SlideShare ist ein Scribd-Unternehmen logo

Detecting evolutionary regime shifts with comparative phylogenetics

•
•
Carl Boettiger
Carl Boettiger

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

BildungLifestyle
1 von 97
Downloaden Sie, um offline zu lesen
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
Introduction Parrotfish: a story A new method Challenges Opportunities Once upon a time. . . Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 2/61
Introduction Parrotfish: a story A new method Challenges Opportunities Phylogeny was a nuisance. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 3/61
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
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
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
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
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
Introduction Parrotfish: a story A new method Challenges Opportunities Regime Shifts Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 6/61
Introduction Parrotfish: a story A new method Challenges Opportunities The (Updated) Phylogeny of Phylogenetic Models Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 7/61
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 1 A Method: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 1 A Method: Detecting a release of constraint Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 1 A Method: Detecting a release of constraint 2 Challenges: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 1 A Method: Detecting a release of constraint 2 Challenges: The edge of identifiability Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 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
Introduction Parrotfish: a story A new method Challenges Opportunities Outline 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
Introduction Parrotfish: a story A new method Challenges Opportunities A key innovation? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
Introduction Parrotfish: a story A new method Challenges Opportunities A key innovation? This guy Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
Introduction Parrotfish: a story A new method Challenges Opportunities A key innovation? This guy These fish Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 10/61
Introduction Parrotfish: a story A new method Challenges Opportunities Fish Suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 11/61
Introduction Parrotfish: a story A new method Challenges Opportunities Fish Suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 12/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 13/61
Introduction Parrotfish: a story A new method Challenges Opportunities These fish don’t suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 14/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 15/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 16/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 17/61
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
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
Introduction Parrotfish: a story A new method Challenges Opportunities An evolutionary regime shift? a large change in the model parameters Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 20/61
Introduction Parrotfish: a story A new method Challenges Opportunities An evolutionary regime shift? a large change in the model parameters In which parameters? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 20/61
Introduction Parrotfish: a story A new method Challenges Opportunities Candidate models Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 21/61
Introduction Parrotfish: a story A new method Challenges Opportunities Unconstrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 22/61
Introduction Parrotfish: a story A new method Challenges Opportunities Constrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 23/61
Introduction Parrotfish: a story A new method Challenges Opportunities Release of constraint Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 24/61
Introduction Parrotfish: a story A new method Challenges Opportunities Accelerating rates Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 25/61
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
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 27/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 28/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 29/61
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
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
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
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
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
Introduction Parrotfish: a story A new method Challenges Opportunities Generalized 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
Introduction Parrotfish: a story A new method Challenges Opportunities Some Mathematical Conveniences Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
Introduction Parrotfish: a story A new method Challenges Opportunities Some Mathematical Conveniences Gaussian process! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
Introduction Parrotfish: a story A new method Challenges Opportunities Some Mathematical Conveniences Gaussian process! Need only E(Xi ) and Cov(Xi , Xj ) Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
Introduction Parrotfish: a story A new method Challenges Opportunities Some 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
Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular integrals! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular integrals! E( f (Xi )dWi × f (Xj )dWj ) Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular 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
Introduction Parrotfish: a story A new method Challenges Opportunities Covariance 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
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 36/61
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
Introduction Parrotfish: a story A new method Challenges Opportunities Challenges Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 37/61
Introduction Parrotfish: a story A new method Challenges Opportunities Where the sidewalk ends Generalizing models any further, we will not have analytic likelihoods Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 38/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 39/61
Introduction Parrotfish: a story A new method Challenges Opportunities Limits of Identifiability? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 40/61
Introduction Parrotfish: a story A new method Challenges Opportunities Can our data support so many parameters? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 41/61
Introduction Parrotfish: a story A new method Challenges Opportunities How 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
Introduction Parrotfish: a story A new method Challenges Opportunities How 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
Introduction Parrotfish: a story A new method Challenges Opportunities How 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
Introduction Parrotfish: a story A new method Challenges Opportunities How 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
Introduction Parrotfish: a story A new method Challenges Opportunities AIC 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
Introduction Parrotfish: a story A new method Challenges Opportunities AIC 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
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
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
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
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
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
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
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
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
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 53/61
Introduction Parrotfish: a story A new method Challenges Opportunities Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 54/61
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
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Building tools, building community Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Building tools, building community Follow @ropensci for more Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
Introduction Parrotfish: a story A new method Challenges Opportunities A wealth of repositories Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 58/61
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
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
Introduction Parrotfish: a story A new method Challenges Opportunities Conclusions 1 Can distinguish mechanisms such as release of constraint. Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 60/61
Introduction Parrotfish: a story A new method Challenges Opportunities Conclusions 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
Introduction Parrotfish: a story A new method Challenges Opportunities Conclusions 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
Introduction Parrotfish: a story A new method Challenges Opportunities Conclusions 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
Introduction Parrotfish: a story A new method Challenges Opportunities Conclusions 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
Introduction Parrotfish: a story A new method Challenges Opportunities Acknowledgments 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

Empfohlen

Reading the Secrets of Biological Fluctuations
Reading the Secrets of Biological FluctuationsReading the Secrets of Biological Fluctuations
Reading the Secrets of Biological FluctuationsCarl Boettiger
 
Natural Selection - Crash Course Biology.htmlI hope you like thi.docx
Natural Selection - Crash Course Biology.htmlI hope you like thi.docxNatural Selection - Crash Course Biology.htmlI hope you like thi.docx
Natural Selection - Crash Course Biology.htmlI hope you like thi.docxvannagoforth
 
Liberty university biol 101 study guide quiz 7 solutions answers slideshare
Liberty university biol 101 study guide quiz 7 solutions answers slideshareLiberty university biol 101 study guide quiz 7 solutions answers slideshare
Liberty university biol 101 study guide quiz 7 solutions answers slideshareLiberty Liberty
 
Investigación con embriones humanos ¿sí o no
Investigación con embriones humanos ¿sí o noInvestigación con embriones humanos ¿sí o no
Investigación con embriones humanos ¿sí o noseminary
 
Graham Slater's Phyloseminar Slides 12-10-2013
Graham Slater's Phyloseminar Slides 12-10-2013Graham Slater's Phyloseminar Slides 12-10-2013
Graham Slater's Phyloseminar Slides 12-10-2013gjslater
 
ESA 2012 talk
ESA 2012 talkESA 2012 talk
ESA 2012 talkCarl Boettiger
 
Regime shifts in ecology and evolution
Regime shifts in ecology and evolutionRegime shifts in ecology and evolution
Regime shifts in ecology and evolutionCarl Boettiger
 
Limits to Detection for Early Warning Signals of Population Collapse
Limits to Detection for Early Warning Signals of Population CollapseLimits to Detection for Early Warning Signals of Population Collapse
Limits to Detection for Early Warning Signals of Population CollapseCarl Boettiger
 

Empfohlen

Reading the Secrets of Biological Fluctuations
Reading the Secrets of Biological FluctuationsReading the Secrets of Biological Fluctuations
Reading the Secrets of Biological FluctuationsCarl Boettiger
 
Natural Selection - Crash Course Biology.htmlI hope you like thi.docx
Natural Selection - Crash Course Biology.htmlI hope you like thi.docxNatural Selection - Crash Course Biology.htmlI hope you like thi.docx
Natural Selection - Crash Course Biology.htmlI hope you like thi.docxvannagoforth
 
Liberty university biol 101 study guide quiz 7 solutions answers slideshare
Liberty university biol 101 study guide quiz 7 solutions answers slideshareLiberty university biol 101 study guide quiz 7 solutions answers slideshare
Liberty university biol 101 study guide quiz 7 solutions answers slideshareLiberty Liberty
 
Investigación con embriones humanos ¿sí o no
Investigación con embriones humanos ¿sí o noInvestigación con embriones humanos ¿sí o no
Investigación con embriones humanos ¿sí o noseminary
 
Graham Slater's Phyloseminar Slides 12-10-2013
Graham Slater's Phyloseminar Slides 12-10-2013Graham Slater's Phyloseminar Slides 12-10-2013
Graham Slater's Phyloseminar Slides 12-10-2013gjslater
 
ESA 2012 talk
ESA 2012 talkESA 2012 talk
ESA 2012 talkCarl Boettiger
 
Regime shifts in ecology and evolution
Regime shifts in ecology and evolutionRegime shifts in ecology and evolution
Regime shifts in ecology and evolutionCarl Boettiger
 
Limits to Detection for Early Warning Signals of Population Collapse
Limits to Detection for Early Warning Signals of Population CollapseLimits to Detection for Early Warning Signals of Population Collapse
Limits to Detection for Early Warning Signals of Population CollapseCarl Boettiger
 
R interface to TreeBASE
R interface to TreeBASER interface to TreeBASE
R interface to TreeBASECarl Boettiger
 
A general model of continuous character evolution
A general model of continuous character evolutionA general model of continuous character evolution
A general model of continuous character evolutionCarl Boettiger
 
Iiasa final
Iiasa finalIiasa final
Iiasa finalCarl Boettiger
 
IIASA Progress Report 2
IIASA Progress Report 2IIASA Progress Report 2
IIASA Progress Report 2Carl Boettiger
 
Scioslides
ScioslidesScioslides
ScioslidesCarl Boettiger
 
Is your phylogeny informative?
Is your phylogeny informative?Is your phylogeny informative?
Is your phylogeny informative?Carl Boettiger
 
Inferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic TreesInferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic TreesCarl Boettiger
 
A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...Carl Boettiger
 
Open Science
Open ScienceOpen Science
Open ScienceCarl Boettiger
 
Concurrency Control in Database Management system
Concurrency Control in Database Management systemConcurrency Control in Database Management system
Concurrency Control in Database Management systemChristalin Nelson
 
Choosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for ParentsChoosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for Parentsnavabharathschool99
 
Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...Seán Kennedy
 
ClimART Action | eTwinning Project
ClimART Action | eTwinning ProjectClimART Action | eTwinning Project
ClimART Action | eTwinning Projectjordimapav
 
Paradigm shift in nursing research by RS MEHTA
Paradigm shift in nursing research by RS MEHTAParadigm shift in nursing research by RS MEHTA
Paradigm shift in nursing research by RS MEHTABP KOIRALA INSTITUTE OF HELATH SCIENCS,, NEPAL
 
Transaction Management in Database Management System
Transaction Management in Database Management SystemTransaction Management in Database Management System
Transaction Management in Database Management SystemChristalin Nelson
 
Integumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.pptIntegumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.pptshraddhaparab530
 
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdfGrade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdfJemuel Francisco
 
Measures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped dataMeasures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped dataBabyAnnMotar
 
Keynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-designKeynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-designMIPLM
 
How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17Celine George
 
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...JojoEDelaCruz
 
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...Postal Advocate Inc.
 

Weitere ähnliche Inhalte

Mehr von Carl Boettiger

R interface to TreeBASE
R interface to TreeBASER interface to TreeBASE
R interface to TreeBASECarl Boettiger
 
A general model of continuous character evolution
A general model of continuous character evolutionA general model of continuous character evolution
A general model of continuous character evolutionCarl Boettiger
 
IIASA Progress Report 2
IIASA Progress Report 2IIASA Progress Report 2
IIASA Progress Report 2Carl Boettiger
 
Is your phylogeny informative?
Is your phylogeny informative?Is your phylogeny informative?
Is your phylogeny informative?Carl Boettiger
 
Inferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic TreesInferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic TreesCarl Boettiger
 
A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...Carl Boettiger
 

Mehr von Carl Boettiger (9)

R interface to TreeBASE
R interface to TreeBASER interface to TreeBASE
R interface to TreeBASE
 
A general model of continuous character evolution
A general model of continuous character evolutionA general model of continuous character evolution
A general model of continuous character evolution
 
Iiasa final
Iiasa finalIiasa final
Iiasa final
 
IIASA Progress Report 2
IIASA Progress Report 2IIASA Progress Report 2
IIASA Progress Report 2
 
Scioslides
ScioslidesScioslides
Scioslides
 
Is your phylogeny informative?
Is your phylogeny informative?Is your phylogeny informative?
Is your phylogeny informative?
 
Inferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic TreesInferring Adaptive Landscapes from Phylogenetic Trees
Inferring Adaptive Landscapes from Phylogenetic Trees
 
A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...A new phylogenetic comparative method: detecting niches and transitions with ...
A new phylogenetic comparative method: detecting niches and transitions with ...
 
Open Science
Open ScienceOpen Science
Open Science
 

Kürzlich hochgeladen

Concurrency Control in Database Management system
Concurrency Control in Database Management systemConcurrency Control in Database Management system
Concurrency Control in Database Management systemChristalin Nelson
 
Choosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for ParentsChoosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for Parentsnavabharathschool99
 
Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...Seán Kennedy
 
ClimART Action | eTwinning Project
ClimART Action | eTwinning ProjectClimART Action | eTwinning Project
ClimART Action | eTwinning Projectjordimapav
 
Transaction Management in Database Management System
Transaction Management in Database Management SystemTransaction Management in Database Management System
Transaction Management in Database Management SystemChristalin Nelson
 
Integumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.pptIntegumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.pptshraddhaparab530
 
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdfGrade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdfJemuel Francisco
 
Measures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped dataMeasures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped dataBabyAnnMotar
 
Keynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-designKeynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-designMIPLM
 
How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17Celine George
 
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...JojoEDelaCruz
 
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...Postal Advocate Inc.
 
Activity 2-unit 2-update 2024. English translation
Activity 2-unit 2-update 2024. English translationActivity 2-unit 2-update 2024. English translation
Activity 2-unit 2-update 2024. English translationRosabel UA
 
Active Learning Strategies (in short ALS).pdf
Active Learning Strategies (in short ALS).pdfActive Learning Strategies (in short ALS).pdf
Active Learning Strategies (in short ALS).pdfPatidar M
 
Textual Evidence in Reading and Writing of SHS
Textual Evidence in Reading and Writing of SHSTextual Evidence in Reading and Writing of SHS
Textual Evidence in Reading and Writing of SHSMae Pangan
 
EMBODO Lesson Plan Grade 9 Law of Sines.docx
EMBODO Lesson Plan Grade 9 Law of Sines.docxEMBODO Lesson Plan Grade 9 Law of Sines.docx
EMBODO Lesson Plan Grade 9 Law of Sines.docxElton John Embodo
 
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)lakshayb543
 
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptx
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptxMULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptx
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptxAnupkumar Sharma
 

Kürzlich hochgeladen (20)

Concurrency Control in Database Management system
Concurrency Control in Database Management systemConcurrency Control in Database Management system
Concurrency Control in Database Management system
 
Choosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for ParentsChoosing the Right CBSE School A Comprehensive Guide for Parents
Choosing the Right CBSE School A Comprehensive Guide for Parents
 
Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...Student Profile Sample - We help schools to connect the data they have, with ...
Student Profile Sample - We help schools to connect the data they have, with ...
 
ClimART Action | eTwinning Project
ClimART Action | eTwinning ProjectClimART Action | eTwinning Project
ClimART Action | eTwinning Project
 
Paradigm shift in nursing research by RS MEHTA
Paradigm shift in nursing research by RS MEHTAParadigm shift in nursing research by RS MEHTA
Paradigm shift in nursing research by RS MEHTA
 
Transaction Management in Database Management System
Transaction Management in Database Management SystemTransaction Management in Database Management System
Transaction Management in Database Management System
 
Integumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.pptIntegumentary System SMP B. Pharm Sem I.ppt
Integumentary System SMP B. Pharm Sem I.ppt
 
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdfGrade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
Grade 9 Quarter 4 Dll Grade 9 Quarter 4 DLL.pdf
 
Measures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped dataMeasures of Position DECILES for ungrouped data
Measures of Position DECILES for ungrouped data
 
Keynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-designKeynote by Prof. Wurzer at Nordex about IP-design
Keynote by Prof. Wurzer at Nordex about IP-design
 
How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17How to Add Barcode on PDF Report in Odoo 17
How to Add Barcode on PDF Report in Odoo 17
 
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
ENG 5 Q4 WEEk 1 DAY 1 Restate sentences heard in one’s own words. Use appropr...
 
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
USPS® Forced Meter Migration - How to Know if Your Postage Meter Will Soon be...
 
Activity 2-unit 2-update 2024. English translation
Activity 2-unit 2-update 2024. English translationActivity 2-unit 2-update 2024. English translation
Activity 2-unit 2-update 2024. English translation
 
YOUVE GOT EMAIL_FINALS_EL_DORADO_2024.pptx
YOUVE GOT EMAIL_FINALS_EL_DORADO_2024.pptxYOUVE GOT EMAIL_FINALS_EL_DORADO_2024.pptx
YOUVE GOT EMAIL_FINALS_EL_DORADO_2024.pptx
 
Active Learning Strategies (in short ALS).pdf
Active Learning Strategies (in short ALS).pdfActive Learning Strategies (in short ALS).pdf
Active Learning Strategies (in short ALS).pdf
 
Textual Evidence in Reading and Writing of SHS
Textual Evidence in Reading and Writing of SHSTextual Evidence in Reading and Writing of SHS
Textual Evidence in Reading and Writing of SHS
 
EMBODO Lesson Plan Grade 9 Law of Sines.docx
EMBODO Lesson Plan Grade 9 Law of Sines.docxEMBODO Lesson Plan Grade 9 Law of Sines.docx
EMBODO Lesson Plan Grade 9 Law of Sines.docx
 
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)
Visit to a blind student's school🧑‍🦯🧑‍🦯(community medicine)
 
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptx
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptxMULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptx
MULTIDISCIPLINRY NATURE OF THE ENVIRONMENTAL STUDIES.pptx
 

Detecting evolutionary regime shifts with comparative phylogenetics

  • 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 Opportunities The (Updated) Phylogeny of Phylogenetic Models Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 7/61
  • 11. Introduction Parrotfish: a story A new method Challenges Opportunities Outline 1 A Method: Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 8/61
  • 12. Introduction Parrotfish: a story A new method Challenges Opportunities Outline 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 Opportunities Outline 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 Opportunities Outline 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 Opportunities Outline 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 Opportunities Outline 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 Opportunities A key innovation? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
  • 18. Introduction Parrotfish: a story A new method Challenges Opportunities A key innovation? This guy Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 9/61
  • 19. Introduction Parrotfish: a story A new method Challenges Opportunities A 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 Opportunities Fish Suck Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 11/61
  • 22. Introduction Parrotfish: a story A new method Challenges Opportunities Fish 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 Opportunities These 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 Opportunities An 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 Opportunities An 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 Opportunities Unconstrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 22/61
  • 34. Introduction Parrotfish: a story A new method Challenges Opportunities Constrained Evolution Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 23/61
  • 35. Introduction Parrotfish: a story A new method Challenges Opportunities Release of constraint Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 24/61
  • 36. Introduction Parrotfish: a story A new method Challenges Opportunities Accelerating 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 Opportunities Generalized 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 Opportunities Some Mathematical Conveniences Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 48. Introduction Parrotfish: a story A new method Challenges Opportunities Some Mathematical Conveniences Gaussian process! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 33/61
  • 49. Introduction Parrotfish: a story A new method Challenges Opportunities Some 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 Opportunities Some 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 Opportunities Averaging removes the random shocks Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 52. Introduction Parrotfish: a story A new method Challenges Opportunities Averaging 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 Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular integrals! Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 34/61
  • 54. Introduction Parrotfish: a story A new method Challenges Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular 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 Opportunities Averaging removes the random shocks n E(Xi ) = eγi θi 1 − eαi ti i=0 Itô Isometry makes stochastic integrals into regular 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 Opportunities Covariance 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 Opportunities Where 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 Opportunities Limits of Identifiability? Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 40/61
  • 63. Introduction Parrotfish: a story A new method Challenges Opportunities Can 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 Opportunities How 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 Opportunities How 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 Opportunities How 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 Opportunities How 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 Opportunities AIC 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 Opportunities AIC 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 Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 82. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 83. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 84. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic Access to data Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 56/61
  • 85. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 86. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic access for everyone Carl Boettiger, UC Davis Detecting Evolutionary Regime Shifts 57/61
  • 87. Introduction Parrotfish: a story A new method Challenges Opportunities Programmatic 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 Opportunities Programmatic 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 Opportunities A 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 Opportunities Conclusions 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 Opportunities Conclusions 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 Opportunities Conclusions 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 Opportunities Conclusions 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 Opportunities Conclusions 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 Opportunities Acknowledgments 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