1. Ben Stöver WS 2012/2013 Ancestral state reconstruction Molecular Phylogenetics – exercise

2. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 1 Ancestral state reconstruction 1. Ancestral state reconstruction 2 Reconstructing character states of acenstral nodes Tree topology is given Terminal character states are given Top left charts: Female gametangia (green: ventral, red: marginal, blue: central) Top right charts: Mycothallus (green: parenchymal, red: epidermal, blue: none) Bottom charts: Scales (yellow: small, green: broad marginal, red: lateral on margin, blue: broad central)

3. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 2 Mesquite 2. Mesquite 3 Modular software system Ancestral state reconstruction with parsimony or likelihood (No Bayesian methods available) Many other features Distributed under GPL

4. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 3.1 BayesTraits – overview 3. BayesTraits 4 Parts of the software: BayesMultistate Reconstructs characters with multiple (more than two) 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) BayesTraits is a command line based software (like PAUP* and MrBayes) Performs maximum likelihood or Bayesian reconstruction.

5. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 3.2 Starting BayesTraits 5 BayesTraits takes two command line parameters. BayesTraits.exe The tree file may also contain a tree distribution (e.g. from MrBayes) The data file contains a table specifying the terminal character states. In the start menu the part of the program to be used must be selected The method is selectes afterwards 3. BayesTraits

6. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 3.3 BayesTraits commands 6 sample :Sets the sample frequency. iterations :Specifies the number of generations for the MCMC- algorithm. burnin :Sets the generation count of the burin. 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 48 sets the state of Node1=0) info :Prints out information of the current settings. run :Starts the analysis. 3. BayesTraits

7. Ben Stöver Ancestal state reconstruction with BayesTraits Fortgeschrittenenmodul Molecular Phylogenetics Winter term 2012/2013 13.02.2012 3.4 Output of BayesTraits 7 BayesTraits generates a text file containing a table with the posterior probabilities of the samples (or likelihoods). Each line describes one sample the MCMC algorithm took. (For ML with a single tree, there will only be one line.) There is one column for each state of each character that was reconstructed. 3. BayesTraits