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


    <data
id="anolis_morph"
dataType="standard">
                            <sequence id="seq_Anolis_acutus1" taxon="Anolis_acutus" totalcount="2" value="0021021134507100"/>
                            <sequence id="seq_Anolis_aeneus1" taxon="Anolis_aeneus" totalcount="2" value="0000011134306100"/>
                            <sequence id="seq_Anolis_agassizi1" taxon="Anolis_agassizi" totalcount="2" value="0000011134306100"/>
                            <sequence id="seq_Anolis_ahli1" taxon="Anolis_ahli" totalcount="2" value="002104113{34}{56}08211"/>
                            <sequence id="seq_Anolis_aliniger1" taxon="Anolis_aliniger" totalcount="2" value="00{12}0041134407110"/>
                            <sequence id="seq_Anolis_alutaceus1" taxon="Anolis_alutaceus" totalcount="2" value="002104113{56}407110"/>
                            <sequence id="seq_Anolis_angusticeps1" taxon="Anolis_angusticeps" totalcount="2" value="002104113{45}408110"/>
                            <sequence id="seq_Anolis_bahorucoensis1" taxon="Anolis_bahorucoensis" totalcount="2" value="0121011134407110"/>
                            <sequence id="seq_Anolis_barahonae1" taxon="Anolis_barahonae" totalcount="2" value="0021021133307100"/>
                            <sequence id="seq_Anolis_bartschi1" taxon="Anolis_bartschi" totalcount="2" value="0021041134507110"/>
                            <sequence id="seq_Anolis_bimaculatus1" taxon="Anolis_bimaculatus" totalcount="2" value="0021031134507100"/>
                            <sequence id="seq_Anolis_brevirostris1" taxon="Anolis_brevirostris" totalcount="2" value="00210{12}1134507100"/>
                            <sequence id="seq_Anolis_carolinensis1" taxon="Anolis_carolinensis" totalcount="2" value="0021041134407110"/>
                            <sequence id="seq_Anolis_christophei1" taxon="Anolis_christophei" totalcount="2" value="00{12}1041134507110"/>
                            <sequence id="seq_Anolis_coelestinus1" taxon="Anolis_coelestinus" totalcount="2" value="00?0041134406110"/>
                            <sequence id="seq_Anolis_cristatellus1" taxon="Anolis_cristatellus" totalcount="2" value="01211{12}1144508{12}01"/>
                            <sequence id="seq_Anolis_cuvieri1" taxon="Anolis_cuvieri" totalcount="2" value="0021021133307100"/>
                            <sequence id="seq_Anolis_distichus1" taxon="Anolis_distichus" totalcount="2" value="0021011133507100"/>
                            <sequence id="seq_Anolis_equestris1" taxon="Anolis_equestris" totalcount="2" value="0021011133{12}07110"/>
                            <sequence id="seq_Anolis_etheridgei1" taxon="Anolis_etheridgei" totalcount="2" value="0121?41136{34}07110"/>
                            <sequence id="seq_Anolis_garmani1" taxon="Anolis_garmani" totalcount="2" value="0121041133407210"/>
                            <sequence id="seq_Anolis_grahami1" taxon="Anolis_grahami" totalcount="2" value="0121041133{45}07210"/>
                            <sequence id="seq_Anolis_humilis1" taxon="Anolis_humilis" totalcount="2" value="001104114{34}508210"/>
                            <sequence id="seq_Anolis_insolitus1" taxon="Anolis_insolitus" totalcount="2" value="11{12}1041?3{45}?17110"/>
                            <sequence id="seq_Anolis_krugi1" taxon="Anolis_krugi" totalcount="2" value="012131114{34}508101"/>
                            <sequence id="seq_Anolis_limifrons1" taxon="Anolis_limifrons" totalcount="2" value="0011041134407210"/>
                            <sequence id="seq_Anolis_lineatopus1" taxon="Anolis_lineatopus" totalcount="2" value="0121041133407210"/>
                            <sequence id="seq_Anolis_lineatus1" taxon="Anolis_lineatus" totalcount="2" value="0021041133408210"/>
                            <sequence id="seq_Anolis_loysiana1" taxon="Anolis_loysiana" totalcount="2" value="002104113{45}408110"/>
                            <sequence id="seq_Anolis_luciae1" taxon="Anolis_luciae" totalcount="2" value="0000011134306100"/>
                            <sequence id="seq_Anolis_lucius1" taxon="Anolis_lucius" totalcount="2" value="0021041134507110"/>
                            <sequence id="seq_Anolis_luteogularis1" taxon="Anolis_luteogularis" totalcount="2" value="0021011133{12}07110"/>
                            <sequence id="seq_Anolis_marcanoi1" taxon="Anolis_marcanoi" totalcount="2" value="102124113{34}508100"/>
                            <sequence id="seq_Anolis_maynardi1" taxon="Anolis_maynardi" totalcount="2" value="0021041134407110"/>
                            <sequence id="seq_Anolis_microtus1" taxon="Anolis_microtus" totalcount="2" value="?000011133{0123}0310?"/>
                            <sequence id="seq_Anolis_occultus1" taxon="Anolis_occultus" totalcount="2" value="000004114{34}203110"/>
                            <sequence id="seq_Anolis_olssoni1" taxon="Anolis_olssoni" totalcount="2" value="1021041135407110"/>
                            <sequence id="seq_Anolis_ophiolepis1" taxon="Anolis_ophiolepis" totalcount="2" value="102104113{34}508210"/>
                            <sequence id="seq_Anolis_paternus1" taxon="Anolis_paternus" totalcount="2" value="0021041135408110"/>
                            <sequence id="seq_Anolis_pumilis1" taxon="Anolis_pumilis" totalcount="2" value="1011041135508110"/>
                            <sequence id="seq_Anolis_richardi1" taxon="Anolis_richardi" totalcount="2" value="000001113{45}306100"/>
                            <sequence id="seq_Anolis_sagrei1" taxon="Anolis_sagrei" totalcount="2" value="1021041134608211"/>
                            <sequence id="seq_Anolis_sheplani1" taxon="Anolis_sheplani" totalcount="2" value="01{12}1041134?11110"/>
                            <sequence id="seq_Anolis_strahmi1" taxon="Anolis_strahmi" totalcount="2" value="1021241133508100"/>
                            <sequence id="seq_Anolis_stratulus1" taxon="Anolis_stratulus" totalcount="2" value="00210{34}1134507100"/>
                            <sequence id="seq_Anolis_valencienni1" taxon="Anolis_valencienni" totalcount="2" value="0021041133408210"/>
                            <sequence id="seq_Anolis_vanidicus1" taxon="Anolis_vanidicus" totalcount="2" value="01010411354?7110"/>
                            <sequence id="seq_Anolis_vermiculatus1" taxon="Anolis_vermiculatus" totalcount="2" value="0121041133{45}07110"/>
                            <sequence id="seq_Anolis_wattsi1" taxon="Anolis_wattsi" totalcount="2" value="00210{34}1134507110"/>
                            <sequence id="seq_Chamaeleolis_chamaeleonides1" taxon="Chamaeleolis_chamaeleonides" totalcount="2" value="0021410033?12100"/>
                            <sequence id="seq_Chamaeleolis_guamuhaya1" taxon="Chamaeleolis_guamuhaya" totalcount="2" value="0021410033?12100"/>
                            <sequence id="seq_Chamaelinorops_barbouri1" taxon="Chamaelinorops_barbouri" totalcount="2" value="100?041135?14310"/>
                            <sequence id="seq_Diplolaemus_darwinii1" taxon="Diplolaemus_darwinii" totalcount="2" value="000000013020501?"/>
                            <sequence id="seq_Phenacosaurus_nicefori1" taxon="Phenacosaurus_nicefori" totalcount="2" value="000?01114{23}?11100"/>
                            <sequence id="seq_Polychrus_acutirostris1" taxon="Polychrus_acutirostris" totalcount="2" value="1000000101?1?100"/>
                            <userDataType id="StandardData.0" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="10">
                                <charstatelabels id="UserDataType.0" spec="beast.evolution.datatype.UserDataType" characterName="Postfrontal bone (this study)" codeMap="0=0, 1=1, ? =0 1 " states="2" value="present., absent."/>
                                <charstatelabels id="UserDataType.01" spec="beast.evolution.datatype.UserDataType" characterName="Parietal_foramen" codeMap="0=0, 1=1, ? =0 1 " states="2" value="at_fronto_parietal_suture., entirely_within_parietal."/>
                                <charstatelabels id="UserDataType.02" spec="beast.evolution.datatype.UserDataType" characterName="Parietal roof and crests, ordered linear. (These states refer to ontogenetic end" codeMap="0=0, 1=1, 2=2, ? =0 1 2 " states="3" value="crests U-shaped (not meeting posteriorly), roof trapezoidal., crests V-shaped (meeting posteriorly at occipital crest but not, crests Y-shaped (meeting posteriorly and forming midsagittal cr"/>
                                <charstatelabels id="UserDataType.03" spec="beast.evolution.datatype.UserDataType" characterName="Parietal posterior margin, unordered. (Related to character 3 but treated separa" codeMap="0=0, 1=1, ? =0 1 " states="2" value="notched_posteriorly_and_not_extending_over_occipital_region_as, not notched posteriorly with a half-funnel-shaped portion exten"/>
                                <charstatelabels id="UserDataType.04" spec="beast.evolution.datatype.UserDataType" characterName="Dentary sculpturing, unordered" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, ? =0 1 2 3 4 " states="5" value="absent., present as irregular horizontal excavations (cristatellus type), present as a single, forward-directed, semilunar excavation (cy, present as a series of 7-10 semilunar excavations (krugi type), present as irregular rugosities on posterolateral surface (Cham"/>
                                <charstatelabels id="UserDataType.05" spec="beast.evolution.datatype.UserDataType" characterName="Splenial bone, ordered by step matrix A1" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, ? =0 1 2 3 4 " states="5" value="large and broad, includes anterior mylohyoid foramen and anteri, small and narrow, extends from posterior border of single myloh, very small and narrow, restricted to lingual surface of mandibl, very small and narrow, restricted to ventral surface of mandibl, absent (e.g. A. sagrei)."/>
                                <charstatelabels id="UserDataType.06" spec="beast.evolution.datatype.UserDataType" characterName="Angular_bone" codeMap="0=0, 1=1, ? =0 1 " states="2" value="present., absent."/>
                                <charstatelabels id="UserDataType.07" spec="beast.evolution.datatype.UserDataType" characterName="Palatine_teeth" codeMap="0=0, 1=1, ? =0 1 " states="2" value="present., absent."/>
                                <charstatelabels id="UserDataType.08" spec="beast.evolution.datatype.UserDataType" characterName="Modal number of presacral vertebrae, ordered linear" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, 5=5, ? =0 1 2 3 4 5 " states="6" value="27., 26., 25., 24., 23., 22."/>
                                <charstatelabels id="UserDataType.09" spec="beast.evolution.datatype.UserDataType" characterName="Modal number of lumbar vertebrae, ordered linear" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, 5=5, 6=6, ? =0 1 2 3 4 5 6 " states="7" value="0., l., 2., 3., 4., 5., 6."/>
                                <charstatelabels id="UserDataType.010" spec="beast.evolution.datatype.UserDataType" characterName="Modal number of caudal vertebrae anterior to first autotomic vertebra, ordered l" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, 5=5, 6=6, ? =0 1 2 3 4 5 6 " states="7" value="11., 10., 9., 8., 7., 6., 5."/>
                                <charstatelabels id="UserDataType.011" spec="beast.evolution.datatype.UserDataType" characterName="Caudal_autotomy_septa" codeMap="0=0, 1=1, ? =0 1 " states="2" value="present., absent."/>
                                <charstatelabels id="UserDataType.012" spec="beast.evolution.datatype.UserDataType" characterName="Postxiphisternal inscriptional rib formula, modal condition is given (attached c" codeMap="0=0, 1=1, 2=2, 3=3, 4=4, 5=5, 6=6, 7=7, 8=8, 9=9, ? =0 1 2 3 4 5 6 7 8 9 " states="10" value="4_to_3., 5_to_1., 4_to_2., 5_to_0., 4_to_1., 3_to_2., 4_to_0., 3_to_1., 2_to_2., 1_to_3."/>
                                <charstatelabels id="UserDataType.013" spec="beast.evolution.datatype.UserDataType" characterName="Caudal ribs, transverse processes, unordered" codeMap="0=0, 1=1, 2=2, 3=3, ? =0 1 2 3 " states="4" value="present_on_caudal_vertebrae_extending_into_posterior_half_of_se, disappear_after_a_short_series_confined_to_caudal_vertebrae_on, present_on_caudal_vertebrae_extending_into_posterior_half_of_se, extend_into_posterior_half_of_caudal_series_with_the_processes"/>
                                <charstatelabels id="UserDataType.014" spec="beast.evolution.datatype.UserDataType" characterName="Interclavicle" codeMap="0=0, 1=1, ? =0 1 " states="2" value="lateral_processes_in_contact_with_clavicles_for_less_than_half, lateral_processes_in_contact_with_clavieles_for_more_than_half"/>
                                <charstatelabels id="UserDataType.015" spec="beast.evolution.datatype.UserDataType" characterName="Parabasisphenoid (this study)" codeMap="0=0, 1=1, ? =0 1 " states="2" value="basipterygoid_processes_lack_anteroventral_crests., basipterygoid_processes_with_anteroventral_crests_that_approach"/>
                            </userDataType>
                        </data>


    


    


    
<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>


<run id="mcmc" spec="MCMC" chainLength="1000">
    <state id="state" storeEvery="500">
        <tree id="Tree.t:anolis_morph" name="stateNode">
            <trait id="dateTrait.t:anolis_morph" spec="beast.evolution.tree.TraitSet" traitname="date-backward">
                Anolis_acutus=10,
Anolis_aeneus=20,
Anolis_agassizi=0,
Anolis_ahli=0,
Anolis_aliniger=0,
Anolis_alutaceus=0,
Anolis_angusticeps=0,
Anolis_bahorucoensis=0,
Anolis_barahonae=0,
Anolis_bartschi=0,
Anolis_bimaculatus=0,
Anolis_brevirostris=0,
Anolis_carolinensis=0,
Anolis_christophei=0,
Anolis_coelestinus=0,
Anolis_cristatellus=0,
Anolis_cuvieri=0,
Anolis_distichus=0,
Anolis_equestris=0,
Anolis_etheridgei=0,
Anolis_garmani=0,
Anolis_grahami=0,
Anolis_humilis=0,
Anolis_insolitus=0,
Anolis_krugi=0,
Anolis_limifrons=0,
Anolis_lineatopus=0,
Anolis_lineatus=0,
Anolis_loysiana=0,
Anolis_luciae=0,
Anolis_lucius=0,
Anolis_luteogularis=0,
Anolis_marcanoi=0,
Anolis_maynardi=0,
Anolis_microtus=0,
Anolis_occultus=0,
Anolis_olssoni=0,
Anolis_ophiolepis=0,
Anolis_paternus=0,
Anolis_pumilis=0,
Anolis_richardi=0,
Anolis_sagrei=0,
Anolis_sheplani=0,
Anolis_strahmi=0,
Anolis_stratulus=0,
Anolis_valencienni=0,
Anolis_vanidicus=0,
Anolis_vermiculatus=0,
Anolis_wattsi=0,
Chamaeleolis_chamaeleonides=0,
Chamaeleolis_guamuhaya=0,
Chamaelinorops_barbouri=0,
Diplolaemus_darwinii=0,
Phenacosaurus_nicefori=0,
Polychrus_acutirostris=0 
<taxa id="TaxonSet.anolis_morph2" spec="TaxonSet">
<alignment id="anolis_morph2" spec="FilteredAlignment" filter="1-2,4,7-8,12,15-16">
   <data idref="anolis_morph"/>
   <userDataType id="morphDataType.anolis_morph2" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="2"/>
                    </alignment>
                </taxa>
            </trait>
            <taxonset idref="TaxonSet.anolis_morph2"/>
        </tree>
        <parameter id="clockRate.c:anolis_morph" name="stateNode">1.0</parameter>
        <parameter id="origin.t:anolis_morph" lower="0.0" name="stateNode" upper="Infinity">100.0</parameter>
        <parameter id="samplingProportion.t:anolis_morph" dimension="10" lower="0.0" name="stateNode" upper="1.0">0.01</parameter>
        <parameter id="becomeUninfectiousRate.t:anolis_morph" dimension="10" lower="0.0" name="stateNode" upper="Infinity">1.0</parameter>
        <parameter id="R.t:anolis_morph" dimension="10" lower="0.0" name="stateNode" upper="Infinity">2.0</parameter>
    </state>

    <init id="RandomTree.t:anolis_morph" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:anolis_morph" taxa="@anolis_morph2">
        <populationModel id="ConstantPopulation0.t:anolis_morph" spec="ConstantPopulation">
            <parameter id="randomPopSize.t:anolis_morph" name="popSize">1.0</parameter>
        </populationModel>
    </init>

    <distribution id="posterior" spec="util.CompoundDistribution">
        <distribution id="prior" spec="util.CompoundDistribution">
            
            <distribution id="BirthDeathSkySerial.t:anolis_morph_old" spec="beast.evolution.speciation.BirthDeathSkylineModel" R0="@R.t:anolis_morph" becomeUninfectiousRate="@becomeUninfectiousRate.t:anolis_morph" origin="@origin.t:anolis_morph" samplingProportion="@samplingProportion.t:anolis_morph" tree="@Tree.t:anolis_morph" />
            
            
            <distribution id="BirthDeathSkySerial.t:anolis_morph" tree="@Tree.t:anolis_morph" contemp="false" spec="beast.evolution.speciation.BirthDeathSkylineModel">

  <!-- Starting parameters of the BirthDeathSkylineModel for the observed tree -->
  
  <!-- originTime: the start of the sampling+tree growth process -->
  <!-- (This is a nuisance parameter, but its starting value must be older than the start tree root or Beast2 will crash) -->
  <parameter id="originTime" lower="0.0" upper="4600" name="origin">300</parameter>
  
  <!-- birthRates (lambda: speciation or lineage splitting rates, oldest to youngest) -->
  <parameter id="birthRate" name="birthRate" lower="0.0" upper="100" value="1"/>
  <parameter id="birthRateChangeTimes_tops" name="birthRateChangeTimes" value="0"/>
  
  <!-- deathRates (mu: lineage extinction rates, oldest to youngest) -->
  <parameter id="deathRate" name="deathRate" lower="0.0" upper="100" value="0.1"/>
  <parameter id="deathRateChangeTimes_tops" name="deathRateChangeTimes" value="0"/>
  
  <!-- samplingRates (psi: rate of sampling per lineage per my)                  -->
  <!-- sorted from youngest to oldest, but with zero at the end,                 -->
  <!-- as specified by Denise on the beast-users group:                          -->
  <!-- https://groups.google.com/d/msg/beast-users/UyAS0sYDkKk/PB0ktWnssn0J          -->
  <!-- The actual psi samplingRates, though, are in order from oldest to youngest -->
  <parameter id="samplingRate" name="samplingRate" lower="0.0" upper="100" value="0.1"/>
  <parameter id="samplingRateChangeTimes_tops" name="samplingRateChangeTimes" value="0"/>
  
  <!-- rho (probability of sampling each lineage extant at a particular timepoint, typically the present, 0 Ma) -->
  <parameter id="rho" name="rho" lower="0.0" value="1"/>
  <parameter id="rhoSamplingTimes" name="rhoSamplingTimes" value="0"/>
  
  <!-- Are time arrays reversed, for birth, death, psi, rho, and R. Regardless, the parameter values are listed from oldest to youngest time bin. -->
  <reverseTimeArrays id="reverseTimeArrays" spec="beast.core.parameter.BooleanParameter" value="true true true true true"/>
  

    </distribution>


            
            
            <prior id="RPrior.t:anolis_morph" name="distribution" x="@R.t:anolis_morph">
                <LogNormal id="LogNormalDistributionModel.0" name="distr">
                    <parameter id="RealParameter.0" lower="0.0" name="M" upper="0.0">0.0</parameter>
                    <parameter id="RealParameter.01" lower="0.0" name="S" upper="0.0">1.0</parameter>
                </LogNormal>
            </prior>
            <prior id="becomeUninfectiousRatePrior.t:anolis_morph" name="distribution" x="@becomeUninfectiousRate.t:anolis_morph">
                <LogNormal id="LogNormalDistributionModel.01" name="distr">
                    <parameter id="RealParameter.02" lower="0.0" name="M" upper="0.0">0.0</parameter>
                    <parameter id="RealParameter.03" lower="0.0" name="S" upper="0.0">1.0</parameter>
                </LogNormal>
            </prior>
            <prior id="ClockPrior.c:anolis_morph" name="distribution" x="@clockRate.c:anolis_morph">
                <Gamma id="Gamma.0" name="distr">
                    <parameter id="RealParameter.04" lower="0.0" name="alpha" upper="0.0">0.001</parameter>
                    <parameter id="RealParameter.05" lower="0.0" name="beta" upper="0.0">1000.0</parameter>
                </Gamma>
            </prior>
            <prior id="samplingProportionPrior.t:anolis_morph" name="distribution" x="@samplingProportion.t:anolis_morph">
                <Beta id="Beta.0" name="distr">
                    <parameter id="RealParameter.06" lower="0.0" name="alpha" upper="0.0">1.0</parameter>
                    <parameter id="RealParameter.07" lower="0.0" name="beta" upper="0.0">1.0</parameter>
                </Beta>
            </prior>
        </distribution>
        <distribution id="likelihood" spec="util.CompoundDistribution">
            <distribution id="morphTreeLikelihood.anolis_morph2" spec="TreeLikelihood" data="@anolis_morph2" tree="@Tree.t:anolis_morph">
                <siteModel id="morphSiteModel.s:anolis_morph2" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph2" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph2" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph2" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph2" spec="LewisMK" datatype="@morphDataType.anolis_morph2"/>
                </siteModel>
                <branchRateModel id="StrictClockModel.c:anolis_morph" spec="beast.evolution.branchratemodel.StrictClockModel" clock.rate="@clockRate.c:anolis_morph"/>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph3" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph3"
spec="FilteredAlignment"
data="@anolis_morph"
filter="3">
                    <userDataType id="morphDataType.anolis_morph3" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="3"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph3" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph3" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph3" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph3" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph3" spec="LewisMK" datatype="@morphDataType.anolis_morph3"/>
                </siteModel>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph4" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph4"
spec="FilteredAlignment"
data="@anolis_morph"
filter="14">
                    <userDataType id="morphDataType.anolis_morph4" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="4"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph4" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph4" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph4" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph4" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph4" spec="LewisMK" datatype="@morphDataType.anolis_morph4"/>
                </siteModel>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph5" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph5"
spec="FilteredAlignment"
data="@anolis_morph"
filter="5-6">
                    <userDataType id="morphDataType.anolis_morph5" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="5"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph5" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph5" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph5" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph5" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph5" spec="LewisMK" datatype="@morphDataType.anolis_morph5"/>
                </siteModel>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph6" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph6"
spec="FilteredAlignment"
data="@anolis_morph"
filter="9">
                    <userDataType id="morphDataType.anolis_morph6" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="6"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph6" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph6" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph6" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph6" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph6" spec="LewisMK" datatype="@morphDataType.anolis_morph6"/>
                </siteModel>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph7" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph7"
spec="FilteredAlignment"
data="@anolis_morph"
filter="10-11">
                    <userDataType id="morphDataType.anolis_morph7" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="7"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph7" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph7" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph7" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph7" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph7" spec="LewisMK" datatype="@morphDataType.anolis_morph7"/>
                </siteModel>
            </distribution>
            <distribution id="morphTreeLikelihood.anolis_morph10" spec="TreeLikelihood" branchRateModel="@StrictClockModel.c:anolis_morph" tree="@Tree.t:anolis_morph">
                <data
id="anolis_morph10"
spec="FilteredAlignment"
data="@anolis_morph"
filter="13">
                    <userDataType id="morphDataType.anolis_morph10" spec="beast.evolution.datatype.StandardData" ambiguities="34 56 12 45 23 0123" nrOfStates="10"/>
                </data>
                <siteModel id="morphSiteModel.s:anolis_morph10" spec="SiteModel" gammaCategoryCount="1">
                    <parameter id="mutationRate.s:anolis_morph10" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anolis_morph10" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anolis_morph10" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="LewisMK.s:anolis_morph10" spec="LewisMK" datatype="@morphDataType.anolis_morph10"/>
                </siteModel>
            </distribution>
        </distribution>
    </distribution>

    <operator id="treeScaler.t:anolis_morph" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:anolis_morph" weight="3.0"/>

    <operator id="treeRootScaler.t:anolis_morph" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:anolis_morph" weight="3.0"/>

    <operator id="UniformOperator.t:anolis_morph" spec="Uniform" tree="@Tree.t:anolis_morph" weight="30.0"/>

    <operator id="SubtreeSlide.t:anolis_morph" spec="SubtreeSlide" tree="@Tree.t:anolis_morph" weight="15.0"/>

    <operator id="narrow.t:anolis_morph" spec="Exchange" tree="@Tree.t:anolis_morph" weight="15.0"/>

    <operator id="wide.t:anolis_morph" spec="Exchange" isNarrow="false" tree="@Tree.t:anolis_morph" weight="3.0"/>

    <operator id="WilsonBalding.t:anolis_morph" spec="WilsonBalding" tree="@Tree.t:anolis_morph" weight="3.0"/>

    <operator id="StrictClockRateScaler.c:anolis_morph" spec="ScaleOperator" parameter="@clockRate.c:anolis_morph" scaleFactor="0.75" weight="3.0"/>

    <operator id="strictClockUpDownOperator.c:anolis_morph" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
        <up idref="clockRate.c:anolis_morph"/>
        <down idref="Tree.t:anolis_morph"/>
    </operator>

    <operator id="becomeUninfectiousRateScaler.t:anolis_morph" spec="ScaleOperator" parameter="@becomeUninfectiousRate.t:anolis_morph" scaleFactor="0.75" weight="10.0"/>

    <operator id="samplingScaler.t:anolis_morph" spec="ScaleOperator" parameter="@samplingProportion.t:anolis_morph" scaleFactor="0.75" weight="10.0"/>

    <operator id="RScaler.t:anolis_morph" spec="ScaleOperator" parameter="@R.t:anolis_morph" scaleFactor="0.75" weight="10.0"/>

    <operator id="updownBD.t:anolis_morph" spec="UpDownOperator" scaleFactor="0.75" weight="10.0">
        <up idref="R.t:anolis_morph"/>
        <down idref="becomeUninfectiousRate.t:anolis_morph"/>
    </operator>

    <operator id="origScaler.t:anolis_morph" spec="ScaleOperator" parameter="@origin.t:anolis_morph" scaleFactor="0.75" weight="1.0"/>

    <logger id="tracelog" fileName="beast2.log" logEvery="100" model="@posterior" sanitiseHeaders="true" sort="smart">
        <log idref="posterior"/>
        <log idref="likelihood"/>
        <log idref="prior"/>
        <log idref="morphTreeLikelihood.anolis_morph2"/>
        <log idref="morphTreeLikelihood.anolis_morph5"/>
        <log idref="morphTreeLikelihood.anolis_morph7"/>
        <log idref="morphTreeLikelihood.anolis_morph6"/>
        <log idref="morphTreeLikelihood.anolis_morph10"/>
        <log idref="morphTreeLikelihood.anolis_morph4"/>
        <log idref="morphTreeLikelihood.anolis_morph3"/>
        <log idref="clockRate.c:anolis_morph"/>
        <log idref="BirthDeathSkySerial.t:anolis_morph"/>
        <log idref="origin.t:anolis_morph"/>
        <log idref="samplingProportion.t:anolis_morph"/>
        <log idref="becomeUninfectiousRate.t:anolis_morph"/>
        <log idref="R.t:anolis_morph"/>
        <log id="birth.t:anolis_morph" spec="beast.math.statistic.RPNcalculator" expression="R.t:anolis_morph becomeUninfectiousRate.t:anolis_morph *">
            <parameter idref="becomeUninfectiousRate.t:anolis_morph"/>
            <parameter idref="R.t:anolis_morph"/>
        </log>
        <log id="death.t:anolis_morph" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:anolis_morph 1 samplingProportion.t:anolis_morph - *">
            <parameter idref="becomeUninfectiousRate.t:anolis_morph"/>
            <parameter idref="samplingProportion.t:anolis_morph"/>
        </log>
        <log id="sampling.t:anolis_morph" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:anolis_morph samplingProportion.t:anolis_morph *">
            <parameter idref="becomeUninfectiousRate.t:anolis_morph"/>
            <parameter idref="samplingProportion.t:anolis_morph"/>
        </log>
    </logger>

    <logger id="screenlog" logEvery="100">
        <log idref="posterior"/>
        <log id="ESS.0" spec="util.ESS" arg="@posterior"/>
        <log idref="likelihood"/>
        <log idref="prior"/>
    </logger>

</run>

</beast>
