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Ancestral state reconstruction Molecular Phylogenetics – exercise

Ancestral state reconstruction Molecular Phylogenetics – exercise. 1 Ancestral state reconstruction. Reconstructing character states of acenstral nodes Tree topology is given Terminal character states are given.

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Ancestral state reconstruction Molecular Phylogenetics – exercise

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  1. AncestralstatereconstructionMolecularPhylogenetics – exercise

  2. 1. Ancestralstatereconstruction 1 Ancestralstatereconstruction • Reconstructingcharacterstatesofacenstralnodes • Treetopologyisgiven • Terminal characterstatesaregiven • Top leftcharts: Femalegametangia (green: ventral, red: marginal, blue: central) • Top rightcharts: Mycothallus (green: parenchymal, red: epidermal, blue: none) • Bottomcharts: Scales (yellow: small, green: broad marginal, red: lateral on margin, blue: broadcentral)

  3. 2. Mesquite 2 Mesquite • Modular softwaresystem • Ancestralstatereconstructionwithparsimonyorlikelihood • (NoBayesianmethodsavailable) • Manyotherfeatures • Distributed under GPL

  4. 3. BayesTraits 3.1 BayesTraits – overview • BayesTraitsis a commandlinebasedsoftware (like PAUP* andMrBayes) • PerformsmaximumlikelihoodorBayesianreconstruction. • Parts ofthesoftware: • BayesMultistate • Reconstructscharacterswith multiple (morethantwo) states • BayesDiscrete • Analyze correlated evolution between pairs of discrete binary traits • BayesContinues • Analysis of the evolution of continuously varying traits (e.g. length of an organ)

  5. 3. BayesTraits 3.2 StartingBayesTraits • BayesTraitstakestwocommandlineparameters. • BayesTraits.exe <TreeFile> <DataFile> • The treefilemay also contain a treedistribution (e.g. fromMrBayes) • The datafilecontains a tablespecifyingthe terminal characterstates. • In thestartmenuthepartoftheprogramtobeused must beselected • The methodisselectesafterwards

  6. 3. BayesTraits 3.3 BayesTraitscommands • sample <n>: Sets the sample frequency. • iterations <n>: Specifiesthenumberofgenerationsforthe MCMC-algorithm. • burnin <n>: Sets thegenerationcountoftheburin. • revjumphp: Specifies the distribution of prior probabilities (only for MCMC) • AddNode: Defines an exact node to be reconstructed. (e.g.: AddNode Node01 51 52 50 49 47 48) • AddMRCA: Defines a node to be reconstructed that is the most recent common ancestor of the specified taxa (but might also be the acestor of additional taxa.) • fossil: Specifies an ancestral state already known. (e.g.: fossil Node1 0 51 52 50 49 47 48setsthestateof Node1=0) • info: Prints out informationofthecurrentsettings. • run: Starts theanalysis.

  7. 3. BayesTraits 3.4 Output ofBayesTraits • BayesTraitsgenerates a textfilecontaining a tablewiththeposteriorprobabilitiesofthesamples (orlikelihoods). • Eachlinedescribesone sample the MCMC algorithmtook. • (For ML with a singletree, there will onlybeoneline.) • Thereisonecolumnforeachstateofeachcharacterthat was reconstructed.

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