regime shifts in ecology and evolution

Introduction Early Warning Conclusions Acknowledgements

Regime shifts in

ecology & evolution

@cboettig

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Regime

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Shifts

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〈 Ecologist 〉

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started in physics. . .

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Digging for dinosaurs

sponsored by National Geographic

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Peter Wainwright

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Peter’s dives

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A release of constraint?

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How do we get anevolutionary time seriesfrom present-day species?

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XT1 = X0︸︷︷︸where you start

e−α1T1+

θ1(1− e−α1T1

)︸ ︷︷ ︸Where you are going

+

∫ T1

0σ1e

α1(s−T1)dWs︸ ︷︷ ︸Random shocks along the way

Solves as:

E(Xi) =n∑i=0

eγi

[θi(1− eαiti

) ]

Cov(Xi, Xj) =k∑s=0

[eγs+γ′

sσ2s

2αs

(1− e−2αsts

)]

γi = −n∑

j=i+1αjtj

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Candidate models

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Phylogenetic Monte Carlo

← Fits both models

to this data

LogLik(simple)LogLik(complex)

Simulate from

simple model →complex

model →

Likelihood ratio

frequency

Boettiger et al. 2012, Evolution, pmc R package

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Part II

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Coral Bleaching

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Eutrophication

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ddtE(xi) = 2

√r(t)(

√r(t) + θ − xi) (1)

ddtV (xi) = −2

√r(t)V (xi) + σ2(

√r(t) + θ) (2)

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Carver

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Boettiger et al. 2012, PRSICarl Boettiger, UC Davis cboettig@ucdavis.edu Regime shifts in ecology and evolution 38/45

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Unifying challenges in regime shifts

Weak signals

Uncertainty quantificationComputationally intensiveStatistical power is data limited

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Introduction Early Warning Conclusions Acknowledgements

Unifying challenges in regime shifts

Weak signalsUncertainty quantification

Computationally intensiveStatistical power is data limited

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Introduction Early Warning Conclusions Acknowledgements

Unifying challenges in regime shifts

Weak signalsUncertainty quantificationComputationally intensive

Statistical power is data limited

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Introduction Early Warning Conclusions Acknowledgements

Unifying challenges in regime shifts

Weak signalsUncertainty quantificationComputationally intensiveStatistical power is data limited

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Why Open Source?

Reproduceresearch

Find & fix bugs

Extend into newsoftware

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Code

Literature

Discussions

Lab Notebook

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The Open Lab Notebook

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Acknowledgements

Image creditsMichael Najjar

Arkive.org

Millennium Ecosystem Assessment

Flickr user gfpeck

Boettiger et al 2012

Scheffer et al. 2001

Westneat & Alfaro 2005

http://carlboettiger.info/

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