Time-binning rates of continuous character evolution on a phylogeny: the origin of amniotes, not tetrapods, is characterised by increased rates

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Graeme Lloyd

Presentation at International Symposium on Early and Lower Vertebrates (Melbourne 2015).

Science

Time-binning rates of continuous character
evolution on a phylogeny: the origin of
amniotes, not tetrapods, is characterised by
increased rates
@GraemeTLloyd
Graeme T. Lloyd
@Friedman_Lab
Matt Friedman

Acknowledgements
Chris Organ Graham Slater

Questions
1. How can we measure rates of evolution in a
continuous character over multiple time bins?

Questions
2. How did the tempo of tetrapod mandible
evolution change over their early evolution?
1. How can we measure rates of evolution in a
continuous character over multiple time bins?

Questions
2. How did the tempo of tetrapod mandible
evolution change over their early evolution?
3. How does phylogenetic time-scale
choice affect patterns of tempo?
1. How can we measure rates of evolution in a
continuous character over multiple time bins?

Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

Rate data types
Simpson 1944,1953; Westoll 1949

Discrete data: disparity and tempo
Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted

Discrete data: disparity and tempo
Claddis
Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted

Continuous data: mode dominates
Trait
value
Time

Early Burst
Late Burst
Trait
Time
Continuous data: mode dominates

Lee et al 2014
Time-scaling trees: simultaneous

Time-scaling trees: a posteriori
paleotree
strap

Time-scaling trees: a posteriori
Arbitrary
Branch-sharing
Ruta et al 2006; Brusatte et al 2008
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004

Time-scaling trees: a posteriori
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Nowak
Nowak et al 2013
Arbitrary Probabilistic
Branch-sharing
Ruta et al 2006; Brusatte et al 2008
Arbitrary addition(s)
Derstler 1982
Minimum branch-length
Laurin 2004

Time-scaling trees: a posteriori
Hedman method
Lloyd and Friedman in prep
Arbitrary Probabilistic
Branch-sharing
Ruta et al 2006; Brusatte et al 2008

τ7
τ8
τ6
τ5
Traditional approach first
Ruta et al. 2006; Brusatte et al. 2008
Branch-sharing (“equal”)

τ7
τ8
τ6
τ5
root age
τ7
τ6
τ5
Traditional approach first
Share time with preceding
(non-zero length) branch
Ruta et al. 2006; Brusatte et al. 2008
τ8
Branch-sharing (“equal”)

τ6
τ5
τ4
τ2
τ1
τ3
Hedman 2010; Lloyd and Friedman in prep
τ0
Probabilistic time-scaling

τ0
τ6
τ5
τ4
τ2
τ1
τ3
Age (Ma)
τ0
Probabilistic time-scaling
Hedman 2010; Lloyd and Friedman in prep

“Equal” timetree
Probablistic timetree
Results

Slater 2013
BrownianOrnstein-Uhlenbeck
Two-mode evolution

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Time-binning rates of continuous character evolution on a phylogeny: the origin of amniotes, not tetrapods, is characterised by increased rates

1. Time-binning rates of continuous character evolution on a phylogeny: the origin of amniotes, not tetrapods, is characterised by increased rates @GraemeTLloyd Graeme T. Lloyd @Friedman_Lab Matt Friedman

2. Acknowledgements Chris Organ Graham Slater

3. Questions

4. Questions 1. How can we measure rates of evolution in a continuous character over multiple time bins?

5. Questions 2. How did the tempo of tetrapod mandible evolution change over their early evolution? 1. How can we measure rates of evolution in a continuous character over multiple time bins?

6. Questions 2. How did the tempo of tetrapod mandible evolution change over their early evolution? 3. How does phylogenetic time-scale choice affect patterns of tempo? 1. How can we measure rates of evolution in a continuous character over multiple time bins?

7. How fast?

8. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

9. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

10. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

11. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

12. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

13. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted

14. Rate data types Simpson 1944,1953; Westoll 1949

15. Rate data types Simpson 1944,1953; Westoll 1949

16. Rate data types Simpson 1944,1953; Westoll 1949

17. Rate data types Simpson 1944,1953; Westoll 1949

18. Discrete data: disparity and tempo Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted

19. Discrete data: disparity and tempo Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted

20. Discrete data: disparity and tempo Claddis Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted

21. Continuous data: mode dominates

22. Continuous data: mode dominates Trait value Time

23. Early Burst Late Burst Trait Time Continuous data: mode dominates

24. Rate Time Continuous rates

25. Rate Time Continuous rates

26. Raia et al. 2013 Continuous rates

27. Harmon et al. 2008 New method: guts

28. New method: description

29. New method: description

30. New method: description

31. New method: description

32. S1 S2 S31 New method: description

33. Anderson et al. 2013 Data

34. Anderson et al. 2013 Data

35. Time-scaling trees

36. Lee et al 2014 Time-scaling trees: simultaneous

37. Time-scaling trees: a posteriori paleotree strap

38. Time-scaling trees: a posteriori + paleotree strap

39. Time-scaling trees: a posteriori + = paleotree strap

40. Time-scaling trees: a posteriori Arbitrary Branch-sharing Ruta et al 2006; Brusatte et al 2008 Arbitrary addition(s) Derstler 1982 Minimum branch-length Laurin 2004

41. Time-scaling trees: a posteriori cal3 Bapst 2013 Hedman method Lloyd and Friedman in prep Nowak Nowak et al 2013 Arbitrary Probabilistic Branch-sharing Ruta et al 2006; Brusatte et al 2008 Arbitrary addition(s) Derstler 1982 Minimum branch-length Laurin 2004

42. Time-scaling trees: a posteriori Hedman method Lloyd and Friedman in prep Arbitrary Probabilistic Branch-sharing Ruta et al 2006; Brusatte et al 2008

43. τ7 τ8 τ6 τ5 Traditional approach first Ruta et al. 2006; Brusatte et al. 2008 Branch-sharing (“equal”)

44. τ7 τ8 τ6 τ5 root age τ7 τ6 τ5 Traditional approach first Share time with preceding (non-zero length) branch Ruta et al. 2006; Brusatte et al. 2008 τ8 Branch-sharing (“equal”)

45. τ6 τ5 τ4 τ2 τ1 τ3 Hedman 2010; Lloyd and Friedman in prep τ0 Probabilistic time-scaling

46. τ0 τ6 τ5 τ4 τ2 τ1 τ3 Age (Ma) τ0 Probabilistic time-scaling Hedman 2010; Lloyd and Friedman in prep

47. “Equal” time-tree

48. Probabilistic time-tree

49. “Equal” timetree Results

50. “Equal” timetree Results

51. “Equal” timetree Probablistic timetree Results

52. Results with error

53. Results with error

54. S1 S2 Two-tempo evolution

55. Slater 2013 BrownianOrnstein-Uhlenbeck Two-mode evolution

56. Conclusions

57. Conclusions

58. Conclusions

59. Conclusions

60. Conclusions

Time-binning rates of continuous character evolution on a phylogeny: the origin of amniotes, not tetrapods, is characterised by increased rates

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