Running MrBayes

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Running MrBayes

• Get help using help or help ltcommandgt
• Use execute to bring data in a Nexus file into
  MrBayes
• Set the model and priors using lset and prset
• Run the chain using mcmc
• Summarize the parameter samples using sump
• Summarize the tree samples using sumt

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Resources

• Very easy ML-Bayesian comparative tutorial using
  PAUP and MrBayes
• Easy MrBayes 3 tutorial simple analysis,
  analysis of partitioned data datafiles
  primates.nex and cynmix.nex
• Advanced users Last pages of the tutorial
  contain graphical summaries of the MrBayes 3
  models and most common types of proposal
  mechanisms
• Advanced users MrBayes 3 chapter complex
  analysis datafile kim.nex
• Advanced users MrBayes 3 beta 5 command reference

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Morphological models

• Incomplete coding
• Varying state space
• Unordered and ordered characters
• Transformation weighting for arbitrarily labeled
  states

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Incomplete coding
All
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Incomplete coding
Variable
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Incomplete coding
Informative
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Types of characters

• A (All), V (Variable), I (Informative)

V
V
A
I
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Conditional character probability
Cumulative character probability
0.0
1.0
?I
?V
?A
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Branch length estimates
All characters Assuming all
Variable chars Assuming variable
Informative chars Assuming informative
Inferred length
terminal internal
2000 chars
1176 chars
740 chars
True length
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Branch length estimates
Variable characters Assuming all
Informative chars Assuming all
Informative chars Assuming variable
Inferred length
terminal internal
2000 chars
1176 chars
740 chars
True length
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Transformation series
0

• Unordered (Fitch)

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1
Ordered (Wagner)
0
1
2
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Probabilistic models

• Unordered (M3u)

Ordered (M3o)
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Probabilitic models
0
?
?

• Unordered (M3u)

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1
?
?
?
Ordered (M3o)
0
1
2
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Transformation weighting
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Example Bayesian analysis of directional
morphological evolution in the Hymenoptera
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Character systems

• Musculature present ? absent, separate ? fused
• Wing veins present ? absent
• Sclerites present ? absent, separate ? fused
• Articulations / skeletal integration absent ?
  present

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Equal frequencies
Starting state
Process
Probability of state 1
Probability of state 1
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Asymmetric equilibrium
Starting state
Process
Probability of state 1
Probability of state 1
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Driving process
Starting state
Process
Probability of state 1
Probability of state 1
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Data

• Morphological dataset on basal hymenopteran
  relationships from Vilhelmsen (2001, Zool. J.
  Linn. Soc.)
• Divided into five partitions muscles, wing
  veins, sclerites, articulations and others
• Four potentially asymmetric character types
  recoded into binary characters with predicted
  change from state 0 to state 1
• Final dataset had 254 characters

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Partitions
Total 254 chars
Muscles
Wing veins
Others
Sclerites
Articulations
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Tree
91
62
80
98
71
90
98
100
100
85
93
69
100
78
99
99
94
100
78
100
100
100
78
85
62
100
83
100
91
100
51
94
100
100
100
100
93
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Muscles
Starting state
Process
Probability of state 1
Probability of state 1
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Wing veins
Starting state
Process
Probability of state 1
Probability of state 1
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Sclerites
Starting state
Process
Probability of state 1
Probability of state 1
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Articulations
Starting state
Process
Probability of state 1
Probability of state 1
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Simultaneous analysis of fossils and recent taxa
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Simultaneous analysis of extant forms and fossils

• Uncertainty in phylogeny of extant forms
• Uncertainty in placement of fossils
• Model distance fossils to ancestors
• Model preservation probability

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Mapping characters onto phylogenies
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Mapping Uncertainty
parsimony
ML
Bayesian
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Phylogenetic and Mapping Uncertainty
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