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Time-binning rates of continuous character
evolution on a phylogeny: the origin of
amniotes, not tetrapods, is characteris...
Acknowledgements
Chris Organ Graham Slater
Questions
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 rat...
Questions
2. How did the tempo of tetrapod mandible
evolution change over their early evolution?
3. How does phylogenetic ...
How fast?
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate categories
Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
Rate data types
Simpson 1944,1953; Westoll 1949
Rate data types
Simpson 1944,1953; Westoll 1949
Rate data types
Simpson 1944,1953; Westoll 1949
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
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
Continuous data: mode dominates
Trait
value
Time
Early Burst
Late Burst
Trait
Time
Continuous data: mode dominates
Rate
Time
Continuous rates
Rate
Time
Continuous rates
Raia et al. 2013
Continuous rates
Harmon et al. 2008
New method: guts
New method: description
New method: description
New method: description
New method: description
S1 S2 S31
New method: description
Anderson et al. 2013
Data
Anderson et al. 2013
Data
Time-scaling trees
Lee et al 2014
Time-scaling trees: simultaneous
Time-scaling trees: a posteriori
paleotree
strap
Time-scaling trees: a posteriori
+
paleotree
strap
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)
Derst...
Time-scaling trees: a posteriori
cal3
Bapst 2013
Hedman method
Lloyd and Friedman in prep
Nowak
Nowak et al 2013
Arbitrary...
Time-scaling trees: a posteriori
Hedman method
Lloyd and Friedman in prep
Arbitrary Probabilistic
Branch-sharing
Ruta et a...
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. 20...
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” time-tree
Probabilistic time-tree
“Equal”
timetree
Results
“Equal”
timetree
Results
“Equal” timetree
Probablistic timetree
Results
Results with error
Results with error
S1 S2
Two-tempo evolution
Slater 2013
BrownianOrnstein-Uhlenbeck
Two-mode evolution
Conclusions
Conclusions
Conclusions
Conclusions
Conclusions
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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

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

Published in: Science
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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. 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. 2. Acknowledgements Chris Organ Graham Slater
  3. 3. Questions
  4. 4. Questions 1. How can we measure rates of evolution in a continuous character over multiple time bins?
  5. 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. 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. 7. How fast?
  8. 8. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  9. 9. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  10. 10. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  11. 11. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  12. 12. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  13. 13. Rate categories Cloutier 1991; Lloyd et al. 2012; Lloyd submitted
  14. 14. Rate data types Simpson 1944,1953; Westoll 1949
  15. 15. Rate data types Simpson 1944,1953; Westoll 1949
  16. 16. Rate data types Simpson 1944,1953; Westoll 1949
  17. 17. Rate data types Simpson 1944,1953; Westoll 1949
  18. 18. Discrete data: disparity and tempo Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted
  19. 19. Discrete data: disparity and tempo Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted
  20. 20. Discrete data: disparity and tempo Claddis Davis et al. 2012; Lloyd et al. 2012; Lloyd submitted
  21. 21. Continuous data: mode dominates
  22. 22. Continuous data: mode dominates Trait value Time
  23. 23. Early Burst Late Burst Trait Time Continuous data: mode dominates
  24. 24. Rate Time Continuous rates
  25. 25. Rate Time Continuous rates
  26. 26. Raia et al. 2013 Continuous rates
  27. 27. Harmon et al. 2008 New method: guts
  28. 28. New method: description
  29. 29. New method: description
  30. 30. New method: description
  31. 31. New method: description
  32. 32. S1 S2 S31 New method: description
  33. 33. Anderson et al. 2013 Data
  34. 34. Anderson et al. 2013 Data
  35. 35. Time-scaling trees
  36. 36. Lee et al 2014 Time-scaling trees: simultaneous
  37. 37. Time-scaling trees: a posteriori paleotree strap
  38. 38. Time-scaling trees: a posteriori + paleotree strap
  39. 39. Time-scaling trees: a posteriori + = paleotree strap
  40. 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. 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. 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. 43. τ7 τ8 τ6 τ5 Traditional approach first Ruta et al. 2006; Brusatte et al. 2008 Branch-sharing (“equal”)
  44. 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. 45. τ6 τ5 τ4 τ2 τ1 τ3 Hedman 2010; Lloyd and Friedman in prep τ0 Probabilistic time-scaling
  46. 46. τ0 τ6 τ5 τ4 τ2 τ1 τ3 Age (Ma) τ0 Probabilistic time-scaling Hedman 2010; Lloyd and Friedman in prep
  47. 47. “Equal” time-tree
  48. 48. Probabilistic time-tree
  49. 49. “Equal” timetree Results
  50. 50. “Equal” timetree Results
  51. 51. “Equal” timetree Probablistic timetree Results
  52. 52. Results with error
  53. 53. Results with error
  54. 54. S1 S2 Two-tempo evolution
  55. 55. Slater 2013 BrownianOrnstein-Uhlenbeck Two-mode evolution
  56. 56. Conclusions
  57. 57. Conclusions
  58. 58. Conclusions
  59. 59. Conclusions
  60. 60. Conclusions

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