SlideShare una empresa de Scribd 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"

EducaciónEstilo de vida
1 de 97
Descargar para leer sin conexión
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

Recomendados

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
 

Recomendados

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
 
Micro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdfMicro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdfPoh-Sun Goh
 
Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)Jisc
 
Spellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please PractiseSpellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please PractiseAnaAcapella
 
How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17Celine George
 
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...christianmathematics
 
Dyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptxDyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptxcallscotland1987
 
Application orientated numerical on hev.ppt
Application orientated numerical on hev.pptApplication orientated numerical on hev.ppt
Application orientated numerical on hev.pptRamjanShidvankar
 
1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdf1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdfQucHHunhnh
 
Basic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptxBasic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptxDenish Jangid
 
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptxSKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptxAmanpreet Kaur
 
Introduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The BasicsIntroduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The BasicsTechSoup
 
Spatium Project Simulation student brief
Spatium Project Simulation student briefSpatium Project Simulation student brief
Spatium Project Simulation student briefAssociation for Project Management
 
How to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POSHow to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POSCeline George
 

Más contenido relacionado

Más de 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
 

Más de 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
 

Último

Micro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdfMicro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdfPoh-Sun Goh
 
Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)Jisc
 
Spellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please PractiseSpellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please PractiseAnaAcapella
 
How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17Celine George
 
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...christianmathematics
 
Dyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptxDyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptxcallscotland1987
 
Application orientated numerical on hev.ppt
Application orientated numerical on hev.pptApplication orientated numerical on hev.ppt
Application orientated numerical on hev.pptRamjanShidvankar
 
1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdf1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdfQucHHunhnh
 
Basic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptxBasic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptxDenish Jangid
 
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptxSKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptxAmanpreet Kaur
 
Introduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The BasicsIntroduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The BasicsTechSoup
 
How to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POSHow to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POSCeline George
 
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...Nguyen Thanh Tu Collection
 
microwave assisted reaction. General introduction
microwave assisted reaction. General introductionmicrowave assisted reaction. General introduction
microwave assisted reaction. General introductionMaksud Ahmed
 
Unit-V; Pricing (Pharma Marketing Management).pptx
Unit-V; Pricing (Pharma Marketing Management).pptxUnit-V; Pricing (Pharma Marketing Management).pptx
Unit-V; Pricing (Pharma Marketing Management).pptxVishalSingh1417
 
Unit-IV; Professional Sales Representative (PSR).pptx
Unit-IV; Professional Sales Representative (PSR).pptxUnit-IV; Professional Sales Representative (PSR).pptx
Unit-IV; Professional Sales Representative (PSR).pptxVishalSingh1417
 
Third Battle of Panipat detailed notes.pptx
Third Battle of Panipat detailed notes.pptxThird Battle of Panipat detailed notes.pptx
Third Battle of Panipat detailed notes.pptxAmita Gupta
 
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesMixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesCeline George
 
PROCESS RECORDING FORMAT.docx
PROCESS RECORDING FORMAT.docxPROCESS RECORDING FORMAT.docx
PROCESS RECORDING FORMAT.docxPoojaSen20
 

Último (20)

Micro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdfMicro-Scholarship, What it is, How can it help me.pdf
Micro-Scholarship, What it is, How can it help me.pdf
 
Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)Accessible Digital Futures project (20/03/2024)
Accessible Digital Futures project (20/03/2024)
 
Spellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please PractiseSpellings Wk 3 English CAPS CARES Please Practise
Spellings Wk 3 English CAPS CARES Please Practise
 
How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17How to Create and Manage Wizard in Odoo 17
How to Create and Manage Wizard in Odoo 17
 
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
Explore beautiful and ugly buildings. Mathematics helps us create beautiful d...
 
Dyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptxDyslexia AI Workshop for Slideshare.pptx
Dyslexia AI Workshop for Slideshare.pptx
 
Application orientated numerical on hev.ppt
Application orientated numerical on hev.pptApplication orientated numerical on hev.ppt
Application orientated numerical on hev.ppt
 
1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdf1029-Danh muc Sach Giao Khoa khoi 6.pdf
1029-Danh muc Sach Giao Khoa khoi 6.pdf
 
Basic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptxBasic Civil Engineering first year Notes- Chapter 4 Building.pptx
Basic Civil Engineering first year Notes- Chapter 4 Building.pptx
 
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptxSKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
SKILL OF INTRODUCING THE LESSON MICRO SKILLS.pptx
 
Introduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The BasicsIntroduction to Nonprofit Accounting: The Basics
Introduction to Nonprofit Accounting: The Basics
 
Spatium Project Simulation student brief
Spatium Project Simulation student briefSpatium Project Simulation student brief
Spatium Project Simulation student brief
 
How to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POSHow to Manage Global Discount in Odoo 17 POS
How to Manage Global Discount in Odoo 17 POS
 
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...
TỔNG ÔN TẬP THI VÀO LỚP 10 MÔN TIẾNG ANH NĂM HỌC 2023 - 2024 CÓ ĐÁP ÁN (NGỮ Â...
 
microwave assisted reaction. General introduction
microwave assisted reaction. General introductionmicrowave assisted reaction. General introduction
microwave assisted reaction. General introduction
 
Unit-V; Pricing (Pharma Marketing Management).pptx
Unit-V; Pricing (Pharma Marketing Management).pptxUnit-V; Pricing (Pharma Marketing Management).pptx
Unit-V; Pricing (Pharma Marketing Management).pptx
 
Unit-IV; Professional Sales Representative (PSR).pptx
Unit-IV; Professional Sales Representative (PSR).pptxUnit-IV; Professional Sales Representative (PSR).pptx
Unit-IV; Professional Sales Representative (PSR).pptx
 
Third Battle of Panipat detailed notes.pptx
Third Battle of Panipat detailed notes.pptxThird Battle of Panipat detailed notes.pptx
Third Battle of Panipat detailed notes.pptx
 
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesMixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
 
PROCESS RECORDING FORMAT.docx
PROCESS RECORDING FORMAT.docxPROCESS RECORDING FORMAT.docx
PROCESS RECORDING FORMAT.docx
 

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