effects of ancestral character estimation on methods for estimating rates of evolution in discrete...
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Effects of ancestral character estimation on methods for estimating rates of evolution in
discrete morphological characters
Graeme T. Lloyd, Steve C. Wang and Stephen L. Brusatte
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G. G. Simpson
1902 - 1984
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T. S. Westoll
1912 - 1995
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Westoll and lungfish
Westoll 1949
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Simpson modification
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Textbook example
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Other discrete character studies
Derstler 1982 Forey 1988
Ruta et al. 2006 Brusatte et al. 2008
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Translating Westoll’s method
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Evolution is phylogenetic
Phyletic Phylogenetic
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Evolution is phylogenetic
Phyletic Phylogenetic
Use cladogram
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Zero duration branch problem
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Zero duration branch problem
Use Ruta et al. dating technique
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Uncertainty in dating
Time
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Uncertainty in dating
Time
Randomly choose dates and repeat
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Uncertainty in optimisation
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Uncertainty in optimisation
Apply ACCTRAN and DELTRAN
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Uncertainty in topology
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Uncertainty in topology
Apply to multiple MPTs
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Specimen completeness bias
Many elements preserved Few elements preserved
Few changes observedMany changes observed
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Specimen completeness bias
Many elements preserved Few elements preserved
Few changes observedMany changes observedUse Wagner’s patristic dissimilarity
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Lacks null/alt. hypotheses
H0 Halt
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Lacks null/alt. hypotheses
H0 HaltApply equal rates as null hypothesis
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Data
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Lungfish
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Lungfish supermatrix
91 characters
86 ta
xa
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Results
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Rate over time test (ACCTRAN)
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Rate over time test (DELTRAN)
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Likelihood estimation of ancestral states
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Parsimony problems
?
?
?
Changeearly
Changelate
DELTRAN ACCTRAN
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Likelihood
?
?
?
?
?
?
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Likelihood
?
?
?
?
?
?No changes
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Rate over time test (Likelihood)
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Rate over time test (Likelihood)
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Terminal vs internal branches
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Branch length comparison
High
rate
(ste
ep sl
ope)
Low rate
(gentle slope)
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Branch rate comparison
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Branch changes comparison
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Branch duration comparison
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Branch length comparison
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Internal length comparison
Devonian
post-Devonian
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Terminal length comparison
Devonian
post-Devonian
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Conclusions
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Acknowledgements, code, data
Roger Benson
http://www.graemetlloyd.com/