<?xml version="1.0" standalone="yes"?>
<!-- Generated by BEAUTi v1.5.1                                              -->
<!--       by Alexei J. Drummond and Andrew Rambaut                          -->
<!--       Department of Computer Science, University of Auckland and        -->
<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
<!--       http://beast.bio.ed.ac.uk/                                        -->
<beast>
	
	<!-- The list of taxa analyse (can also include dates/ages).                 -->
	<!-- ntax=7                                                                  -->
	<taxa id="taxa">
		<taxon id="CanineOralPV"/>
		<taxon id="FelisPV1"/>
		<taxon id="LynxPV1"/>
		<taxon id="PumaPV1"/>
		<taxon id="RacoonPV1"/>
		<taxon id="AsianLionPV1"/>
		<taxon id="SnowLeopardPV1"/>
	</taxa>
	
	<taxa id="Felis/Lynx/Puma">
		<taxon idref="FelisPV1"/>
		<taxon idref="LynxPV1"/>
		<taxon idref="PumaPV1"/>
	</taxa>
	<taxa id="Lion/Leopard">
		<taxon idref="AsianLionPV1"/>
		<taxon idref="SnowLeopardPV1"/>
	</taxa>
	<taxa id="Cats">
		<taxon idref="AsianLionPV1"/>
		<taxon idref="FelisPV1"/>
		<taxon idref="LynxPV1"/>
		<taxon idref="PumaPV1"/>
		<taxon idref="SnowLeopardPV1"/>
	</taxa>
	
	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=7 nchar=1434                                                       -->
	<alignment id="alignment" dataType="nucleotide">
		<sequence>
			<taxon idref="CanineOralPV"/>
			ATGGCAAGGAAAAGACGCGCAGCCCCTCAAGATATATACCCTGCTTGTAAAGTGTCCAACACTTGCCCCGCTGATATTTTGAATAAAATGGAGCAAAATACGCTTGCAGATAAAATCCTCAAATATGGTAGTGCTGGTGTTTTTTTGGGGGGTCTAGGAATATCAACAGGCAAAGGGGTAGGGGGGCGCACAGGTTACATTCCTTTGGGAAGTGGAGTGGGTGTAGGCACAAGGGTCACAACAATAAGACCTACTGTCCCAATAAGCAGTGTGGGGTCTCCTGACTTTATTCCTGTAGATGCAGTAGACCCTCTAGGGCCTGCAGTCATACCCCCAGAAAGATTTCCTATAGCAGTAGAGGATCCTTTTACTCTACCTCCACCACGTTTCCCAACTGCAGTAGAAGAAGATGTAATTGAGCTGCAGCCTATTGGCCCTAAGATTACCACTGATGCTCAGCCTGCAATATTGGAAGTCATACCAGAGACTAGGCCTCCTAAAGTAATCACTAGGCATCAGTACAGTAACCCTGCATTTGAGGTGTCCATTACTTCTAACTCTGGTGCAGGGGAGTCTTCTGCTTCTGACCATGTGCTGGTGGAAGGTTTTTCTGGTGGCCACTCAATTGGTGAACACATTCCATTGCAAGACCTTGCACCCAGCAGGTCATTCTCTGAGACCATAGAAGATGAAACTGCTTTTAGCAGCAGTACTCCTAAACAAGGCAGTTACTATAATAGGCGAAGATATCAGCAAGTACAAGTTACTGACCCTGTGTTTATTTCAAGACCACGGTCACTTGTCACGTTTGATAACCCAGCCTTTGATGAATCTGTTGACCTGATATTTGAAAGAGATGTTGCAGAAATAACT---GCAGCACCTCATGCAGACTTTACAGATATCACAAAGCTCACAAAGCCTGCATATCACAGAGGCCCATCTGGCCATGTCCGTGTCAGTAGGCTTGGACATAGAGCTAATATAAAAACTAGAAGTGGTCTTACAATAGGGCCACAAAGCCATTTTTACTACGATGTCAGCAGCATTGACCCTGCAGAATCTTTTGAGCTGCAGGCACTTGGCAATGTATCCAGTGCTGAACAAACAGGAGAAGCAGTAATCTCCTCTGGCACAGGAGACTTTGAAATTATAAGCCTTTACAATGATGAGGATTTAATAGACGTGTTTGAGGATGTAGCTAGAGATTTGCATTTATTAGTTGGAGAAAGAAGG---CAGCAACCGATCCAAGTTCAACGTTACATAAAGCCTTTTTCTTTTGTTGAGGGAGTACACATATCAGATTTTTGGCTGCCTCCTGTAACGCCTGACAGCACACCTGCAATAGTGATTGACATTTTGGACTCCTCTGCAGATTACTATCTGCATCCAAGTTTAATAAAAAAACGCAAACGCAAACATTTTTTTTTT
		</sequence>
		<sequence>
			<taxon idref="FelisPV1"/>
			ATGCTTAGGCAAAAACGTGCAGCCCCAAAAGATATTTACCCACAATGCAAGATATCCAACACCTGCCCGCCCGACATCCTGAATAAAGCTGAGCAAAACACGCTTGCAGATAAAATTTTAAAATATGGCTCTGCTGGTGTTTTTTTGGGGAGTCTGGGTATTGGGACGGGGCGTGGGACCGGGGGATCCTTGGGCTATGTGCCATTAGGCCAGGGGGTGCGTTTGGGGACTCGGGTGACTACAGTTAGGCCCACCCTGCCTGTGAGTAGTGTAGGCACTACAGATGTAATCCCTGTGGACGCTGTGGATCCTTTGGGGCCTGCAGTGCTTCCAGGCAGAATTTTTCCAACAGCTGTAGAAGATCCTGTCACTATTCAGCCCCCTAGATTTCCCTCTGTGGTGGACGAA---CCTGTAACTGTCTCCACACCCACACCTAAGGTGACCACAGATGCACAGCCTGCAGTGCTGGAAGTTGTCCCTGAAACCCGAGAGCCCAGAATTTTGTCCAGGACTCAATACAGTAATCCAGCCTTTGAGGTGTCCCTGACGGCTTCTGCAGGGTCTGGGGAAACATCTGCCTCGGACCATATTCTTGTAGATGCATTTTCAGGGGGACAGGTCATAGGTGAGCAGATACCCCTGCAGGAACTGGGTACT---AGGTCATTCTCCACAACTATTGAGGAGGAAACCACTTTTACAACTAGTACACCTAGGACAGAGAGGGTCTTCACATCCAGGCGGCTGCAGCAGGTTCGGGTGCAGGACCCCACTTTCTTAAGTCATCCGAGGTCACTGGTAACCTTCCAAAACCCAGTATTTGATGAGTCAGTAGACTTGCTGTTCGAACAAGACGTGGCGGAGCTAGCTTTGGCAGCTCCAAATGAAGATTTCAGGGACTTGGTGTCTCTCTCCAAGCCCTACTTTTCGCGCACGCAAGAGGGTAGAGTGAGGATAAGCAGGCTAGGTACCAAAGCCACTATGCGTACGCGGAGTGGTCTTGTTATTGGTCCACAAAGCCATTACTATTATGACCTTAGCGATATAGCTCCTGCAGAAAACTTAGAATTAACCCCCATAGGCGACATGTCTTTGGGAGAGCAATCTGGGCAAGCCGTCATTTCCTCTGGCACGAGCGACATGGAGATTATAAGCTTGTACCCTGAGGAGTTTTTACTTGACGAGATCGAATCCGTTGCCAATGATTTGCAGCTGGTAATTGGAGACAGACGGGCGCAGCAACCGATTTCGGTTCCAAACTTGCAAAGGCCTAGCCCGCAGGTGGAAGGCGTGCATGTGGCAGGGCCCCCTGCCATTCCCACGGACCCTACAAAAACACCAGCTATTGTCATAGAAGTATGGGCATCAGGGGCTACTTATTCTCTGCACCCATCTTTGTTGCGAAAAAGAAAACGCAAACGCATTTCTTTG
		</sequence>
		<sequence>
			<taxon idref="LynxPV1"/>
			ATGCTACGGCGAAAACGTGCAGCCCCCCATGATATCTACCCCCAATGCAAAATCTCCAACACCTGCCCGCCCGATATTCTCAATAAAGCTGAGCAAAACACGCTTGCAGATAAAATTTTAAGATATGGCTCTGCTGGTGTTTTTTTGGGTAGTTTGGGGATTGGTACAGGGCGTGGGTCTGGGGGGACATTAGGCTATGTGCCTGTTGGCCAGGGGGTGAGATTGGGAACGAGGGTGACCACAGTGAGGCCCACCCTGCCAATCAGCAGTGTTGGCAGTGCTGATGTGATCCCTATTAATGCAGTGGATCCTTTGGGGCCTGCAGTGCTTCCAGGTGATTATTTTCCCACTGCTGTAGAAGATCCTGTTGTCATACAGCCCCCACGGTTTCCTTCTGTTGTGGAGGAC---CCTGTGCCCGCGCAGTCCGAAACGCCCAAGGTGACCACTGATGGGCAACCAGCTGTCCTGGAAGTAGTTCCTGAGACTAGAGAGCCACGCATACTCTCCAGAAGCCAGTACAGCAATCCCGCTTTTGAGGTCTCTCTCACTGCATCTGCAGGGTCGGGCGAAACCTCCGCCTCCGACCACATTGTGGTTGAGGGCTTCAACGGGGGCCATGTTATAGGGGAGCAAATACCACTGAGGGAATTGGGGACT---AGGTCATTTTCCACTACTGTTGAA---GAAACATCCTTCAGCACAAGCACACCTAGGACCGATAGGGTCCTGCAAGGCAGACGCATCCAGCAGGTCCGTGTGCACGACCCCAGCTTCTTGGACAGACCACGGTCCTTGGTCACGTTCCAGAACCCAGCTTTTGATGAGTCAGTGGACCTTCTGTTTGCACAAGATGTGGCAGATATTGCTTTGGCAGCACCCCATGAAGATTTTAGGGATTTGGTATCTCTCAGCAAACCGATATTTTCCCGTACCCAGGAGGGGCGGGTGCGGGTTAGCCGCCTGGGTACTAAGGGCACAATGCGTACACGCAGTGGCCTGGTCATAGGGCCGCAGAGCCACTACTTTTATGACCTCAGTGATATTGCTCCTGCAGAAAACCTAGAATTATCCCCTGTAGGCAATATGTCTTTAGGTGAACAAACAGGACAGGCTGTCGTTTCCTCTGGCACGAGTGACATGGAGATTATTAGCCTATATCCTGAGGAGGTTTTGCTAGATGAAATCGAATCCGTTGCCAACGACCTGCAGCTAGTGTTTGGAGACAGAAGGGCTCAGCAACCGATTTCGGTCCCGCACATACAAAGACCTAGCCCTCAGGTGGAGGGCGTGCATGTGTCATTGCCCCCTTCCATTCCCACAGTGCCTGACAAAACACCAGCTATTCTCATAGAAATCTGGGATTCAGGGTCTAATTACTCACTGCATCCCTCTTTGCTAAAAAAGAGAAAACGCAAACTGCTTTTTCTG
		</sequence>
		<sequence>
			<taxon idref="PumaPV1"/>
			ATGCTTAGGCGAAAACGTGCAGCCCCCAAAGATATTTACCCCCAATGCAAAATCTCCAACACCTGCCCACCCGATGTACTCAATAAAGCTGAGCAAAGCACGCTTGCAGATAAAATTTTAAAATATGGCTCTGCTGGTGTTTTTTTGGGGAGTCTGGGAATTGGTACGGGGCGTGGGTCAGGGGGAACTTTGGGATATGTGCCTGTGGGACAAGGGGTTCGCCTGGGAACACGTGTGTCAACTGTGAGGCCCTCATTGCCAATAAGCAGTGTGGGCACTGCAGATGTCATTCCCATAGATGCAGTAGATCCTTTGGGGCCTGCAGTGCTACCTGGCAATGTGTTTCCCACAGCTGTTGAAGACCCCTTCACAATTCAGCCCCCACGCTTTCCTTCTATTGTTGAAGAG---CCTGTGAGTGTGCACTCTGAAACACCCAAGGTGACCATAGATGGTCAGCCTGCTGTGCTGGAAGTAGTCCCTGAAACCAGAGAACCACGTATCTTGTCCAGAAGCCAGTATGGGAACTCAGCTTTTGAAGTATCTCTCACAGCCTCTGCAGGGTCAGGTGAAACTTCATCCTCAGACCACATTTTAGTGCATGGCTTCACAGGGGGCCATGTTATCGGAGAACAGATTCCCTTGCAAGAATTGGGGGGT---AGATCCTTTTCTAGTACCCTAGAGGCAGAAACAACCTTCACCACAAGCACACCTAAGGCGGATAGGGTCTTCACATCCAGGCGGCTGGAGCAAATTCCAGTGCGTGACCCCGGTTTCATAAGCAGGCCCAGGTCTTTGGTGACATTCCAGAACCCCACATTTGATGAGTCAGTGGACTTGTTCTTTGAAAGGGACGTGGCAGAGCTTGCTCTGGCAGCCCCGAATGAGGATTTTAGAGACTTGGTGTCTCTAAGTAAACCCACCTTTTCTCGCACCCTGGAGGGGAGGGTGAGAGTCAGCCGGCTAGGAACTAAGGCCACTATGCGTACGCGCAGTGGTCTGGTCATAGGTCCACAAAGCCACTACTACTACGACCTTAGTGATATTGCACCTGCAGAAAACCTCGAATTAACCCCCATAGGCAACATGTCTTTGGGTGAACAATCAGGCCAGGCTGTCATTTCCTCTGGCACCAGTGATCTAGAGATTATCAGCTTGTACCCGGAGGAGTTTTTACTTGCTGAAATAGAGTCTGTTGCCAATGATCTGCAGCTGGTGTTTGGAGACAGAAGGGCGCAGCAACCGATTTCGGTCCCGCACATACAAAGACCTAGCCCTCAGGTGGAGGGAGTGTATGTGTCGGTGCCCCCTACCATTCCCACGGATCCTAACAAAACACCAGCCATAATTCTAGAGATTTGGGGCTCAGGGGAAAATTACTCCCTGCACCCATCTTTGCTGAAAAGGCGAAAACGCAAACGGCTCATTTTG
		</sequence>
		<sequence>
			<taxon idref="RacoonPV1"/>
			ATGACTCGCAAACGCCGCGCCGCTCCTCGTGATATATACCCCTCTTGCAAACTGGCAAATACTTGTCCTCCTGATATTGTCGACTCGATTGAAAATAATACTTTGGCAGATAAGATCCTAAAATATGGTAGTGCTGGTGTTTTTTTTGGGAGTCTGGGGATTGGCACTGGGAGGGGTACTGGGGGTAGCACTGGCTACATTCCTCTGGGAGCTGGGGTGCGGCTGAACACGAGGGTGTCCACAGTGAGGCCTAGCTTGCCCATAAGCAGTGTACATCCCACTGATGTCATTCCAGTCGATGCTGTGGATCCTTTGGGTCCTGCAATCGTCCCATTATCAGAGCTGCCCTCCATAGTTGAGGACCCGGATCCTATACTACCCCCTCGCTTTCCCACTGCTGTTGAGGAAAGTGTCATAGACTTTTCACCTGCTTCTCCAAAGGTCACCACAACAGACACCTCAGCACTCATAGAGGTTACTCCTGAAACGAGGCCTCCCAGAATAATATCCAGATCACAGTACTCTAATCCATCATTTGAGGTGCACATCACATCTACATCGGGGTCTGGGGAGTCCTCTGCAGTTGACCACGTATTGATTGATGGCTATTCTGGGGGTGAGGTCATAGGGGAGGAGATTCCGTTGATAGACTTGCAGTCTACAAGGACTTTTAGCACCACTGAGGTTAGGGAGACCTCCTTCTTCACCAGCACCCCACGAGGTGAGACCCTGTATAAC---AGACGCGTGCAGCAGGTTCAGGTTGTTGACCCTGCATTCCTGTCACGTCCTGGTGCACTCGTGACATTTGACAATCCTGCATACACGGACGATGTGGAGTTAATTTTTGAGCAGGATTTAGATGATCTTGCACGTGCAGCTCCACATGAGGATTTTAGAGACATTGTGTCTCTAGGCAGGCCTGTTTATGGCCGTAATCCACAGGGTGGGGTTCGAATAAGCAGGCTAGGACAAAAAGCAACTATGAGAACAAGGAGTGGTTTAAGAATTGGGCCCCAAAGCCACTTTTTTTATGATATAAGTGAAATTGCTGAGCCAGAG---CTTGAGCTTGTGCCATTGGAGCCACCCTTTGTTGGAGAGCAAACAGGGGAATCAGTAGTGGGGTCTGCACTTGGCGAATTTGAAACAATAAGCTTATATCCTGAGGACACACTTATTGATGAGTATGAAGTAGTTGGCAGTGACTTGCAACTGATAATTGGGGATTCTGGAGGTGAGCGACCGATACCGGTCGCTGACTTTGCCAGGCCCCCAGCAAAGCTGGATGGGGTTCAGGTGTCTCGCTCAGCCACTGTGCCAGTTATTCCTGAGGACACTCCATTAATCATTATTGAGGTTTTGGATGGGAGTGGAGACTATTTTCTGCACCCCTCACTTTTTCGTAAAAGG---CGCAAACGACCTTTTTTT
		</sequence>
		<sequence>
			<taxon idref="AsianLionPV1"/>
			ATGCTAAGGCGAAAACGTGCAGCCCCCTCAGATATCTACCCCCAATGCAAAATTTCCAATACCTGCCCCCCTGATATACTCAATAAAGCTGAGCAAAACACGCTTGCAGATAAAATTTTAAAATATGGTTCGGCTGGTGTTTTTTTGGGAAGTTTGGGAATCAGCACTGGGCGAGGGACGGGGGGCTCATATGGCTATGTGCCTGTTGGACAAGGGGTGCGGTTAGGAACCAGAGTCTCAACTGTCAGGCCTACATTGCCTATTAGCAGCGTGGGCACTGCTGATGTGATTCCTGTGGATGCTGTAGATCCTTTGGGACCAGCAGTTCTTCCAGGAAATGTGTTTCCCACAGCTGTAGAAGACCCTATTCCTATACAACCTCCCAGATTTCCTTCAGTTGTTGAGGAC---CTTCTTCCTGTGCAGCCAGAAACACCCAAAGTGACAACAGATGGACAACCAGCAGTATTAGAAGTTGTCCCTGAAACAAGAGAGCCTCGCATCTTAACAAGAACCCAATATAGCAACCCAGCTTTTGAGGTGTCTTTGACCACTTCTGCTGGCTCAGGAGAAACATCAGCTTCAGACCACATTTTAGTTGAAGGGTTTTCTGGTGGGCACACAATAGGCGAGCGCATTCCCCTGCAAGAATTGTCACCC---AGGTCATTCTCTACCACTGTTGAGGAAGAAACAACCTTTACCACTAGCACTCCTGCAGCTGAAAGGGTCTTTCAGTCTAGGCAATTTCAGCAGGTAAGGGTGCAAGACCCTGCGTTTTTGGCGAGGCCAAGGTCATTGGTCACGTTCCAAAACCCTGTTTTTGATGAGTCAGTTGACTTACTTTTTGAGCAAGACGTGGCAGATATTGTTTTGGCAGCACCTCATGAGGATTTTAGAGATTTGGTGTCCCTCAGCAAACCTGTGTACTCTCGGACACAAGAAGGCAGGGTGAGGGTCAGTCGATTGGGAACAAAAGCCAGCATGCGCACACGCAGTGGATTGGTCATTGGGCCACAAAGCCATTACTACTATGACCTTAGTGATATAGCTCCTGCAGAAAACATAGAGCTGTCCCCCATAGGCAACTTTTCTTTAGGGGAACAATCAGGACAATCAGTCATCTCCTCTGGCACCAGTGACATGGAGATTATAAGCTTGTATCCTGAGGAGTTGTTACTTGATGAGATCGAATCCGTTGCCAATGATCTGCAGCTGGTGTTTGGAGACAGAAGGGTGCAGCAACCGATTTCGGTCCCAAACATACAAAGGCCTAGCCCGCAGGTGGAGGGCGTGCATGTGTCAGGGCCCCCTACCATTCCCACACATCCCGAAACAACACCAGCAATTGTGATAGATATCTGGGAATCAGGGAATAGTTATTCTCTGCACCCATCTTTGCTGAGAAAGAGAAAACGCAAACGGCTTTTTTTG
		</sequence>
		<sequence>
			<taxon idref="SnowLeopardPV1"/>
			ATGCTAAGGCGAAAACGTGCAGCCCCTTCTGATATTTACCCACAATGCAAAATTTCCAATACCTGCCCGCCTGACATACTCAATAAAGCTGAGCAAAACACGCTTGCAGATAAAATTTTAAAATATGGATCGGCTGGTGTTTTTTTGGGGAGTCTGGGAATTAGTACTGGGCGAGGGACGGGGGGCTCCTATGGGTACGTGCCTGTTGGGCAGGGAGTGCGGTTGGGGACACGGGTGTCAACGGTCAGACCTACTCTCCCTATCAGCAGTGTGGGCTCTGCAGACGTGATTCCTGTTGATGCAGTGGATCCACTGGGGCCTGCTGTTCTTCCAGGCAATGTTTTCCCCACGGCTGTCGAAGACCCTGTCACTATCCAACCTCCCCGATTTCCATCCATCGTTGAGGAC---CTTCTACCTGTGCAACCTGAGACTCCCAAAGTAACCACAGATGATCAGCCAGCGGTGCTCGAGGTGGTCCCTGAAACCAGAGAGCCCCGCATCCTCACTCGAACACAGTATAGCAACCCAGCTTTAGAGGTGTCTCTCACTGCTTCTGCTGGCTCCGGTGAAACCTCAGCTTCAGACCACATCTTAGTGGAAGGCTTCTCTGGCGGGCATTTCATAGGCGAGCGTATTCCCTTGCAAGAGTTGTCCCCA---AGGTCATTTGCTACCACTGTAGAAGAAGAAACCACCTTCACTACTAGCACCCCTGCAGGTGACAGGGTCTTGTATTCAAGACACATTCAGCAAATCAGAGTGCAAGACCCAACTTTTCTGTCAAGGCCAAGGTCTTTGGTGACGTTCCAGAACCCTGTATTTGATGACTCAGTGGACTTAATTTTTGAGCAGGATGTGGCAGATGTTGCTCTGGCAGCACCTCATGAAGACTTTAGAGATTTGGTCTCTCTCAGCAGACCTGTCTTTTCTCAAACACAAGAAGGCAGGGTGAGGGTCAGCCGACTCGGGACGAGAGCTACCATGCGTACACGCAGTGGGCTGGTCATTGGTCCTCAGAGCCATTACTACTATGACCTGAGTGACATAGCTCCTGCAGAAAACATTGAGCTTTCTCCCATTGGCAACTTTTCTTTAGGTGAGCAATCAGGCCAATCTGTCATCTCCTCTGGCACTAGTGATCTGGAGATTATCAGTTTGTACCCTGAGGAGTTGTTACTAGACGAGATCGAATCCGTTGCCAATGATCTGCAGCTGGTCTTTGGAGACAGAAGGGCGCAGCAACCGATTTCGGTCCCGCACATACAAAGGCCTAGCCCGCAGGTGGAAGGCGTCCATGTGTCTAAGCCCCCCAGCATTCCCACACTTCCTGAAAAAACACCAGCTATTGTGATCGAAATCTGGGGATCAGGAAACAGCTACTCTCTGCACCCATCTTTGCTGAGTAAGAGGAAACGCAAACGGCTTTCTTTG
		</sequence>
	</alignment>
	
	
	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=535                                                           -->
	<patterns id="FPV.patterns" from="1">
		<alignment idref="alignment"/>
	</patterns>
	
	<!-- A prior on the distribution node heights defined given                  -->
	<!-- a Yule speciation process (a pure birth process).                       -->
	<yuleModel id="yule" units="substitutions">
		<birthRate>
			<parameter id="yule.birthRate" value="1.0" lower="0.0" upper="1000000.0"/>
		</birthRate>
	</yuleModel>
	<!-- This is a simple constant population size coalescent model              -->
	<!-- that is used to generate an initial tree for the chain.                 -->
	<constantSize id="initialDemo" units="substitutions">
		<populationSize>
			<parameter id="initialDemo.popSize" value="100.0"/>
		</populationSize>
	</constantSize>
	
	<!-- Generate a random starting tree under the coalescent process            -->
	<!-- Has calibration                                                         -->
	<coalescentTree id="startingTree">
		<constrainedTaxa>
			<taxa idref="taxa"/>
			<tmrca monophyletic="false">
				<taxa idref="Felis/Lynx/Puma"/>
			</tmrca>
			<tmrca monophyletic="false">
				<taxa idref="Lion/Leopard"/>
			</tmrca>
			<tmrca monophyletic="false">
				<taxa idref="Cats"/>
			</tmrca>
		</constrainedTaxa>
		<constantSize idref="initialDemo"/>
	</coalescentTree>
	
	<!-- Generate a tree model                                                   -->
	<treeModel id="treeModel">
		<coalescentTree 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>
	
	<!-- Generate a speciation likelihood for Yule or Birth Death                -->
	<speciationLikelihood id="speciation">
		<model>
			<yuleModel idref="yule"/>
		</model>
		<speciesTree>
			<treeModel idref="treeModel"/>
		</speciesTree>
	</speciationLikelihood>
	
	<!-- The uncorrelated relaxed clock (Drummond, Ho, Phillips & Rambaut, 2006) -->
	<discretizedBranchRates id="branchRates">
		<treeModel idref="treeModel"/>
		<distribution>
			<logNormalDistributionModel meanInRealSpace="true">
				<mean>
					<parameter id="ucld.mean" value="0.038" lower="0.0" upper="100.0"/>
				</mean>
				<stdev>
					<parameter id="ucld.stdev" value="0.1" lower="0.0" upper="10.0"/>
				</stdev>
			</logNormalDistributionModel>
		</distribution>
		<rateCategories>
			<parameter id="branchRates.categories" dimension="12"/>
		</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 HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
	<HKYModel id="hky">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<alignment idref="alignment"/>
				<frequencies>
					<parameter id="frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</kappa>
	</HKYModel>
	
	<!-- site model                                                              -->
	<siteModel id="siteModel">
		<substitutionModel>
			<HKYModel idref="hky"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
			<parameter id="alpha" value="0.5" lower="0.0" upper="100.0"/>
		</gammaShape>
	</siteModel>
	
	<treeLikelihood id="FPV.treeLikelihood" useAmbiguities="false">
		<patterns idref="FPV.patterns"/>
		<treeModel idref="treeModel"/>
		<siteModel idref="siteModel"/>
		<discretizedBranchRates idref="branchRates"/>
	</treeLikelihood>
	
	
	<tmrcaStatistic id="tmrca(Felis/Lynx/Puma)">
		<mrca>
			<taxa idref="Felis/Lynx/Puma"/>
		</mrca>
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>
	<tmrcaStatistic id="tmrca(Lion/Leopard)">
		<mrca>
			<taxa idref="Lion/Leopard"/>
		</mrca>
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>
	<tmrcaStatistic id="tmrca(Cats)">
		<mrca>
			<taxa idref="Cats"/>
		</mrca>
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>
	<!-- Define operators                                                        -->
	<operators id="operators">
		<scaleOperator scaleFactor="0.75" weight="1">
			<parameter idref="kappa"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="1">
			<parameter idref="alpha"/>
		</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="1.0" 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="yule.birthRate"/>
		</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>
		<randomWalkIntegerOperator windowSize="1" weight="10">
			<parameter idref="branchRates.categories"/>
		</randomWalkIntegerOperator>
		<uniformIntegerOperator weight="10">
			<parameter idref="branchRates.categories"/>
		</uniformIntegerOperator>
	</operators>
	
	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="800000" autoOptimize="true">
		<posterior id="posterior">
			<prior id="prior">
				<normalPrior mean="7.15" stdev="1.36">
					<statistic idref="tmrca(Felis/Lynx/Puma)"/>
				</normalPrior>
				<normalPrior mean="3.72" stdev="1.05">
					<statistic idref="tmrca(Lion/Leopard)"/>
				</normalPrior>
				<oneOnXPrior>
					<parameter idref="kappa"/>
				</oneOnXPrior>
				<speciationLikelihood idref="speciation"/>
				
			</prior>
			<likelihood id="likelihood">
				<treeLikelihood idref="FPV.treeLikelihood"/>
			</likelihood>
		</posterior>
		<operators idref="operators"/>
		<!-- write log to screen                                                     -->
		<log id="screenLog" logEvery="10000">
			<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="Root Height" sf="6" width="12">
				<parameter idref="treeModel.rootHeight"/>
			</column>
			<column label="Rate" sf="6" width="12">
				<parameter idref="ucld.mean"/>
			</column>
		</log>
		<!-- write log to file                                                       -->
		<log id="fileLog" logEvery="200" fileName="FPV.log">
			<posterior idref="posterior"/>
			<prior idref="prior"/>
			<likelihood idref="likelihood"/>
			<parameter idref="treeModel.rootHeight"/>
			<tmrcaStatistic idref="tmrca(Felis/Lynx/Puma)"/>
			<tmrcaStatistic idref="tmrca(Lion/Leopard)"/>
			<tmrcaStatistic idref="tmrca(Cats)"/>
			<parameter idref="yule.birthRate"/>
			<parameter idref="kappa"/>
			<parameter idref="alpha"/>
			<parameter idref="ucld.mean"/>
			<parameter idref="ucld.stdev"/>
			<rateStatistic idref="meanRate"/>
			<rateStatistic idref="coefficientOfVariation"/>
			<rateCovarianceStatistic idref="covariance"/>
			<treeLikelihood idref="FPV.treeLikelihood"/>
			<speciationLikelihood idref="speciation"/>
			
		</log>
		<!-- write tree log to file                                                  -->
		<logTree id="treeFileLog" logEvery="200" nexusFormat="true" fileName="FPV.trees" sortTranslationTable="true">
			<treeModel idref="treeModel"/>
			<discretizedBranchRates idref="branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
	</mcmc>
	
	<report>
		<property name="timer">
			<mcmc idref="mcmc"/>
		</property>
	</report>
	
</beast>
