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Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
Detecting evolutionary regime shifts with comparative phylogenetics
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Detecting evolutionary regime shifts with comparative phylogenetics

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Talk presented at Evolution 2012 conference in the SSB Symposium: "New phylogenetic …

Talk presented at Evolution 2012 conference in the SSB Symposium: "New phylogenetic
methods for quantitative
trait evolution"

Published in: Education, Lifestyle
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  • 1. Introduction Parrotfish: a story A new method Challenges Opportunities Detecting evolutionary regime shifts with comparative phylogenetics @cboettig Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 1/61
  • 2. Introduction Parrotfish: a story A new method Challenges Opportunities Once upon a time. . . Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 2/61
  • 3. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogeny was a nuisance. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 3/61
  • 4. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogeny was a nuisance. something we “corrected for” Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 3/61
  • 5. Introduction Parrotfish: a story A new method Challenges Opportunities Then we turned our attention to the parameters Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 4/61
  • 6. Introduction Parrotfish: a story A new method Challenges Opportunities Then we turned our attention to the parameters 2 Diversification σ α Stabilizing selection θ Adaptive Optimum λ phylogenetic signal κ speciational change δ accelerating / decelerating rates Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 4/61
  • 7. Introduction Parrotfish: a story A new method Challenges Opportunities The parameters were allowed to change, Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 5/61
  • 8. Introduction Parrotfish: a story A new method Challenges Opportunities The parameters were allowed to change, we became interested in where the changes occur. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 5/61
  • 9. Introduction Parrotfish: a story A new method Challenges Opportunities Regime Shifts Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 6/61
  • 10. Introduction Parrotfish: a story A new method Challenges OpportunitiesThe (Updated) Phylogeny of Phylogenetic Models Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 7/61
  • 11. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 12. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Detecting a release of constraint Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 13. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Detecting a release of constraint 2 Challenges: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 14. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Detecting a release of constraint 2 Challenges: The edge of identifiability Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 15. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Detecting a release of constraint 2 Challenges: The edge of identifiability 3 Opportunities: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 16. Introduction Parrotfish: a story A new method Challenges OpportunitiesOutline 1 A Method: Detecting a release of constraint 2 Challenges: The edge of identifiability 3 Opportunities: Large, synthetic data sets Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 17. Introduction Parrotfish: a story A new method Challenges OpportunitiesA key innovation? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
  • 18. Introduction Parrotfish: a story A new method Challenges OpportunitiesA key innovation? This guy Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
  • 19. Introduction Parrotfish: a story A new method Challenges OpportunitiesA key innovation? This guy These fish Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
  • 20. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 10/61
  • 21. Introduction Parrotfish: a story A new method Challenges OpportunitiesFish Suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 11/61
  • 22. Introduction Parrotfish: a story A new method Challenges OpportunitiesFish Suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 12/61
  • 23. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 13/61
  • 24. Introduction Parrotfish: a story A new method Challenges OpportunitiesThese fish don’t suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 14/61
  • 25. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 15/61
  • 26. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 16/61
  • 27. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 17/61
  • 28. Introduction Parrotfish: a story A new method Challenges Opportunities Did this innovation release the constraints of suction feeding? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 18/61
  • 29. Introduction Parrotfish: a story A new method Challenges Opportunities. . . and release a burst of jaw evolution? Parrotfish Intramandibular Pharyngeal Joint Jaw Wrasses Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 19/61
  • 30. Introduction Parrotfish: a story A new method Challenges OpportunitiesAn evolutionary regime shift? a large change in the model parameters Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 20/61
  • 31. Introduction Parrotfish: a story A new method Challenges OpportunitiesAn evolutionary regime shift? a large change in the model parameters In which parameters? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 20/61
  • 32. Introduction Parrotfish: a story A new method Challenges Opportunities Candidate models Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 21/61
  • 33. Introduction Parrotfish: a story A new method Challenges OpportunitiesUnconstrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 22/61
  • 34. Introduction Parrotfish: a story A new method Challenges OpportunitiesConstrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 23/61
  • 35. Introduction Parrotfish: a story A new method Challenges OpportunitiesRelease of constraint Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 24/61
  • 36. Introduction Parrotfish: a story A new method Challenges OpportunitiesAccelerating rates Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 25/61
  • 37. Introduction Parrotfish: a story A new method Challenges Opportunities 2 Brownian Motion 2 Ornstein-Uhlenbeck 1 1 trait value trait value 0 0 -1 -1 -2 -2 0 20 40 60 80 100 0 20 40 60 80 100 time time 2 Accelerated Evolution 2 Release of Constraint 1 1 trait value trait value 0 0 -1 -1 -2 -2 0 20 40 60 80 100 0 20 40 60 80 100 time time Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 26/61
  • 38. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 27/61
  • 39. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 28/61
  • 40. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 29/61
  • 41. Introduction Parrotfish: a story A new method Challenges Opportunities XT1 = X0 e−α1 T1 + where you start θ1 1 − e−α1 T1 + Where you are going T1 σ1 eα1 (s−T1 ) dWs 0 Random shocks along the way Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 30/61
  • 42. Introduction Parrotfish: a story A new method Challenges Opportunities XT1 = X0 e−α1 T1 + where you start θ1 1 − e−α1 T1 + Where you are going T1 σ1 eα1 (s−T1 ) dWs 0 Random shocks along the way Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 30/61
  • 43. Introduction Parrotfish: a story A new method Challenges Opportunities XT2 = X1 e−α2 T2 + where you were θ2 1 − e−α2 T2 + possibly new optimum T2 σ2 eα2 (s−T2 ) dWs T1 possibly new shocks Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 31/61
  • 44. Introduction Parrotfish: a story A new method Challenges Opportunities XT2 = X1 e−α2 T2 + where you were θ2 1 − e−α2 T2 + possibly new optimum T2 σ2 eα2 (s−T2 ) dWs T1 possibly new shocks Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 31/61
  • 45. Introduction Parrotfish: a story A new method Challenges Opportunities XT2 = X1 e−α2 T2 + where you were θ2 1 − e−α2 T2 + possibly new optimum T2 σ2 eα2 (s−T2 ) dWs T1 possibly new shocks n γi = − αj t j j=i+1 Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 31/61
  • 46. Introduction Parrotfish: a story A new method Challenges OpportunitiesGeneralized OU model n XN = eγi θi 1 − eαi ti + i=0 ti σi eαi (s−ti ) dWs i 0 Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 32/61
  • 47. Introduction Parrotfish: a story A new method Challenges OpportunitiesSome Mathematical Conveniences Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 48. Introduction Parrotfish: a story A new method Challenges OpportunitiesSome Mathematical Conveniences Gaussian process! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 49. Introduction Parrotfish: a story A new method Challenges OpportunitiesSome Mathematical Conveniences Gaussian process! Need only E(Xi ) and Cov(Xi , Xj ) Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 50. Introduction Parrotfish: a story A new method Challenges OpportunitiesSome Mathematical Conveniences Gaussian process! Need only E(Xi ) and Cov(Xi , Xj ) Evolution on different branches is independent Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 51. Introduction Parrotfish: a story A new method Challenges OpportunitiesAveraging removes the random shocks Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 52. Introduction Parrotfish: a story A new method Challenges OpportunitiesAveraging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 53. Introduction Parrotfish: a story A new method Challenges OpportunitiesAveraging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0Itô Isometry makes stochastic integrals intoregular integrals! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 54. Introduction Parrotfish: a story A new method Challenges OpportunitiesAveraging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0Itô Isometry makes stochastic integrals intoregular integrals! E( f (Xi )dWi × f (Xj )dWj ) Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 55. Introduction Parrotfish: a story A new method Challenges OpportunitiesAveraging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0Itô Isometry makes stochastic integrals intoregular integrals! E( f (Xi )dWi × f (Xj )dWj ) Cov(Xi , Xj ) = n ti eγi σi eαi (u−ti ) dWu × i i=1 0 m sj eγj σj eαj (v−sj ) dWv j j=1 0 Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 56. Introduction Parrotfish: a story A new method Challenges OpportunitiesCovariance matrix determines the likelihood Cov(Xi , Xj ) = k 2 σs eγs +γs 1 − e−2αs ts s=0 2αs Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 35/61
  • 57. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 36/61
  • 58. Introduction Parrotfish: a story A new method Challenges Opportunities OUwie Beaulieu et al. 2012, Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 36/61
  • 59. Introduction Parrotfish: a story A new method Challenges Opportunities Challenges Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 37/61
  • 60. Introduction Parrotfish: a story A new method Challenges OpportunitiesWhere the sidewalk ends Generalizing models any further, we will not have analytic likelihoods Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 38/61
  • 61. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 39/61
  • 62. Introduction Parrotfish: a story A new method Challenges OpportunitiesLimits of Identifiability? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 40/61
  • 63. Introduction Parrotfish: a story A new method Challenges OpportunitiesCan our data support so many parameters? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 41/61
  • 64. Introduction Parrotfish: a story A new method Challenges OpportunitiesHow do we choose between multiple complex models? Before we can ask which is the right model, Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 42/61
  • 65. Introduction Parrotfish: a story A new method Challenges OpportunitiesHow do we choose between multiple complex models? Before we can ask which is the right model, we must ask if we have enough data to tell. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 42/61
  • 66. Introduction Parrotfish: a story A new method Challenges OpportunitiesHow do we choose between multiple complex models? Before we can ask which is the right model, we must ask if we have enough data to tell. Information citeria don’t address this. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 42/61
  • 67. Introduction Parrotfish: a story A new method Challenges OpportunitiesHow do we choose between multiple complex models? Before we can ask which is the right model, we must ask if we have enough data to tell. Information citeria don’t address this. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 42/61
  • 68. Introduction Parrotfish: a story A new method Challenges OpportunitiesAIC scores for four model comparisons (a) BM vs. OU.3 (b) OU.3 vs. OU.4 0.15 0.08 0.10 Density Density 0.04 0.05 0.00 0.00 0 10 20 30 40 50 -10 0 10 20 30 δ δ (c) OU.3 vs. OU.15 (d) BM vs. OU.1 0.04 0.20 0.03 0.15 Density Density 0.02 0.10 0.01 0.05 0.00 0.00 0 50 100 150 -5 0 5 10 15 δ δ Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 43/61
  • 69. Introduction Parrotfish: a story A new method Challenges OpportunitiesAIC scores for four model comparisons (a) BM vs. OU.3 (b) OU.3 vs. OU.4 False Pos (37%) False Pos (43.75%) 0.15 False Neg (0%) False Neg (8.25%) 0.08 0.10 Density Density 0.04 0.05 0.00 0.00 0 10 20 30 40 50 -10 0 10 20 30 δ δ (c) OU.3 vs. OU.15 (d) BM vs. OU.1 0.04 False Pos (47.75%) False Pos (19.95%) 0.20 False Neg (0%) False Neg (76.65%) 0.03 0.15 Density Density 0.02 0.10 0.01 0.05 0.00 0.00 0 50 100 150 -5 0 5 10 15 δ δ Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 44/61
  • 70. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 45/61
  • 71. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 46/61
  • 72. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th LogLik(complex) LogLik(simple) Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 47/61
  • 73. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 48/61
  • 74. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 49/61
  • 75. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo m fro → ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 50/61
  • 76. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo x p le m comdel → fro → mo ate l mul mode Si ple sim del s h mo ts bot a ← Fi is dat to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 51/61
  • 77. Introduction Parrotfish: a story A new method Challenges Opportunities Phylogenetic Monte Carlo x p le om comdel → e fr → mo ulat odel Sim ple m sim l s mode ts both ← Fi is data to th LogLik(complex) LogLik(simple) frequency Likelihood ratio Boettiger et al. 2012, Evolution, pmc R package Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 52/61
  • 78. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 53/61
  • 79. Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 54/61
  • 80. Introduction Parrotfish: a story A new method Challenges Opportunities Software has made comparative methods ubiquitous. . . So how about data? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 55/61
  • 81. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 82. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 83. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 84. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 85. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 86. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 87. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic access for everyone Building tools, building community Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 88. Introduction Parrotfish: a story A new method Challenges OpportunitiesProgrammatic access for everyone Building tools, building community Follow @ropensci for more Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 89. Introduction Parrotfish: a story A new method Challenges OpportunitiesA wealth of repositories Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 58/61
  • 90. Introduction Parrotfish: a story A new method Challenges Opportunities and what about the Parrotfish? Was it a release of constraint after all? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 59/61
  • 91. Introduction Parrotfish: a story A new method Challenges Opportunities and what about the Parrotfish? Was it a release of constraint after all? Of course! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 59/61
  • 92. Introduction Parrotfish: a story A new method Challenges OpportunitiesConclusions 1 Can distinguish mechanisms such as release of constraint. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
  • 93. Introduction Parrotfish: a story A new method Challenges OpportunitiesConclusions 1 Can distinguish mechanisms such as release of constraint. 2 Pushing the limits of analytic solutions, Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
  • 94. Introduction Parrotfish: a story A new method Challenges OpportunitiesConclusions 1 Can distinguish mechanisms such as release of constraint. 2 Pushing the limits of analytic solutions, 3 and more worryingly, the limits of our data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
  • 95. Introduction Parrotfish: a story A new method Challenges OpportunitiesConclusions 1 Can distinguish mechanisms such as release of constraint. 2 Pushing the limits of analytic solutions, 3 and more worryingly, the limits of our data 4 New and diverse data sources would alleviate, but not solve these issues Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
  • 96. Introduction Parrotfish: a story A new method Challenges OpportunitiesConclusions 1 Can distinguish mechanisms such as release of constraint. 2 Pushing the limits of analytic solutions, 3 and more worryingly, the limits of our data 4 New and diverse data sources would alleviate, but not solve these issues 5 Continue to foster a community of data sharing and code sharing Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
  • 97. Introduction Parrotfish: a story A new method Challenges OpportunitiesAcknowledgments Jeremy Beaulieu Peter Wainwright Graham Coop Peter Ralph Brian O’Meara Duncan Temple Lang Slides, source code, and more and many more http://carlboettiger.info Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 61/61

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