MajorIntroductionMethodsFormatRunningRunningcommandtimeMarkovtraittraitsGeneralisedSquaresforcontinuouslytraitsTestingsamplingMCMCmechanismandmixinganalysisMixing ID: 91731
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(Beta,unfinished)(M.Pagel@Reading.ac.uk)Meade(A.Meade@Reading.ac.uk) MajorIntroductionMethodsFormatRunningRunningcommandtimeMarkovtraittraitsGeneralisedSquaresforcontinuouslytraitsTesting:samplingMCMCmechanismandmixinganalysisMixing.........................................................................................................................AcceptanceRateJumpMultistateMultistateMCMCexampleexamplestatereconstructiondiscretevaluesexamplesindependentdependentJumpreduction(Model(Model (ModelMCMCsignificancekappa,EstimatingunknownExample:EstimatingunknownExample:EstimatingunknownIndependentListproblemFrequentlyReferences deviationautomaticallytunedpolytomysnewMultipleIndependentmodelinternalcontinuousmodelsbugimprovementsTreesarehavebranchdiscretemultistateestimateswillcomputerperformingamongphylogenyavailable.appliedtheadoptnumberdiscretecontinuouslytestedmodelsancestralcorrelationsThemethodintouncertaintyaboutevolutionApproachMarkovMonteCarlo(MCMC)posteriordistributionsmaximum(ML)methodspointphylogenies.TheconventionalMCMCtheMarkovdistributionmodelsevolutionparametersmodelsbelow).withexplored,appliedtreesmodelsestimatedtestedtakingphylogeneticuncertaintyintoaccount.   BayesPhylogeniespackagegeneratealignmentdata methodsMultiStatetraitsadoptnumberdiscretephylogenetictrees.usefulreconstructingancestralappliedtraitsadoptmorediscrete2004.Systematic53,usedevolutionbetweendiscretebinaryMostthebutcouldhigh,features.mightincludetestsgeneticculturalthecorrelationsamongtraits,theother(see1999.models(ref)detectvariationstree,accountinglineagemanualdesignedprogramsimplementtheseDetailedaboutmethodspapersend(someavailablewebsite).SyntaxcommandsBayesTraitsNexustreesincludepolytomybutbranchlengths.includedthetreebutlinkednumberthesectionnumberexampleareincludedwithprogram.Formatfromtext(ASCII),taxonthetree.mustspelledexactlytheandthem.speciesname,firstcolumndata,thisadditionaltakeA,Cdatamustexactlytakeintegerspoints.MultiStateremainingdatadatacontinuousremovedtree.Continuousincludedwith ExampleMultiStatedata BBC  â CCB     AB datasite.datatreatedtraitcouldtheforuncertain.ThesignifiescanbutExample(binary)data  â 10 01    11 ExampleContinuous 2 34    1 commandpromptterminal(OSLinux),doubleclickingTheprogram,placeStartthecommandpromptterminalchangedirectorydataandtype.OSXTreeFilenamethefilenamethedata multiplecomplexcommandscommandfile,typingthemtime.commandtextfile,commandsexampleincludedThe 1 1 MultiState,Artiodactyinputthecommand.discretecontinuousmodelschangefromanygivenanyotherstaterateparametersrates1994discussion).Theestimatingtransitionratestheeachbelowtheadoptandamongandtheseestimatestree,thesefromthisindicatestheysignificantcomponentbuttheExamplemodelevolutionadoptsstatesState 2  ââ q q states,thematrixtwelvebinarytraitjust forevolutionbinary(logcontinuousMarkovwhichtraitsindependentlyEachdescribedoneabove,but twoand1.createscoefficientspertraitsthatthechangeonedependsbackgrounddependentcanadoptfourcombinationthe(0,0;0,1;1,0;1,1).representedprogramdescribechangesotherconstant.mainestimateddiagonalelementsdualoccur,beingthattheseratestraitschangingexactlythesameoverperiodshowever.(1994)Barker(2005)forfurtherthisState 0,11, 1,1  ââ ââââ ââââ  ââ therateparametersuponthemeasurementphylogeny.branchfactorctheratesdecreasedthefactorc.parametersMarkovdiscussedmodelBayesTraitsimplements(Tuffley147:6391,1998).variantcontinuouswithinandbetweenbranches.elegantthatattention,findlimitedwithcomparativethemodelrequiremodelContinuousanalysescontinuouslyvaryingdata(GLS)approachBrownianPagel,1997,1999).nonindependencespeciesaccountedamongspecies.thephylogeneticthechange(theBrownianratechange,andancestralstaterootcancovariancecorrelation.approachmeansthatcanacrossspeciesandinterpretedtheobtainedContinuous.approachContinuouspossibletransformphylogenytheadequacyunderlying phylogeneticrequired,andaboutexample,evolutionpunctuationalgradual,adaptiveconstant.   HypothesisTesting:Factorsdoeshypothesesyoubutinformationneededtests.conjunctionwiththeexamplesthetwooftenused.(LR)likelihoodsderivednestedexpressedthatother).calculated2[logfittingdistributeddegreesequaldifferencethenumberbetweentheHowever,circumstances1994,1997Pagel,2005)thefewerincludetheInformationnotdescribetestsmanyphylogeneticinferenceexample,Phylogenies,2004).InformationthatMCMCoftenBayeslogictest,exceptthan   integralparameterspracticethislikelihoodcanapproximatedharmonicallowingMarkovrunlargenumbercheckthatharmonicBayesTraitsthetheharmonicprogramignoredduringtheperiodwhentheconvergence.Therunningharmonicmeansfromfinaliterationthevaluestheindependentanddependentthencompared.just   2(log[harmoniclog[harmonicmean(simple factor Interpretation Strong testingcontroversialanalysis,otherAIK,considered. WhenMCMCdistributionsthechosen.theparametersdependentuponbranchthingsequal,brancheswillparametersversa.thetheprior(e.g.,uniform,exponential)theuninformativepriorsareandwhenthethedataButcomparativethereonepointsmanyhundredsthousandssequence   softunderbellyanalyses.guidingprinciplechoicemustgoodthatoftenrunyourtreestheaveragetheparameters.optionconstrainparameterspriornarrowerandbiologicalgroundsperhapsbutindicationmidpoint.rulewhenconstrainedinformed(nonvaluestruncatedeitherupperlowerconstrainedrange,mustchanged.programexponential,betadistributedexponentialthenwhereastakeuniexponential.exponentialusefulgeneralthanthoughtvalue,intermediatemeanused.(uniform,beta)parametersthedistribution.exponentialmeantheparameterq01uniformtheq10uniform100thesamecandoestakeBecausedifficultdistributions,allowshyperhyperdrawntheexponentialusingelegantsometheuncertaintyarbitrarinessMCMCpriorshyperMeade,2004ancestralcharacterSystematicBiology,53,673684. Whenhyperapproachspecifyforuniformdistributionthatdistribution.forexponentialexponentialprioruniformtheHyperPriorAllmeanandfromhyperbothinterval10.MCMCrunwhileconvergence.impossiblehardmanyburnthatminimumseldomThelengthburnincommand.burnMorecomplexlargertreesperiods.iterationsMarkovthereprintingeachlineoutput.Insteadthinnedthatoutputindependent.samplecommand.printthetheautocorrelationamongcheckedevenExcel).comparativedatasets,everyadequaterun1010000default,changedcommand,whichthenumberiterationsruninfinitewhichMixing,timeschangesuccessfulanalysis.changesparameterlargelikelihooddramatically,convergencetheThistheacceptanceratebecomingbetweenotheraccepted.Thesmallchangesproposechangemuch,leadinghighidealratebetweenconvergence.valuebetweendatatrees,parametersbodymanymagnitudeobtainedtimegenomeThisverymechanism.parameterbiggerleadingloweracceptanceleadhighercontinuousparameterstreeacceptancerate,cannottuned.attemptsautomaticallytunetheproposalmechanismrateparameteracceptanceapproximatelybut RateDevcommand.Thecommandtakesnumber,commandtheMonitoringAcceptanceschedulewhichmixing,containsschedule,percentageoperatorsfollowedheader.headernumbertimesthepercentagetimetunetheacceptancethatparameter,iterationrunningacceptancerateTheschedulechainmixingcorrectly.constantbattlecomparativemethodsbetweencomplexityanddataneededmanyespeciallydiscretethemanyparameters,cannotestimatedthemodelparameterised.Indicationsinclude,estimatedparameters,parameterstradingeachsuboptimallikelihoods,convergenceModelcomplexityparametersrestrictcommandensuringratiohigh.restrictionmultistatediscretemodelsnumberparameters,manysupported.BayesTraitsnumberincreaseavailableestimateremainingones.Thecommand(res)usedrestrictcommandparameternames,suppliedparametersalpha2followingcommandindependentrestrictedconstants,theunrestricted(UnRes)usedrestrictionsModeltestingparameterjustified,numberreduced. JumpMCMCcomplexmodelnumberandimpossiblereverseMCMCwasintegratemodelparameterdescription(ref).RevJumpcommandusedjumpMCMC,commandtakethecommandexponentialTheexponential â RJHP exp 0 100 MultistateprogramArtiodactyl.treestreefiletheThefollowingMultiStatemaximumlikelihoodoptionsdisplayinginformation.Thiswhatexpect.runThefollowedheader Output number,500this for DG GD D G outputprinted.Oncebeentheterminate. MultistateexampleprogramArtiodactyl.treestreeandArtiodactyl.datamultistateMCMC(2).defaultexponentialprinted Output Iteration MeanRunningharmonic number DG GD thestate thestate Iteration No 110007.933077.933071873.7025612.54460.3510230.648977 120008.988468.593984953.1209734.9149590.4756280.524372 130008.374168.525943.7993834.4897980.4173930.582607 1400010.28069.3123117.0761327.544980.4999720.500028 1500010.71229.789126.9455885.8652190.484360.51564 10060008.944819.903884008.976618.4075630.4735170.526483 10070008.532449.903131470.336441.4777020.0121160.987884 10080008.035629.902283382.4540933.3349730.2708690.729131 10090008.411399.901511072.2174074.1835070.3659740.634026 10100009.728129.901357.505419.5387850.4841140.515886 OutputdesignedexcelJMP.RundependthescheduledArtiodactyl.txt.Schedule.txtcreated,checkchainmixingbetweenqGDestimatedbothqDGqGDsignificantlyfromanalysistakeqDG.used shouldbutparametersqGDtheiteration.Thecalculatingmeans.harmonicanalysisqDG9.90135,harmonicqDG8.965492.qGD,becausethantheqGD.D. mean(complexex mean(simple model)]  Log  BF = 2(â9.901358.965492)   1.871716lesssimplerharmonicbetweendependingrandomillustrativepurposes.harmonicmeanscalculatedandtestedreliabilityusingmultipleindependentTheymodelAddMRCAAddNodecommandsancestralstatesmultistatediscretemodels.ThethetwocommandsThecommandsidentifyandlisttaxanumbernode.graphicsgeneratecommandclickingappropriateArtiodactyl.treesmultistatecommandsdefinedFKWhaleThenodecalledidenticalbutnumbertaxadefinenode.followingcommandscolumnsP(D)andP(G),thereconstructing   presentGoat,commandsreconstructionpresentbecausepresenttrees.commandreconstructstheMostRecentpresentMRCA.Anynumbercanreconstructedanalysiseffecteachnodesexternalavailableonecommandtakesnodetaxadefinenode,foundmethod.Thecommanddefinedfossilisedsignificant,state.discreterequiresnumberinsteadThetablebelowthenumberstherecorrespondingleftunchanged, â Number âââ X âââ XX XX X XX XX X XXX0 XX0X X0XX 0XXX usedtraitssignificanceestablishedlikelihoodsmodels,independently,assumesexamplesMCMCbutused.matingwrittenindependentevolveindependently,thetraitindependentsecondtrait.independentparameters,alpah2beta2.transitions1,0 Parameter Transitions alpha1 1110 alpha2 2210 10 2 1  â 0 1 2 BayesTraitstheindependentSetexponentialanalysis,commands. Run willmultistateheadercontain. Output Iteration MeanRunningharmonic number transition transition P(0,0)thestate0,0 P(0,1)thestate0,1 P(1,0)thestate1,0 P(1,1)thestate1,1 dependentassumesthecorrelatedchangedependentdependentmodelq34,q43. Parameter Dependent Transitions 1=0201 2=0101 1=0210 2=1101 2=0110 1=1201 2=1110 1=1210 Q0 QQ  â 0QQ BayesTraitsthedependentmodel(3)analysis(2).Setexponentialanalysis,commands. Run willindependentmodelexceptthatthedependentareestimatedtheindependent.calculateFactorbetweenindependentdependentindependentsharmonicdependentharmonic2(log[harmonicmean(complexlog[harmonicmean(simple42.4745.51)   suggestsevolution.HarmonicbetweenMCMCreductionthedatacomplexitymodelunlikelyindependentanddependentmodelsestimatedThepreviousexample,demonstratedcouldsimplifiedandrestrictionssignificant.TherearepossibleindependentdependentReverseMCMCMCMC)resultsautomaticallyjumpcommandtakespriorcommandexponentialMCMCcanused RJHP exp 0 100 theprimatesandwiththedependentMCMCthecommandswillcontaincolumns. Output ParametersNumber ZeroNumber stringparameterrestrictions modeldependent(D)independent(I)    numberswhicharegroupsareexamplefordependentoneforparameter,the'1twozero.groupparameters(q12,q42),groupformedparameters(q21,q31),parametercancheckedtheparameterdataindependentMCMCandcomparedependentMCMC.described(ref),theswitchingratebetweenThemodelthedifferenttree.commandusedthemodel,columnsincludedtheOffThebetweenstatesBayesTraitstheMammal.treesMammalBody.txt,thesampletreestherebodyillustrativepurposesSelectmodelmaximumlikelihoodstartanalysis   Output number,this for theroot corrected BayesTraitstheMammal.treesMammalBody.txt,Model(2), Output Iteration MeanRunningharmonic number 1 corrected continuouscorrelatedresultsdefault)RuntreeMammal.treesandSelectmodelMCMCtheinformationprintedheader   Output Iteration MeanRunningharmonic number 1 1 correctedthe correctedthe correlation analysisthecorrelation TestCorrel Run shouldsimilartheTraitcorrelationtestedharmonicmeanstheproducedharmonic73.29analysisharmonic135.03,wouldFactorsuggestinghighlyusedtesttraitsdistanceModelultrametrictreestipbetweentaxa.fictionalMammalModelB.txtcanusedtestsignificantdirectionaltrendpreformingModelModelRegressioncontinuoususedtestsignificanceunknownThefirstdependentMammalBrainBodyGt.txtmammalbrain,time.MammalBrainBodyGt.txtSelect(6)andanalysis.header Output Iteration MeanRunningharmonic number Intercept coefficientfortrait coefficientfortrait motion squared squared s.e.AlphaStandardAlpha s.e.Standard s.e.Standard significancenumberwayssignificantmodel,harmonicmeanstrait.Thethethetimecoefficientcoefficientscommand.numberlambdaTheseparametersallowtempo,mode,phylogenetic threedefault.Thesethatlengthsdescribeconstantmodeltraitfollowedbranchlengths,they(e.g.,estimatingthebetweensignificantlyimprovesdatathemodel.differentiallyphylogeneticbranchpunctuationalversustraitKappabranchesshorterindicatingthatbranchescontributelongbranch).Kappa1.0longerbranchesones.theextremeKappatraitevolutionindependentlengthbranch.Kappawithpunctuationaldeltaphylogeny â distancethedetecttimetips,radiations.Delta(earlierphylogeny)contributeevolutionthisradiation:changeindicatesthatcontributeThisacceleratingevolutiontimeway,thatdetectsdifferentialovertimethewhichconstant.phylogenycorrectlypredictsthepatternsamongspeciestrait.Thisparameterindicatesassumptionsunderlyingthecomparativemethodsindependenttruephylogenytrait.wereindependent,parametertakephylogeneticcanlambdatreebeingrepresentedbigphylogeny.expectedlambdamotion)beingrepresentationIntermediatethelambdadifferentphylogeny.thetraitsthenlambdaestimatedsimultaneouslyestimatingthecharacterisetraitslambdacanestimatedeach. Parameter contributionphylogenyphylogenyindependent)phylogeneticphylogenydefined branchpunctuationalbranchesbrancheschange totaltotaldefinedchange(adaptive scalingandinterpretationphylogenythreeparametersestimatedMCMC,threeeitherparameteritsestimation(theyestimateddefault,1.0)scalingparameterfollowednumberthecommandestimatescommandestimateskappa,thecommandestimatesdelta,0.5Modeltestingsignificantsignificant,lambdasignificantlyfromunknownmodelsestimateunknowninternaldata.Estimatingunknowndistributionestimatedfromdata,areunknownTheprocesspreventestimateddatamodelparameters.Estimatingwithmodelmodelthemodelbutanalysis.SaveModelscommandspecifiedLoadModelscommandmodelsThemodelspecifiedwhencreatingandestimatingunknowncheckingimplemented.unknowninternalnodesBayesTraitstheMammalBody.txtSelectmodelMCMCanalysiscommandsMamBodyModels.bin SaveModels MamBodyModels.bin Run MamBodyModels.bincreated.estimatedata,treemodel(4)analysis(2).TheAddMRCAcommandestimateinternaltakesthenodeoutputlisttaxadefinecommandstheNodedefinedtaxa,reconstructcalledNodedefinedtaxa,analysis. AddMRCA Node-01 Whale Hippo Llama Ruminant Pig headercontain Output Iteration MeanRunningharmonic number number 1 motion Est â valuesNode Est â valuesNode unknownforestimated,nodes.MammalBrainBodyNoTapir.txtbeencreatedfortreeMammalBrainBodyNoTapir.txtSelectandcommandmodelsanalysis Run MammalBrainBodyPredTapir.txtcontainsthebutthequestiondatausedindicateshouldestimated.andMammalBrainBodyPredTapir.txtdatamodel(6)(2).commandbelowanalysis Run willcontainEstTapirwithpredicted IndependentindependentmodelsML.theMammal.treesSelectIndependentcontrast(7)MCMCanalysis.independentcontrastindependent.contain Output Iteration MeanRunningharmonic number 1 2 motion motiontrait modelrateschangetimewherethedifferedsignificantly,description(ref).MCMCidentifytheevolutionsignificantly.onlysingletreerequiresroughlythereincluded.anddataselectIndependentcontrast(7)MCMCruncommands VarRates Run willcontain Output Iteration MeanRunningharmonic number 1 motion VarRatesareas filescreated,Marsupials.txt.PP.treesthemodifiedincreasedchange,havedecreasedTheMarsupials.txt.PP.txtdetaileddescriptionchanges,formatnumberuniqueandtaxanumberinternalnodes,uniquenodebranchlengthroot),numberwhichdefinelistID.Thesectionresultsthethe Output the Priorprior Pramchangethe phylogenetic motion Scaleprior(unchanging,diagnostics changetreethere Output nodechange change thechangecreated Branchchangenodebranch designedcomputerextractinformationfromthefile.Commandcomment.Shortcut:Example:comment.ancestorShortcut:taxanumbernodereconstruct.Example:Taxa2Shortcut:taxanumbernodereconstruct.Example:AddNodeNode1AddNNode1interceptShortcut:Example: numberiterationsburnMCMCinfiniteShortcut:Example:maximumnumberShortcut:Example:CapRJRatesShortcut:Example:deviationparameterusedperturbingestimateddata.Thisnotrecommended.Shortcut:number,Example:EstimateShortcut:estimatenumberExample:EqualTreeschainThisposteriordistributiontree.Shortcut:NumberiterationsburneachExample:EqualTrees20000midpointsample.Shortcut:Example:runningtheanalysis Shortcut:Example:internalShortcut:whichdefinenode.fixingaboveinformation.Example:Hylobates_gabriellaeHylobates_leucogenysEstimategammaheterogeneity.Shortcut:numbercategoriesparameterExample:commands,Shortcut:Example:parameterShortcut:distributioneachparameterfromExample:gamma100commonShortcut:distributionparameterExample:Shortcut:Example:numberShortcut:numberchaininfinitetermination.Example:1000000 parameterShortcut:estimatenumberExample:parameterShortcut:estimatelambda,numberExample:0.8modelsmodelShortcut:Example:ModelFile.binnumbertimesmaximumlikelihoodhighertakelongerrunShortcut:NumbermaximumlikelihooddefaultExample:frequenciesShortcut:frequenciesestimates,est,unifrequencies,empirical,Example:Shortcut:distributionparameters,include,beta,gamma,Example:UniformShortcut: distributionparameters,commandExample:thenumbercategoriesdivideinto,default100.Shortcut:Example:rateparameter,effectingacceptancerate.SettingShortcut:automaticallyestimateparameter,valuenamespecificparametercontinuousExample:RestrictRestrictparameterparametersShortcut:parameterrestrictExample:Restrictalpha1Restrictalpha1alpha2Restrictbeta11.5RestrictAllRestrictparameterShortcut:Example:RestrictAllalpha1RevJumpanalysisShortcut:Example:RevJumpRevJumpGammaRevJumpHPanalysishyperShortcut:Example:RevJumpHPexpRevJumpHPgamma theShortcut:Example:Shortcut:Example:modelsShortcut:modelsExample:ModelFile.binModelFile.binShortcut:treesExample:randomShortcut:numberExample:39362SymmetricalcreatesymmetricalShortcut:Example:SymmetricalnamesnumbersShortcut:Example:correlationbetweentesting.Shortcut:Example: UnRestrictparameterrestrictionShortcut:UNResExample:q01UnRestrictAllShortcut:UnResAllExample:variablemodelShortcut:Example: FrequentlyQuestionsrunningprogramclickingprogramcommandclickingit.Runningnexusblock.template.descriptionsnumbernamemustnotspecifiedbutnotdataCheckspellingtaxanumbersnexusbecausefile.causestreefile.mainmemoryerrorsrunningmemory,duetreescomplexintensivemodels.memoryversionprogram.runningtheprogramsmallernumbertreesThecauseerrorprogrammingpleasethecommandused.notmixingbetweenproblemcausedlikelihoodsignificantlythanthesample.likelihood,bettermuchThisproblemnumberwhenthesupported,chancecombinationcreatebetterlikelihoodpreventingmixing.problemdeterminethechaingetslikelihood.optionsthereason.secondcommandspendequalamounttree.treecommandproduceposteriorparametersintegrated References