Effects of ancestral character    estimation on methods for estimating rates of evolution indiscrete morphological charact...
G. G. Simpson          1902 - 1984
T. S. Westoll            1912 - 1995
Westoll and lungfish                   Westoll 1949
Simpson modification
Textbook example
Other discrete character studiesDerstler 1982                         Forey 1988                Ruta et al. 2006   Brusatt...
Translating Westoll’s method
Evolution is phylogenetic    Phyletic       Phylogenetic
Evolution is phylogenetic       Use cladogram
Zero duration branch problem
Zero duration branch problemUse Ruta et al. dating technique
Uncertainty in dating            Time
Uncertainty in datingRandomly choose dates and repeat
Uncertainty in optimisation
Uncertainty in optimisationApply ACCTRAN and DELTRAN
Uncertainty in topology
Uncertainty in topology   Apply to multiple MPTs
Specimen completeness biasMany elements preserved   Few elements preservedMany changes observed      Few changes observed
Specimen completeness biasUse Wagner’s patristic dissimilarity
Lacks null/alt. hypotheses    H0             Halt
Lacks null/alt. hypothesesApply equal rates as null hypothesis
Data
Lungfish
Lungfish supermatrix                                 91 characters                       86 taxa
Results
Rate over time test (ACCTRAN)
Rate over time test (DELTRAN)
Likelihood estimation of ancestral states
Parsimony problems  DELTRAN           ACCTRAN                ?                ?                              Change       ...
Likelihood                     ?         ?           ?             ?                     ?                 ?
Likelihood                           ?             ?             ?                   ?                           ?      No...
Rate over time test (Likelihood)
Rate over time test (Likelihood)
Terminal vs internal branches
Branch length comparison
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/
Upcoming SlideShare
Loading in …5
×

Effects of ancestral character estimation on methods for estimating rates of evolution in discrete morphological characters

486 views

Published on

Published in: Education, Technology, Spiritual
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
486
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
5
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Effects of ancestral character estimation on methods for estimating rates of evolution in discrete morphological characters

  1. 1. Effects of ancestral character estimation on methods for estimating rates of evolution indiscrete morphological characters Graeme T. Lloyd, Steve C. Wang and Stephen L. Brusatte
  2. 2. G. G. Simpson 1902 - 1984
  3. 3. T. S. Westoll 1912 - 1995
  4. 4. Westoll and lungfish Westoll 1949
  5. 5. Simpson modification
  6. 6. Textbook example
  7. 7. Other discrete character studiesDerstler 1982 Forey 1988 Ruta et al. 2006 Brusatte et al. 2008
  8. 8. Translating Westoll’s method
  9. 9. Evolution is phylogenetic Phyletic Phylogenetic
  10. 10. Evolution is phylogenetic Use cladogram
  11. 11. Zero duration branch problem
  12. 12. Zero duration branch problemUse Ruta et al. dating technique
  13. 13. Uncertainty in dating Time
  14. 14. Uncertainty in datingRandomly choose dates and repeat
  15. 15. Uncertainty in optimisation
  16. 16. Uncertainty in optimisationApply ACCTRAN and DELTRAN
  17. 17. Uncertainty in topology
  18. 18. Uncertainty in topology Apply to multiple MPTs
  19. 19. Specimen completeness biasMany elements preserved Few elements preservedMany changes observed Few changes observed
  20. 20. Specimen completeness biasUse Wagner’s patristic dissimilarity
  21. 21. Lacks null/alt. hypotheses H0 Halt
  22. 22. Lacks null/alt. hypothesesApply equal rates as null hypothesis
  23. 23. Data
  24. 24. Lungfish
  25. 25. Lungfish supermatrix 91 characters 86 taxa
  26. 26. Results
  27. 27. Rate over time test (ACCTRAN)
  28. 28. Rate over time test (DELTRAN)
  29. 29. Likelihood estimation of ancestral states
  30. 30. Parsimony problems DELTRAN ACCTRAN ? ? Change early ? Change late
  31. 31. Likelihood ? ? ? ? ? ?
  32. 32. Likelihood ? ? ? ? ? No changes ?
  33. 33. Rate over time test (Likelihood)
  34. 34. Rate over time test (Likelihood)
  35. 35. Terminal vs internal branches
  36. 36. Branch length comparison
  37. 37. Branch rate comparison
  38. 38. Branch changes comparison
  39. 39. Branch duration comparison
  40. 40. Branch length comparison
  41. 41. Internal length comparison Devonian post-Devonian
  42. 42. Terminal length comparison Devonian post-Devonian
  43. 43. Conclusions
  44. 44. Acknowledgements, code, data Roger Benson http://www.graemetlloyd.com/

×