Ancestral state reconstruction
Molecular Phylogenetics – exercise
Ben Stöver
WS 2012/2013
Ancestal state reconstruction with BayesTraits
1. Ancestral state reconstruction
2
1 Ancestral state reconstruction
• 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)
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics
Ancestal state reconstruction with BayesTraits
2. Mesquite
3
2 Mesquite
• Modular software system
• Ancestral state reconstruction with
parsimony or likelihood
• (No Bayesian methods available)
• Many other features
• Distributed under GPL
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics
Ancestal state reconstruction with BayesTraits
3. BayesTraits
4
3.1 BayesTraits – overview
• BayesTraits is a command line based software (like PAUP* and MrBayes)
• Performs maximum likelihood or Bayesian reconstruction.
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)
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics
Ancestal state reconstruction with BayesTraits
3. BayesTraits
5
3.2 Starting BayesTraits
• BayesTraits takes two command line parameters.
• BayesTraits.exe <TreeFile> <DataFile>
• 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
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics
Ancestal state reconstruction with BayesTraits
3. BayesTraits
6
3.3 BayesTraits commands
• sample <n>:
Sets the sample frequency.
• iterations <n>: Specifies the number of generations for the MCMCalgorithm.
• burnin <n>:
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.
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics
Ancestal state reconstruction with BayesTraits
3. BayesTraits
7
3.4 Output of BayesTraits
• 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.
Ben Stöver
13.02.2012
Winter term 2012/2013
Fortgeschrittenenmodul Molecular Phylogenetics