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