This document summarizes a study that estimated rates of evolution in discrete morphological characters of lungfish using different methods while accounting for uncertainty. It compared parsimony-based ancestral state reconstruction using ACCTRAN and DELTRAN to likelihood estimation. It tested for differences in evolutionary rates over time, between terminal and internal branches, and among branch lengths, rates, changes and durations. The study analyzed 91 morphological characters from 86 lungfish taxa in a supermatrix and found higher estimated rates in Devonian branches compared to post-Devonian using likelihood but not parsimony methods.

1. 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

2. G. G. Simpson
1902 - 1984

3. T. S. Westoll
1912 - 1995

4. Westoll and lungfish
Westoll 1949

5. Simpson modification

6. Textbook example

7. Other discrete character studies
Derstler 1982 Forey 1988
Ruta et al. 2006 Brusatte et al. 2008

8. Translating Westoll’s method

9. Evolution is phylogenetic
Phyletic Phylogenetic

10. Evolution is phylogenetic
Use cladogram

11. Zero duration branch problem

12. Zero duration branch problem
Use Ruta et al. dating technique

13. Uncertainty in dating
Time

14. Uncertainty in dating
Randomly choose dates and repeat

15. Uncertainty in optimisation

16. Uncertainty in optimisation
Apply ACCTRAN and DELTRAN

17. Uncertainty in topology

18. Uncertainty in topology
Apply to multiple MPTs

19. Specimen completeness bias
Many elements preserved Few elements preserved
Many changes observed Few changes observed

20. Specimen completeness bias
Use Wagner’s patristic dissimilarity

21. Lacks null/alt. hypotheses
H0 Halt

22. Lacks null/alt. hypotheses
Apply equal rates as null hypothesis

23. Data

24. Lungfish

25. Lungfish supermatrix
91 characters
86 taxa

26. Results

27. Rate over time test (ACCTRAN)

28. Rate over time test (DELTRAN)

29. Likelihood estimation of ancestral states

30. Parsimony problems
DELTRAN ACCTRAN
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?
Change
early
?
Change
late

31. Likelihood
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? ?
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?
?

32. Likelihood
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?
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No changes
?

33. Rate over time test (Likelihood)

34. Rate over time test (Likelihood)

35. Terminal vs internal branches

36. Branch length comparison

37. Branch rate comparison

38. Branch changes comparison

39. Branch duration comparison

40. Branch length comparison

41. Internal length comparison
Devonian
post-Devonian

42. Terminal length comparison
Devonian
post-Devonian

43. Conclusions

44. Acknowledgements, code, data
Roger Benson
http://www.graemetlloyd.com/