sequence>
			<taxon idref="Dipsosaurus_dorsalis_RAG1_FJ356747"/>
			CAAGATGGATTTCCCGTCCTAAAGATTGCACTGAGTGGGTAGATACTAACTGGCCTTGAATATATTGCAAGTTATGACGGTTCCCTACGTATCTCAACTATTAAATTGTGCTCAGAGAGAATGATCTCATTGTTGAACTCACTTAGCTCGTGTGTAGAACTCATAATTAGACAGGGTCTCGCTTTTCTTCTAGGAGGACTTAGGCAAGGG-GTATTAAAGGAGTAAACCAGTAGAGTCCCGGTCCTCGCTAACTTACTAGACTCGCTCTCGTCAAAAACGCATCACCTTACTAAGACTCATTCTTTTTTTGACTGACCGCCGCTGTGATAGTTTGGGCTAAACTCTTCACAGAACAGCTGCACATCAGAACATAGAGATGGCCAAACAAAAATTTGAAAGATCGTGTATGCGATGATATACAATTGGATAGAGGAACTTATTCGACACTTTCCTCGCTAGCGTAATATGAGACGACTATATTAACAGATCTATGGAACGATCCTAAAACTTTGTACAATATTTCAGCATAGATCCTGTGTTCGGTGAACCAACGATGTGTCCCACTCTGGTAGTTTAGATTTGATCTCTTCTGAATACTCACGCCTCTTCGACAGTTAACGCTAGGTTATGCTGTTTAACTGAGACTGTTTGAAGGCGACTAGATGGTACAAACACCCACTATCAGTCTAAGCTACACTTCTCTGTTAACGATCGCTCTCCCAGTTAACAAGTGAGGCTCCTGTTTATTCAGGGTTAATTTGTTTAATCGCTCTCTATATYGACGTGTTACCACTTAAGAARGAGAATCCACCAGGGCGGTAAGGTGTTCAGCGCGGTGAATTAAAGTAGAGACTAATGCGCTGGAAGGGTATCAAACAAAATGTTCTTATTAGAGTAACTCATGCGTTTCTCACTCTTAATTGATATTTTGCTAATGTGCATCACCAAGTCAAAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Anolis_cupreus_RAG1_JN112651"/>
			----ATGGATTTCCTGTCCTAGAGATTGCACTGAGTTGGTGGATACTAACTGGCACGGAATATCTTGCAAGTAACGACGGTCCCTTACATATTTTGACCATTAAATTGGGCTCAAAGAGAATGTTCTCATAGTTGAATTCACTTAGTTCGTGTGTAGAACTTATAATTAGACAGGGGCTTACTTTTCTACTAGGAGGACTTAGGCAAGAG-GTATTAAAGGAGTAAACCAGTAGAATCTCGGTCCCCGCTAACCTACTAGACTCGATGCCGTCAAAAGCGCACTAGCCCACGAAGACTTATTCCTCTGTTGGCTGACTGTCGCTGTGATAAATTAGGCTGAACCCTTCACAAAACAGCTGCACATCAAAATATCGAGATAGCCAAACGRAAATTTGAAAGATCGTGTATGTGGTGACATACAATTGGATAAAAGGACTTATTCAACACTTTCCCCACTAGCGTAATCTGAGACGACTATATTAGCCGATCTATGGAACGATCCTCAAACTTTGGACAATGTTCCAGCATAGATATTATGTTCGGTGAACTAACGAAGCATCCCATTCTGGTAGCTTTGATTTGATCTCTTTTGAATACTCACGCCTCTTCTACAGTTAATGCTAGATTGTGCTGGTTAACTGTCATCGTTTGAAAGCGACTAGATTGTACAAACACCTGCTATTAATCTAAGTTACACCTCTCTTTTAACTACTTCGCTTCCAGTTTACAAATAGGACCCCTGCTTAATCACGTTTAGTTTGTTTAATCGCTCTCTATATCGACGTGTTACCACTTAAAAGAGAGGACTCACCAGGGCGGTGAGGTGTTCAGTGCGGTGACCTAAAGTGGATACCAACGCTCGGGACGGGTACCCAACAAAACGTTCTTAGTAGGGTAACTCATTTATGTCTTACTTT---------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Stenocercus_guentheri_RAG1_HQ876440"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGATATGAACCGTCTGCATTAGCCGATCTATGGTACGATCCTCAAACTTTGTACAATGTTTCAACATGGATATTATGTTAGGTGAACCAACGATGCGTCCTACTCTGGTAGCTTAGATTTGATCTCATTCGATTGTTCGCGCCTTTTCTACAGTTAACGCTAGGTTGTGCTGGTTAACTAACACCGTTTGAAAGCGGTTAGATTGTACAAACACTTGCTATTAATCTAAGTTACACCTCTTAGTTAACGATTGCGCTTCCAGTTTATAAGTGGGACCACTGTTTAATCAGGGTTAGTTTGTTTAATCGCTCTCTATATCGAGGTGTCACCACCTAAAAGAGAGGAATCACCAGG---------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_torquatus_RAG1_JF806210"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAGACGACTCTATTAGCCAATCTATAGAACGATCCTCAAACTTTGTACAATGTTTCAACATGGATATTATGTTCGGTGAACCAACGATGTGTCCCACACTGGTAGTTTAGATTTGATCCCAGCTGAATACTCACGCCTCTTCTTCAGTTAACGCTAAGTTATGCTGGTTAACTGTCACTGTTTGAAAGCGATTAGATTGTATAAACACCTGCTATTAGTCTAAGCTATACTTTTTTGTTAACGACCGCGCTCCCAGTTGACAAGTGGGGCCCCTGTTTAGTCAGGGTTAGTTTGTTTGATCGCTCTCTATATCGACGTGTTAGCACTTAAAAGAGAGGATTCACCAG----------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Enyalioides_laticeps_RAG1_GU457971"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATATGAGACGACTATATTAGCCGATCTATAGAACGATCCTCAAATTTTGTATAATGTTTCAGCACAGATATTATGTTCGGTGAACCAACGATGCGTCCCACTCTGGTAACTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAGTTAACGCTAGGTTATGCTGGTTAACCGACACCGTTTGAAAGCGACTAGATTGTACAAGCACCTGCTATTAGTCTAAGTTACACTTCTTTGTTAACGACCGCGCTCCCAGTTGACAAGTGGGGCCCCTGCTTAGTTAGGGTTAGCTTATTTGATCGCTCTCTATATCGACGTGTTACCACTTAGAAGAGAGGATTCACCAGGGCGGTAAGGT-----------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Urostrophus_gallardoi_RAG1_JN112661"/>
			-AGAATGGATTTCCTGTCCTAAGGATTGCACTGAGTGAGTAGACACTAACCGGCAATGAATATATTGCAAGTAATGACAGTCCCCTACGCATCTTGACCATTAAATTGAGTTCAGAGAGAATGATCTCATCGTTGAACCCACTTAGTCCGTGTGTAGAACTCATAATTAGATAGGGTCTCGCTTTTCTCTTAGGAGGAATTAGGCAAGGG-GTATTAAAGGAGTAAACCAGTAAAGTCCCGGTCCTCGCTCACTTACTGGAATCGCTGCCGTTAAAAACACACCACCTTACTAAGACTCATTCTTCTTTTGGCTGACCGYCGCTATGATAGATTGAGCTGAATTCTTCACGGAACAGTTTCACATCAAAACATAGAAATAGCCAAACGAAAATTTAAAAAATCRTGTATGCAGTCACATACATTTGGATAGAGGGACTTTTTTGACACTTTCCTCGCTAGCATAATATAAGACGACTCTATTAGCCAATCTATGGAACGATCCTCAATCTTTGTACAATGTTTCAACATGGATATTATGTTCGGTGAACCAACGATGTGTCCCACTCTGGTAGCTTAGATTTGATCTTAGCTGAATACTCACGCCTCTTCTAAAGTTAACGCTAGGTTATGCTGGTTAACTGTCACCGTTTGAAAGCGATTAGATTGTATAAACACCTGCTATTAGTCTAAGCTATACTTTTTAGTTAACGACCGCGCTCTCAGTTGACAAGTGGGGCCTCYGTTTAATCAGGATTAGGTTGTTTGATCGCTCTCTATATCGACGTGTTAGCACCTAAAAGAGAGGATTCACCAGGGCAGTAAGGTATTCAGCGCGGTGAATTAAAGTGGACACCAACGCTTTAGAAGGGTGTCCAACTAAACGTTCTTATCAGGGTRACTCATTCGTCTCTCACTCT---------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Liolaemus_lineomaculatus_RAG1_FJ356740"/>
			CAGAATGGATTTCTCGTCCTARAGATTGCACTGAGTGGGTAGACACTATCTAGC-----------TGCAAATATCGATGATCCCCTACATATCTTGGGCATTAAATTATGCTCAGAGAGAATGATCTCATTGTTGAACGCACTTAGTTCCTGTGTAGAATTCATAATTAGACAAGGTCTCATTTTTCTCTTATGAGGACTTAGACAAGGG-GTATTAAGGAAGTCAACCAGCAGAGTCCCTGTCCTTGTTAACTTACTAGACTCGCTGCAGTTAAAGACTCACCACCCTACCAAGATTCATTCTTCTTTTGGTTAACCGCCCTTATGATAGATCGGGTTGAACCCTTCACAGAACAYCTGCACATTTAAACGTAGGGATAGCCAAACGGACATTTCAAAGATCATGTATACAGTGACATACAAATGGATAGAGGGACTTATTTGATACTTTCCTCGCCAGTGTAATATGAAACGACTATATTAGTCGATCTATGGAACGATCCTCAAAATTTGTACAATCTTTCAACATAAATATTATGTTCGGTGAACCAACAATACGTCCCACTCTGGTAGATTAGATTTGATCTGAGCTAAACACTCACGCCTCTACTACAGTTAACGCTAGGTTATGCTGGTTAACTGACACCGTTTGAAAGCGATTAGATTGTACAAACACCTGCTATTAGTTTAAGTTATACTTCTCTGTTAACGACCGCGCTTCCAGTTGACAAATGGGACCCTTGTTTATTTAAGGTAAGTTTGTTTGATCGCTCTCTATATCGACGTGTGAACACTTATAAGAGAGGATTCGTCAGGGTGGTAAGGTGCTCAGCGCGGTGAATTAAAGTGGATACCAACGCTCTAGAAGGGTATTCAACAAAGCGTTCTTGCTAGGGTAACTTATGCGTCTCTCACTCTTAATTAATATTTTGATGCTGTGCATCGCTAAGTCAAAACTAGAT-------------
		</sequence>
		<sequence>
			<taxon idref="Polychrus_marmoratus_RAG1_FJ356748"/>
			CAGATTGGATCTCCTGTCCTAAGGATTGCACTTAGTGGGTAGACACTATTTGGCATTGAGTATCTGGCAAATAACGACGATCTTCTGTATATTTTGACCATTAAATTATACTCAGAGAGAATGATTTCATTGTTGAACTCACCAAGTTCGTGTAGGGAATTTATAATTAAACGGAGTCTCGCTTTTCTTCTAGGAGGACTTAGGCAAGGGGGTATCAAAGGAGTGAACCAGTAGAGTCYCGGTCCTCGCTAACTTGCTGGACTCGCTGCCGTCAAAAACGCACCACYCTACCAAGACTTAACCTCCTTTTGGCTGACTGCCGTTATGATAGACTGGGYTGAACCCTTCACAGAACAGCTGCACATCAAAACATAGAGATAACCAAACGAAAATTTGAAAAATCGTGTATGCAGTGACATACAATTGGATAGAAGAACTTATTCGACACTTTCTTCGCTAGCGTAATATGAGACGACTTTATTAGCTGATCTATGGAACGATCTTCAAGCTTTGTACAATGTTTCAACACAGATATTATGTTCGGTGAACCGACGATGGGTCCCACTCTGGTAGCTTAGATTTGATCTCATCTGAATACTTACGCCTCATYTACAGTTAACGCTAGGTCAAGCCGGTTAACTGACACCGTTTGAAAGCGACTAGATTGTACAAACACCTGCTATTAGTTTAAGCTACACTTCTCTGTTAACGATCGCACTTCCAGTTGACAAGCGGGGCCCCTGTTTAATCAGGGTCAGTTTGTTTGATCGCTCTCTCTATCGACGTGTTACCACTTAGAAAAGAGGATTTACCAGGGTGGTAAGGTGTTCGACGCGGTGAATTAAAGTGGATACCAAYGCTCTGGAAGGCTATCCAACAAACCGTTCTTATTAGAGTAACTCATCCGTCCCTCACTTTTAGTTAATATTTAGGTGATGTGCATTACTAAGTCGAAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Crotaphytus_collaris_RAG1_FJ356749"/>
			CAGAATGGATTACCTGTCCTAAAGATAGCACTGATTGTGTAGACACTAACAGGCATTGAATATCTTGCAAGTAATGACGGTTCCCTACATATCTTGACCATTAAATTGTGCTCAGAGAGAATGATCTCAGTGTTGAACTCACCAAGTTCATGTGTAGAACTCATAATTAGTCAGGGTTTCGCTTTTCTCCTAGGAGGACGTAGGCAAGGG-GTATTAAAGGAGTAAACCAGTAGACTCCCGGTCCTCGCTAACTAACTAGACTCGCTCCCGTCAAAGGCGCACCACCCTACCAAGACTCATCCTTCTTTTGGCTGACCACCGCTATGATAGATTGGGCTGAGCTTTTCACAGAACAGCTGCACATCAAAACATAGAGATAGCCAAACGAAAATTTGAAAGATCGTGTATGCAGTGACATACAACTGAATAGAGAGACTTATTCGACACTTTCCTCGCTAGCGTAATATGAAACGACTATATTAGCCGATCTATGGAACGATCCTCAAATCTTGTACAATGTTCCAACATGGATATTATGTTCGGTGGACCAACGATGCGTCCCACTCGGGTAGCTTAGATGTGATCTCATCTGAATACTCGTGCCTTTTCTACAGTTAACGCTAGGTTATGCTGGTTAACTGCCACCGTTTGAAAACGACTAGATTGTATAAACACTTGCTGTTAAACCAAGCTATACCTCACTGTTAACGAATGCGCTTCCAATTTACAAGTGGGGCCCCTAGTTGATTAGGATTAGTTTGTTTAATCACTCTCTATATCGACGTGTTACCAACTAGAAGAGAGGATTCACCAGGGCGGTAAGGTGTTCAGCGCGATGAATTAAAATGGATACCAACGCTCTGGAAGGGTATACAACAAAACGTCCTTATTAATGTAACTCATGCGTCTCTCACTTTTAATTAATAATTTGATGACGTGCATCACTAAGTCAAAACTAGATCAGA---------
		</sequence>
		<sequence>
			<taxon idref="Sauromalus_ater_RAG1_AY662591"/>
			----------------TCCTAAAGTTTGCACTAAGTGGGTAGACACTATCAGGCATTGAATGTCTTGCAAGTAACGACGGTCCCCTACATATATTGACTATTAAATTGTGCTCAGAGAAAATGATCTCATTGTTGAACTCACCTAACTCCTGTATAGAACTCATAATTAGACAGAGTCTCGCCTTTTTTCTAGGAGGACTTAGACAAGGG-GTATTAAAGGAGTAAACCAGTAGAATCCCGGTCCTCGCTAACTTGCTAGACTCGCTGTCGTTAAAAACGCATCACCCTATCAAGACTCATTCTTCTTTTGGCTGACCGCCGCTGTGATAGTTTGGGTTGAACTCTTCACGGAACAGCTGCACATCAGAACATTGAGATAGCCAAACGAAAATTTGAAAGATCGTGTATGTAGCGACATACAGCTGGATAGAGGGATTTATTCGACACTTTCCTCGCTAGTGTGATATGAGACGACTGTATTAGCTGATCTATGGAACGATTCTCAAATTTTGTACAATGTTTCAGCATAGATATTATGTTCGGTGAACCAACGATGTGTCCCATACTGGTAGCTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAGTTGACGCTAAGTTATGCTGTTTAACTGAGACCGTTTGAAAGCGACTAGATTGTACAAACACCTGCTATTAGTCTAAGCTACAGTTTTCTGTTAACGATCGCGCTCCCAGTTGACAAGTGGGGCTCCCATTTAATCAGGGTTAATTTGTTTGATCGCTCTCTATATCGACGTGTTACCACTTAAGAGAGAGAATTCACCAGGGCGGTAAGGTGTTCAGCGTGCTGAATTAAAGTGGAGATTAACGCTCTGGAAGGGTATCAAACAATATGTTCTTATTAGAGTCACTTATGCGTCTCTCACTTTTAATTGATATTTTGATGATGTGCATCATTAAGTCAAA--------------------
		</sequence>
		<sequence>
			<taxon idref="Oplurus_cuvieri_RAG1_JQ073188"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTATATAAACCGATCTATGGAACGATCCCCAAACTTTGTACAATATTCTAACATAGATATTATGTTCGGTGAACCAACGATCCGTCCCATTCTGGTAGCTTAGATTTGATCTTATCTGAATACTCACGCCTCTTCTATAGTTAACGCCAGGTTATGTTGGTTAACTGACACCGTTTGAAAGCAACTAGATTGTACAAACACCTGCTATTAGTCTAAACTATACCTCTTTGTTAACGACCGCGCTCCCAGTTGACTAGTGGGGCTCCTGTTTAGTCAGGGTTAGTTTGTTTAATCGCTCTCTATATTAACGCGTTAGCACCTAAAAGAGAGGATTCACCAGGGCAGTAAGGTGTTCAGCGCGGTGAACTAAAGTGGAGATCAACGTTTTGGAAGGGTATTCAACAAGACATTTTTATTAGGGTAACTCATGCGTCTCTCACTTTTAATTAATATTTTGATGATGTGCATCACTAAGTCGAAATTAGATCA-----------
		</sequence>
		<sequence>
			<taxon idref="Anolis_equestris_RAG1_JN112653"/>
			-AGAATGGATTT-----CCTAAAGATTGCACTGAGTTGGTGGATACTAACCGGCACGGAATATCTTGCAAGTAACGACGGTCCCCTACATATTTTGACCATTAAATTGGGCTCAGAGAGAATGTTCTCATAGTTGAATTCACTTAGTTTATGTGTAGAACTCATAATTAGACAGGGGCTCGCTTTTCTACTAGGAGGACTTAGGCAAGGG-GTATTAAAGGAGTGAACCAGTAGAATCCCGGTCCCCGCTAACCTACTAGAATCGCTGCCGTCAAAAACGCACCACCCCACCAAGACTTATTCTTCTTTTGGCTGACCACCGCTATGATAAATTGGGCTGAACCCTTCACAAAACAGCCGCACATGAAAACATCGAGATAGCCAAACGAAAATTTGAAAGATCGTGTATGTGCTGACATACAATTGGACAGAAAGGCTTATTCGACGCTTTCCTCGTTAGCGTAATCTGAGACGACTACATTAGCCGATCTATGGAACGATCCTCAAACTTTGGACAATGTTCCAGCATAGATATTATGTTCGGTGAACCAACGAAGTGCCCCACTCTAGTAGCTTGGATTTGATCTCTTCCGAATACTCACGCCTCTTCTACAGTTAACGATAGGTTGTGCTGGTTAACTGTCACCGTTTGAAAGCGACTAGATTGTACAAACACCTGCTATTAATCTAAGTTACACCTTTCTCTTAACTACTGCGCTCCCAGTTTACAAATAGGGCCCCTCTTTAGTCACGGTTAGTTTGTTTAATCGCTCTCTATATCGACGTGTTACCATTTAAAAGAGAGGATTCACCAGGGCGGTGAGGTGTTCAGCGCGGTGAAC-------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Phrynosoma_mcallii_RAG1_AY662590"/>
			CAAAATGGGTTTCCTGTCCTAAA----GCACTGAGTGAGTAGACACTAACTGGCATGGAATATCATGAAAGTAACGACGGTCCCCTACATATCTTGACCATTAAATTGTGCTCAGAGAGAATGATCTCATTGTTGGACTCTCTTAGTTCGTGTGTAGAACTCATAGTTAGATAAGGTCTCACTTTTTTCCTAGGAGGATTTAGGCAAGGG-GTATTAAAAAAGTAAACCAGTAGAGTCCCGGTCCTCACTAACTTACTAGATTCGTTACCGTTAAAGACACACCACCTTACCAAGACTCATTCTTCTTTCGACTGACCGCCGCTATGATAGATTGAACTGAACTCCTCGCAGAACAGCTGCACATCAAAACATAGAGATAGCCAAACGAATATTTAGAAGATCGTGTATGCACTGACATATAATTGGATAGAGGGACCTATTCGGCATTTCTCTCACTAGCGTAATATGGAACGATTACATTAGCCGTTCCATGGAACGATCCTCAAACTTTGTACAAGGTTCCAATATAGATATTATGTTCGGTGAACCAACGACGCGTTTCACTCTGGTAACTTAGATTTGATTTCATCTGAATACTCACGCCTCTTATACAGTTAACGCTAGATCATGCTGGTTGACTGACACCGTTTGAAAGCGACTAGATTGTACCAACATCTACTCTTGGATTAAGCTACACTTCTCCGTTAACGACCGTGTTCCCTGTTAACAAGTGAGAACCCTGTTTAGTCAGGGTTAGTTTGTTTAATCGCTTTCTATATCGATGTGTTAGCATTTAAAAGAGAGGATTCACCAGGGCGGTGAGGTGTTCAGCGCAGTGAATTAAAGTGGATACTAACGCTCGGGAAGGGTATCCAACAAAACGTTCTCGCTAGGACAACTCATGCGTCTCTCACCTTTAATTAATCTTTTGATAATGTGCAACATT----------------------------
		</sequence>
		<sequence>
			<taxon idref="Chalarodon_madagascariensis_RAG1_JQ073189"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCTATAAACCGATCTATGGAACGATCCCCAAACTTTGTACAATATTCCAACATAGATATTATGTTCGGTGAACCAACGATCCGTCTCATTCTGGTAGCTTAGCTTTGATCTTATTTGAATATTCACGCCTCTTCTATAGTTAACGCCAGGTTAYGCTGGTTAACTGACACCGTTTGAAAGCAACTGGATTGTACAAACACCTACTATTAGTCTAAACTATACCTCTTTGTTAACGACCGCGCTCCCAGTTGACAATTGGGGCTCCTGTTTAGTCAGAGTTAGTTTGTTTAATCGCTCTCTATATTAACGTGTTAGCACCTAAAAGAGAGGATTCACCAGGGCAGTAAGGTGTTCAGCGCGGTGAACTAAAGTGGAGATCAACGTTTTGGAAGGGTATTCAATAAGACGTTTTTACTARGGTAACTTATGCGTCTCTCACTTTTAATTAATATTTTGATGATGTTCGTCACTAAGTCGAAA-------------------
		</sequence>
		<sequence>
			<taxon idref="Uranoscodon_superciliosus_RAG1_JF806215"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTATTAGCCGTTCTATGGAATGATCCTCTAACTTTATACTATGGTCCAACATTGATATCATGTACGGTGAACCAACGATGCGTCCCACTCTGGTAGCTTAGATCTGATCTTATCTGAATACTCACGCTTCTTCTACAGTTAAGGCTAAGTTATGCTGGTTAACCAACACCGCTTGAAAGCGACTAGATTGTACAAACACTTGCTATTAGTCTAAGCTGCACTTCTTTGTTAACGACTGCGCTCCCAATTTACAAATGGGGCCCCTGTTTACTCAGGATTAGTTCGTGTAATCGCTCTTTATATCGAGGTGTTACCACCTAAAAGAGAGGAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiosaurus_catamarcensis_RAG1_JF806207"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCTCTATTAGCCAATCTATAGAACGATCCTCAAACTTTGTACAATGTTTCAACATAGATATTATGTTCGGTGAACCAACGATGTGTCCCACACTGGTAGTTTAGATTTGATCTCAGCCGAATACTCACGCCTCTTCTACAGTTAACGCTAAGTTATGCTGGTTAACTGTCACCGTTTGAAAGCGATTAGATTGTATAAACACCTGCTATTAGTCTAAGCTATACTTTTTTGTTAACGACCGCGCTCCCAGTTGACAAGTGGGGCCCCTGTTTAGTCAGGATTAGTTTGTTTGATCGCTCTCTATATCGACGTGTTAGCATTTAAAAGAGAGGAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Uma_scoparia_RAG1_JF806214"/>
			-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATTACATTAGCTGTTCTATGGAACGATCCTCAAACTTTGTATAAGGTTCCAATATAAATATTATGTTCGGTGAACAAACGATGCGTTTCACTCTGGTAACTTAGATTTGATTTCATCTGAATACTCACGCCTCTTATACAGTTAACGCTAGATCATGCTGGTTGACCGACACCATTTGAAAGCGACTAGATTGTACCAACATCTACTCTTAGAGTAAGCTACACTTCTTCGTTAACGACCGTGTTCCCTGTTAACAAGTGAGACCCCTGTTTAGTCAGGGTTAGTTTGTTTGATCGCTTTCTATATCGACGTGTTAGCATTTAAAAGAGAGGGTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_basiliscus_RAG1_JF806202"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCCATTAGCCGATCTATGGAACGATCCTTAAACTTTGTACAATGTTTCATCATAGATATTTTGTTCGGTGAACCAACGATGCGTCTCGYTCTGGTAGCTTAGATTTGATCTCATCTAAATACTCACGCCTCTTCTACAGTTAATGCTAAGTTATGCTGGTTAACTGACACCGTTTGAAAGCGACTAGATTGTACGAGCACATACTATTAGTCTAAGCTATACTTCCCGGTTAACGGCAGCGCTTCCAGTTGACAAGCGGGACCCTTGTTTAGTCAGGGTTAGTTTGTGTGATCGCTCTCTATATCGATGTGTTACCACCTAAAAGAGAGGAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_carinatus_RAG1_AY662598"/>
			CAGAATGGATTTCCTGTCCTAAAGATTGCACTGAGTGGGTAAAGGCTAACTGGCATCGAATATTTTGCCAGTAACGACGGTCCCCTACATATCTTGACCATTAAATTGTGCTCAGAGAGACTGATCTCATTGGTGAACTCACTTGGTTCTTGTGTAGAACTCATAACTAGACAGGGTCTCACTTTTCTGCGAGGAAGACTTAGGCAAGGC-GTATTAAAGGAGTAGACTGGTAGAGTCCCGATCCTCGCTAACTTGCTAGACTCGCTGCTGTCAAAAGCGCGCCACCCCACCAAGACTCATTCTTCTTTTGGCTCATCGCTGTTATGATAGATTGGGCTGAACCCTTCACGGAACAACTGTACATCAAAACATTGAAATAGCCAAACAAAAATTTGAAAGATCATGTCTGCAGTGAGATACGACTGAATAGAGATACAGATTCGACACTTTTCTCGTTAGCGTAATATGAGTCGAGTCTATTAATCGATCTATGGAGCGATCCTCAACCTTTATACAATGTTCCAACACAGATATTATGTTCGGTGAACCGACGATGCGTCCCACTTTAGTAGCTTCGATTTGATTTTATCTAAATACTCACGCTTTTTCTACAGTTAACGATAGGTTGTGCTGGTTAACCGACACTGTTTGAAAGCGACTAAATTGTACAAGCACCTGCTATTAGTCTAAGTAACACCTCTCTGTTAACGATTGCGCTCACAGTTAACAAGTAGGACCCCGGTTTAATCAGGGCTAGCTTGTTTAATCGCTCTCTATATCGACGTGTTACCACTTAAAAGAGGGAATTCACCAGAGCGGCAAGGTGTTCAGCGCGGTGAATTAAAGTGGACACCAACGCTCTAGACGGGTATCCAACAAAATGTTCTTAGTAGAGTAACTCATGCATCTCTCATTTTTAATTAATATTTTGATGATGTGCATCGCT----------------------------
		</sequence>
		<sequence>
			<taxon idref="Leiocephalus_raviceps_RAG1_FJ356744"/>
			CAGAATGGATTTCCTGTCCTAAAGATTGCACTGAGTGGGTAAAGGCTAACTGGCATCGAATATTTTGCCAGTAATGACGGTCCCCTACATATCTTGACCATTAAATTGTGCTCAAAGAGACTGATCTCATTGGTGAACTCAATTAGTTCTTGTGTAGAACTCATAATTAGAGAGGGTATCACTTTTCTGCGAGGAAGACTTAGGCAAGGT-ATATTAAAGGAGTACACTGGTAGAGTCCCGGTCCTCGCTAACTTGCTAGACTCGCTGCTGTCAAAAGCGCGCCACCCCACCAAGACTCATTCTTCTTTTGGCTCATCGCCGTTATGACAGATTGGGCTGAACCCTTCACAAAATAACTGTACATCAAAACATTGGAATAGCCAAATAAAAATTTGAAAGATCATGTTTGCAGTGAGATACGACTGGATAGAGATACAGATTCGACACTTTGCTCGCTAGCGTAATATGAGTCGAGTCTATCAACCGATCTATGGAACGATCCTCAATCTTTATACAATGTTCCAACACAGATATTATATTCGGTGAACCGACGATGTGTCCCACTTTGGTAGCTTCGATTTGATTTCATCTAAATACTCACGCTTTTTCTATAGTTAACAATAGGTTGTGCTGGTTAACTGACACTGTTTGAAAGAGACTAAATTGTACAAGCACCTGCTATTAGTGTAAGCTACACCTCTCTGTTAACGATTGCGCTCACAGTTAACAAGTAGGACCCCGGTTTAATCAGAGCTAGCTTGTTTAATCGCTCTCTATATCGACGTGTTACCATTTAAAAGAGGGAATTCACCAGAGCGGCAAGGTGTTCAGCGCGGTGAATTAAAGTGGACACCAACGCTCTAGACGGGTATCCAACAAAATGTTCTTAGTAGAGTAACTCATGCATCTCTCATTTTTAATTAATATTTTGATGATGTGCATCGCTAAGTCGAAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Basiliscus_galeritus_RAG1_FJ356743"/>
			CAAAATGGATTTCCTGTCCTAAAGATTGAACTGAGGGTGTAGACACTAACCGGCATTGAATGTCTTGCAAGTAACGACGGTCCCCTACATATCTTGACCATTAATTTGTGCTCAGAGAGAATGATCTCATTGTTGAGCTCACTAAGTTCGTGTGTAAAACTCATAATTAGACAGAGTCTCACTTTTCTCCTAGGAGGACTTAGGCAGGGG-GTATTAAAAGAGAAAACCAGTGGAATCCCGGTCTTCGCTAACTCCCTAGACCCGCTGCCATCAAAGACGCATCACCCTACCAAGACTCATTCTTCTTTTGGCTGACCGCCGCTATGATAGATTGGGCCGAACTCTTCACAGAACAGGTGCACATCAAAACATAGAGATAGCCAAACGAAAATTTGAAAGATCGTGTATGCAGTGACATACAATTGGATAGAGGGACTTATTCGACACTTTCCTCGCTAGCGTAATATGAGACGACTCCATTAGCCGATCTGTGGAACGATCCTCAAACTTTGTACAATGTTTCACCATAGATATTCTGTTCGGTGAACCAACGATGCGTCTCGCTCTGGTAGCTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAGTTAATACTAAGTTATGCTGGTTAACTGACACCGTTTGAAAGCGACTAGATTGTACAAGCACATACTATTAGTCTAAGCTATACTTCCCGGTTAACAGCAGCGCTCCCAGTTGACAAGCGGGGCCCTTGTTTAGTCAGGGTTAGTTTGTGTTATCGCTCTCTATATCGATGTGCTACCACCTAAAAGAGAGGATTCACCAGGGCGGTCCAGTGTTCAGCGCGGTGAATTAAAGTGGACACCAACGCTCTGGAAGGGTATCCGACAAAACGTTTTTATTGGGGTAACTCATGCGTCTCTCACCTTTAATTAGTATTTTGATGATGTGCATCACTAAGTCAGAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Pristidactylus_scapulatus_RAG1_JN112660"/>
			-AGAATGGATTTCCTGTCCTAAAGATTGCACTGAGTGAGTAGACACTAACTGGCATTGAATATCTTGCAAGTAACGACGGTCCCCTACGTATCTTGACCATTAAATTGTGTTCAGAGAGAATGATCTCATCGTTGAACTCACTTAGTCCGTGTATAGAACTCATAATTAGATAGGGTTTCGCTTTTCTCTTAGGAGGACTTAGGCAAGGG-GTATTAAAGGAGTAAACTAGTAGAGTCCTGGTCCTCGCTCACTTACTAGACTCGCTGCCGTTAAAAACATACCACCCTACCAAGACTCATTCTTCTTTTGGCTGACCGCCGCTATGATAGATTGGGATGAACTCTTCACAGAACAGCTTCACATCAAAACATAGAAATAGCCAAACGAAAATTTAAAAGATCGTGTATGCAGTCGCATACATTTGGATAGAGGAACTTATTTGACACTTTCCTCGCTAGCGTAATATGAGACGACTATATTAGCCAATCTATAGAACGATCCTCAAACTTTGTACAATGTTTCAACATGGATATTATGTTCGGTGAACCAACGATGTGTCCCACACTGGTAGTTTAGATTTGATCTCAGCTGAATACTCGCGCCTCTTCTACAGTTAACGCTAAGTTATGCTGGTTAACTGTCACCGTTTGAAAGCGATTAGATTGTATAAACACCTGCTATTAGTCTAAGCTATACTTTTTTGTTAACGACCGCTATCCCAGTTGACAAGTGGGGCCCCTGTTTAGTCAGGGTTAGTTTGTTTGATCGCTCTTTATATCGACGTGTTAGCACTTAAAAGAGAGAATTCACCAGGGCAGTAAGGTGTTCAGCGCGGTGAATTAAAGTGGACACCAACGCTTTAGACGGGTATCCAACTAAACGTTCTTATCAGGGTCACTCATTCGTCTTTCACTCT---------------------------------------------------------
		</sequence>
		<sequence>
			<taxon idref="Diplolaemus_darwinii_RAG1_JQ073190"/>
			------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTATATTAGCCAATCTATAGAACGATCCTCAAACTTTGTACAATGTTTCAACATGGATATTATGTTCGGTGAACCAACGATGTGTCCCACACTGGTAGTTTAGATTTGATCTCAGCTGAATACTCACGCCTCTTCTACAGTTAACGCTAAGTTATGCTGGTTAACTGTCACCGTTTGAAAGCGATTAGATTGTATAAACACCTGCTATTAGTCTAAGCTATACTTTTTTGTTAGCGACCGCGCTCCCAGTTGACAAGTGGGGCCCCTGTTTAGTCAGGGTTAGTTTGTGTTATCGCTCTCTATATCGATGTGCTACCACCTAAAAGAGAGGATTCACCAGGGCGGTCCAGTGTTCAGCGCGGTGAATTAAAGTGGACACCAACGCTCTGGAAGGGTATCCGACAAAACGTTTTTATTGGGGTAACTCATGCGTCTCTCACCTTTAATTAGTATTTTGATGATGTGCATCACTAAGTCAGAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Morunasaurus_annularis_RAG1_FJ356741"/>
			CAAGATGGATTTCCTGTCCTAAAGATTGCACTGAGTGGGTAGACACTAAATGGCATTGAATATTTTGCAAGTAACGACTGTCCCCTACATATTTTGACCATTAAATTATGCTTAGAGAGAATGATCTCATTGTTGAACTTACTTAGTTCATGTGTAGAATTTATAGTTAGACAGGGTCTCGCTTTTCTTCTAGGAGGAGTTAGGCAAGGG-GTATCAAGGGAGTAGACCAGTGGAGTCCCGGTCCTCGCTAACTTGCTAGACTCGCTACCGTCAAAAGCGCACCACCCGACCAAGACTCATTCTTCTTTTGGCTGACCGCCGCCATGGTAGATCGGGCTGAACTCTTCACAGAACGGCTGCACATCAAAACATAGAGATAGCCAAACGAAAATTTGAAAGATCGTGTATGCAGTGACATACAATTGGATAGAGGGACTTATTCGACACCTTCCTCGCTAGCGTAATACGAGACGACTATATTAGCCGATCTATAGAACGATCCTCAAACTTTGTATAATGTTTCAGCACAGATATTATGTTCGGTGAACCAACGATGCGTCCCACCCTGGTAGCTTAGATTTGATCTCATCTGAATACTCACGCCTCTTCTACAGTTAACGCTAGGTTATGCTGGTTAACCGACACCGTTTGAAAGCGACTAAATTGTACAAACACCTGGTATTAGTCTAAGCTACACTTCTCTGTTAACGACCGCGCTCCCAGTTGACAAGTGGGGCCCCCGTTTAGTCAGGGTTAGCTTGTTTGATCGCTCTCTATATCGACGTGTTACCACTTAAAAAAGAGGATTCACCAGGGCGGTAAGGTGTCCAGCGCGGTGAACTGAAATGGACACCAACGCTCTAGGAGGGTATCCAACAACACGTCTTAATTAGAGTAACTCATGCGTCTCTCATTTTTAATTAATGTTTTGATGACGTGCATCACTAAGTTGAAACTAGATCAG----------
		</sequence>
		<sequence>
			<taxon idref="Petrosaurus_mearnsi_RAG1_HQ876437"/>
			-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTACATTAGCCGATCTATGGAACGATCCTCAAACTTTGTACAAGGTTCCAATATAGATACTATGTTCGGTGAACCAACGATGCGTCCCACTCTGGTAGCTTAGATTTGATTTCATCTGAATACCCACGCCTCTTATACAGTTAACGCTAGATCAAGCTGGTTGTCCGACACCGCTTGAAAGCGACTAGATTGTACCATCATCTACTCTTAGATTAAGCTACATTTCTCGGTTAACGACCGTGCTCCCTGTTAACAAGTGAGGCCCCAGTTTAGTCAGGGTTAGTTTGTTTGATCGCTCTCTATATCGACGTGTTAGCATTTAAAAGAAAGGATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------
		</sequence>
	</alignment>

	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=281                                                           -->
	<patterns id="position_1.patterns" from="1" strip="false">
		<alignment idref="alignment1"/>
	</patterns>

	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=225                                                           -->
	<patterns id="position_2.patterns" from="1" strip="false">
		<alignment idref="alignment2"/>
	</patterns>

	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=607                                                           -->
	<patterns id="position_3.patterns" from="1" strip="false">
		<alignment idref="alignment3"/>
	</patterns>

	<!-- A prior on the distribution node heights defined given                  -->

	<!-- Stadler, T; On incomplete sampling under birth-death models and connections to the sampling-based coalescent;
JOURNAL OF THEORETICAL BIOLOGY (2009) 261:58-66-->
	<birthDeathModel id="birthDeath" units="years">
		<birthMinusDeathRate>
			<parameter id="birthDeath.meanGrowthRate" value="0.2" lower="0.0"/>
		</birthMinusDeathRate>
		<relativeDeathRate>
			<parameter id="birthDeath.relativeDeathRate" value="0.5" lower="0.0"/>
		</relativeDeathRate>
		<sampleProbability>
			<parameter id="birthDeath.sampleProbability" value="0.01" lower="0.0" upper="1.0"/>
		</sampleProbability>
	</birthDeathModel>

	<!-- This is a simple constant population size coalescent model              -->
	<!-- that is used to generate an initial tree for the chain.                 -->
	<constantSize id="initialDemo" units="years">
		<populationSize>
			<parameter id="initialDemo.popSize" value="100.0"/>
		</populationSize>
	</constantSize>

	<!-- Construct a starting tree that is compatible with specified clade heights-->
	<rescaledTree id="startingTree">

		<!-- The user-specified starting tree in a newick tree format.               -->
		<newick usingDates="false">
			((Polychrus_marmoratus_RAG1_FJ356748:30.343504000000003,(Hoplocercus_spinosus_RAG1_AY662592:15.381447950000002,(Morunasaurus_annularis_RAG1_FJ356741:7.484446977999994,Enyalioides_laticeps_RAG1_GU457971:7.484446977999994):7.897000971000004):14.962056050000001):45.656496,((Dipsosaurus_dorsalis_RAG1_FJ356747:27.484364069999998,Sauromalus_ater_RAG1_AY662591:27.484364069999998):29.06560599,((((Uranoscodon_superciliosus_RAG1_JF806215:11.805570059999994,Stenocercus_guentheri_RAG1_HQ876440:11.805570059999994):11.813589649999997,(Gambelia_wislizenii_RAG1_HQ876434:11.848092550000004,Crotaphytus_collaris_RAG1_FJ356749:11.848092550000004):11.771067160000001):13.279316569999999,((Anolis_cupreus_RAG1_JN112651:11.841655239999994,Anolis_equestris_RAG1_JN112653:11.841655239999994):11.850672459999998,(Leiocephalus_raviceps_RAG1_FJ356744:11.883760719999998,Leiocephalus_carinatus_RAG1_AY662598:11.883760719999998):11.808566979999995):13.206148579999997):13.522271260000004,(((Basiliscus_basiliscus_RAG1_JF806202:17.52252289999999,Basiliscus_plumifrons_RAG1_HM161150:17.52252289999999):17.20293969,(Basiliscus_galeritus_RAG1_FJ356743:17.115127810000004,Corytophanes_cristatus_RAG1_JF806205:17.115127810000004):17.610334780000002):6.411221036999997,(((Petrosaurus_mearnsi_RAG1_HQ876437:13.631899650000001,Uta_stansburiana_RAG1_JF806216:13.631899650000001):13.82088736,(Phrynosoma_mcallii_RAG1_AY662590:13.692101309999998,Uma_scoparia_RAG1_JF806214:13.692101309999998):13.760685700000003):13.600634939999999,((Liolaemus_lineomaculatus_RAG1_FJ356740:20.384401829999995,(Phymaturus_palluma_RAG1_JF806209:10.262907209999995,Phymaturus_somuncurensis_RAG1_AY662594:10.262907209999995):10.121494629999994):20.58576642,((Oplurus_cuvieri_RAG1_JQ073188:20.788069370000002,(Chalarodon_madagascariensis_RAG1_JF806204:10.144495939999999,Chalarodon_madagascariensis_RAG1_JQ073189:10.144495939999999):10.643573430000004):20.098839999999996,(Diplolaemus_darwinii_RAG1_JQ073190:20.499635389999995,(Pristidactylus_scapulatus_RAG1_JN112660:10.400365609999994,(Pristidactylus_torquatus_RAG1_JF806210:5.076475274999993,(Leiosaurus_catamarcensis_RAG1_JF806207:2.528304535999993,Urostrophus_gallardoi_RAG1_JN112661:2.528304535999993):2.5481707389999997):5.323890337999998):10.09926978):20.387273980000003):0.08325888117000346):0.08325369907999658):0.0832616721000008):9.284063905000004):6.129222528999996):19.45002994);
		</newick>
	</rescaledTree>

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

	<!-- Taxon Sets                                                              -->
	<tmrcaStatistic id="tmrca(Corytophanidae)" includeStem="false">
		<mrca>
			<taxa idref="Corytophanidae"/>
		</mrca>
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>
	<tmrcaStatistic id="tmrca(Chalo_Uros)" includeStem="false">
		<mrca>
			<taxa idref="Chalo_Uros"/>
		</mrca>
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>

	<!-- Generate a speciation likelihood for Yule or Birth Death                -->
	<speciationLikelihood id="speciation">
		<model>
			<birthDeathModel idref="birthDeath"/>
		</model>
		<speciesTree>
			<treeModel idref="treeModel"/>
		</speciesTree>
	</speciationLikelihood>

	<!-- The uncorrelated relaxed clock (Drummond, Ho, Phillips & Rambaut (2006) PLoS Biology 4, e88 )-->
	<discretizedBranchRates id="branchRates">
		<treeModel idref="treeModel"/>
		<distribution>
			<logNormalDistributionModel meanInRealSpace="true">
				<mean>
					<parameter id="ucld.mean" value="1.0" lower="0.0"/>
				</mean>
				<stdev>
					<parameter id="ucld.stdev" value="0.3333333333333333" lower="0.0"/>
				</stdev>
			</logNormalDistributionModel>
		</distribution>
		<rateCategories>
			<parameter id="branchRates.categories"/>
		</rateCategories>
	</discretizedBranchRates>
	<rateStatistic id="meanRate" name="meanRate" mode="mean" internal="true" external="true">
		<treeModel idref="treeModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</rateStatistic>
	<rateStatistic id="coefficientOfVariation" name="coefficientOfVariation" mode="coefficientOfVariation" internal="true" external="true">
		<treeModel idref="treeModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</rateStatistic>
	<rateCovarianceStatistic id="covariance" name="covariance">
		<treeModel idref="treeModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</rateCovarianceStatistic>

	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="position_1.gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="position_1.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="position_1.ac" value="1.0" lower="0.0"/>
		</rateAC>
		<rateAG>
			<parameter id="position_1.ag" value="1.0" lower="0.0"/>
		</rateAG>
		<rateAT>
			<parameter id="position_1.at" value="1.0" lower="0.0"/>
		</rateAT>
		<rateCG>
			<parameter id="position_1.cg" value="1.0" lower="0.0"/>
		</rateCG>
		<rateGT>
			<parameter id="position_1.gt" value="1.0" lower="0.0"/>
		</rateGT>
	</gtrModel>

	<!-- site model                                                              -->
	<siteModel id="position_1.siteModel">
		<substitutionModel>
			<gtrModel idref="position_1.gtr"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
			<parameter id="position_1.alpha" value="0.5" lower="0.0"/>
		</gammaShape>
		<proportionInvariant>
			<parameter id="position_1.pInv" value="0.5" lower="0.0" upper="1.0"/>
		</proportionInvariant>
	</siteModel>

	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="position_2.gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="position_2.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="position_2.ac" value="1.0" lower="0.0"/>
		</rateAC>
		<rateAG>
			<parameter id="position_2.ag" value="1.0" lower="0.0"/>
		</rateAG>
		<rateAT>
			<parameter id="position_2.at" value="1.0" lower="0.0"/>
		</rateAT>
		<rateCG>
			<parameter id="position_2.cg" value="1.0" lower="0.0"/>
		</rateCG>
		<rateGT>
			<parameter id="position_2.gt" value="1.0" lower="0.0"/>
		</rateGT>
	</gtrModel>

	<!-- site model                                                              -->
	<siteModel id="position_2.siteModel">
		<substitutionModel>
			<gtrModel idref="position_2.gtr"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
			<parameter id="position_2.alpha" value="0.5" lower="0.0"/>
		</gammaShape>
		<proportionInvariant>
			<parameter id="position_2.pInv" value="0.5" lower="0.0" upper="1.0"/>
		</proportionInvariant>
	</siteModel>

	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="position_3.gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="position_3.frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="position_3.ac" value="1.0" lower="0.0"/>
		</rateAC>
		<rateAG>
			<parameter id="position_3.ag" value="1.0" lower="0.0"/>
		</rateAG>
		<rateAT>
			<parameter id="position_3.at" value="1.0" lower="0.0"/>
		</rateAT>
		<rateCG>
			<parameter id="position_3.cg" value="1.0" lower="0.0"/>
		</rateCG>
		<rateGT>
			<parameter id="position_3.gt" value="1.0" lower="0.0"/>
		</rateGT>
	</gtrModel>

	<!-- site model                                                              -->
	<siteModel id="position_3.siteModel">
		<substitutionModel>
			<gtrModel idref="position_3.gtr"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
			<parameter id="position_3.alpha" value="0.5" lower="0.0"/>
		</gammaShape>
		<proportionInvariant>
			<parameter id="position_3.pInv" value="0.5" lower="0.0" upper="1.0"/>
		</proportionInvariant>
	</siteModel>

	<!-- Likelihood for tree given sequence data                                 -->
	<treeLikelihood id="position_1.treeLikelihood" useAmbiguities="false">
		<patterns idref="position_1.patterns"/>
		<treeModel idref="treeModel"/>
		<siteModel idref="position_1.siteModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</treeLikelihood>

	<!-- Likelihood for tree given sequence data                                 -->
	<treeLikelihood id="position_2.treeLikelihood" useAmbiguities="false">
		<patterns idref="position_2.patterns"/>
		<treeModel idref="treeModel"/>
		<siteModel idref="position_2.siteModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</treeLikelihood>

	<!-- Likelihood for tree given sequence data                                 -->
	<treeLikelihood id="position_3.treeLikelihood" useAmbiguities="false">
		<patterns idref="position_3.patterns"/>
		<treeModel idref="treeModel"/>
		<siteModel idref="position_3.siteModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</treeLikelihood>

	<!-- Define operators                                                        -->
	<operators id="operators" optimizationSchedule="default">
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.gt"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="position_1.frequencies"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.alpha"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_1.pInv"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.gt"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="position_2.frequencies"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.alpha"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_2.pInv"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.gt"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="position_3.frequencies"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.alpha"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="position_3.pInv"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="ucld.mean"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="ucld.stdev"/>
		</scaleOperator>
		<subtreeSlide size="11.0" gaussian="true" weight="15">
			<treeModel idref="treeModel"/>
		</subtreeSlide>
		<narrowExchange weight="15">
			<treeModel idref="treeModel"/>
		</narrowExchange>
		<wideExchange weight="3">
			<treeModel idref="treeModel"/>
		</wideExchange>
		<wilsonBalding weight="3">
			<treeModel idref="treeModel"/>
		</wilsonBalding>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="treeModel.rootHeight"/>
		</scaleOperator>
		<uniformOperator weight="30">
			<parameter idref="treeModel.internalNodeHeights"/>
		</uniformOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="birthDeath.meanGrowthRate"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="birthDeath.relativeDeathRate"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="birthDeath.sampleProbability"/>
		</scaleOperator>
		<upDownOperator scaleFactor="0.75" weight="3">
			<up>
				<parameter idref="ucld.mean"/>
			</up>
			<down>
				<parameter idref="treeModel.allInternalNodeHeights"/>
			</down>
		</upDownOperator>
		<swapOperator size="1" weight="10" autoOptimize="false">
			<parameter idref="branchRates.categories"/>
		</swapOperator>
		<uniformIntegerOperator weight="10">
			<parameter idref="branchRates.categories"/>
		</uniformIntegerOperator>
	</operators>

	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="1000000" autoOptimize="true" operatorAnalysis="RAG1_nucleotide_chrono.ops">
		<posterior id="posterior">
			<prior id="prior">
				<uniformPrior lower="5.0" upper="35.0">
					<statistic idref="tmrca(Corytophanidae)"/>
				</uniformPrior>
				<uniformPrior lower="40.0" upper="62.0">
					<statistic idref="tmrca(Chalo_Uros)"/>
				</uniformPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_1.ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="position_1.ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_1.at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_1.cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_1.gt"/>
				</gammaPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_1.frequencies"/>
				</uniformPrior>
				<exponentialPrior mean="0.5" offset="0.0">
					<parameter idref="position_1.alpha"/>
				</exponentialPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_1.pInv"/>
				</uniformPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_2.ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="position_2.ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_2.at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_2.cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_2.gt"/>
				</gammaPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_2.frequencies"/>
				</uniformPrior>
				<exponentialPrior mean="0.5" offset="0.0">
					<parameter idref="position_2.alpha"/>
				</exponentialPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_2.pInv"/>
				</uniformPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_3.ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="position_3.ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_3.at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_3.cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="position_3.gt"/>
				</gammaPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_3.frequencies"/>
				</uniformPrior>
				<exponentialPrior mean="0.5" offset="0.0">
					<parameter idref="position_3.alpha"/>
				</exponentialPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="position_3.pInv"/>
				</uniformPrior>
				<exponentialPrior mean="0.3333333333333333" offset="0.0">
					<parameter idref="ucld.stdev"/>
				</exponentialPrior>
				<exponentialPrior mean="10.0" offset="0.0">
					<parameter idref="ucld.mean"/>
				</exponentialPrior>
				<uniformPrior lower="0.0" upper="100000.0">
					<parameter idref="birthDeath.meanGrowthRate"/>
				</uniformPrior>
				<uniformPrior lower="0.0" upper="1.0">
					<parameter idref="birthDeath.relativeDeathRate"/>
				</uniformPrior>
				<betaPrior shape="1.0" shapeB="1.0" offset="0.0">
					<parameter idref="birthDeath.sampleProbability"/>
				</betaPrior>
				<speciationLikelihood idref="speciation"/>
			</prior>
			<likelihood id="likelihood">
				<treeLikelihood idref="position_1.treeLikelihood"/>
				<treeLikelihood idref="position_2.treeLikelihood"/>
				<treeLikelihood idref="position_3.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="rootHeight" sf="6" width="12">
				<parameter idref="treeModel.rootHeight"/>
			</column>
			<column label="ucld.mean" sf="6" width="12">
				<parameter idref="ucld.mean"/>
			</column>
		</log>

		<!-- write log to file                                                       -->
		<log id="fileLog" logEvery="1000" fileName="RAG1_nucleotide_chrono.log" overwrite="false">
			<posterior idref="posterior"/>
			<prior idref="prior"/>
			<likelihood idref="likelihood"/>
			<parameter idref="treeModel.rootHeight"/>
			<tmrcaStatistic idref="tmrca(Corytophanidae)"/>
			<tmrcaStatistic idref="tmrca(Chalo_Uros)"/>
			<parameter idref="birthDeath.meanGrowthRate"/>
			<parameter idref="birthDeath.relativeDeathRate"/>
			<parameter idref="birthDeath.sampleProbability"/>
			<parameter idref="position_1.ac"/>
			<parameter idref="position_1.ag"/>
			<parameter idref="position_1.at"/>
			<parameter idref="position_1.cg"/>
			<parameter idref="position_1.gt"/>
			<parameter idref="position_1.frequencies"/>
			<parameter idref="position_1.alpha"/>
			<parameter idref="position_1.pInv"/>
			<parameter idref="position_2.ac"/>
			<parameter idref="position_2.ag"/>
			<parameter idref="position_2.at"/>
			<parameter idref="position_2.cg"/>
			<parameter idref="position_2.gt"/>
			<parameter idref="position_2.frequencies"/>
			<parameter idref="position_2.alpha"/>
			<parameter idref="position_2.pInv"/>
			<parameter idref="position_3.ac"/>
			<parameter idref="position_3.ag"/>
			<parameter idref="position_3.at"/>
			<parameter idref="position_3.cg"/>
			<parameter idref="position_3.gt"/>
			<parameter idref="position_3.frequencies"/>
			<parameter idref="position_3.alpha"/>
			<parameter idref="position_3.pInv"/>
			<parameter idref="ucld.mean"/>
			<parameter idref="ucld.stdev"/>
			<rateStatistic idref="meanRate"/>
			<rateStatistic idref="coefficientOfVariation"/>
			<rateCovarianceStatistic idref="covariance"/>
			<treeLikelihood idref="position_1.treeLikelihood"/>
			<treeLikelihood idref="position_2.treeLikelihood"/>
			<treeLikelihood idref="position_3.treeLikelihood"/>
			<speciationLikelihood idref="speciation"/>
		</log>

		<!-- write tree log to file                                                  -->
		<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="RAG1_nucleotide_chrono.trees" sortTranslationTable="true">
			<treeModel idref="treeModel"/>
			<trait name="rate" tag="rate">
				<discretizedBranchRates idref="branchRates"/>
			</trait>
			<posterior idref="posterior"/>
		</logTree>
	</mcmc>
	<report>
		<property name="timer">
			<mcmc idref="mcmc"/>
		</property>
	</report>
</beast>
