regime shifts in ecology and evolution
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Introduction Early Warning Conclusions Acknowledgements
Regime shifts in
ecology & evolution
@cboettig
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 1/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 2/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 3/45
Introduction Early Warning Conclusions Acknowledgements
Regime
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 4/45
Introduction Early Warning Conclusions Acknowledgements
Shifts
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 5/45
Introduction Early Warning Conclusions Acknowledgements
〈 Ecologist 〉
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 6/45
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started in physics. . .
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 7/45
Introduction Early Warning Conclusions Acknowledgements
Digging for dinosaurs
sponsored by National Geographic
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 8/45
Introduction Early Warning Conclusions Acknowledgements
Peter Wainwright
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 9/45
Introduction Early Warning Conclusions Acknowledgements
Peter’s dives
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 10/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 11/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 12/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 13/45
Introduction Early Warning Conclusions Acknowledgements
A release of constraint?
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 14/45
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Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 15/45
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Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 16/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 17/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 18/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 19/45
Introduction Early Warning Conclusions Acknowledgements
How do we get anevolutionary time seriesfrom present-day species?
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 20/45
Introduction Early Warning Conclusions Acknowledgements
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
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 21/45
Introduction Early Warning Conclusions Acknowledgements
Candidate models
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 22/45
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Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 23/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 24/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 25/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 26/45
Introduction Early Warning Conclusions Acknowledgements
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
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 27/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 28/45
Introduction Early Warning Conclusions Acknowledgements
Part II
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 29/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 30/45
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Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 31/45
Introduction Early Warning Conclusions Acknowledgements
Coral Bleaching
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 32/45
Introduction Early Warning Conclusions Acknowledgements
Eutrophication
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 33/45
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Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 34/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 35/45
Introduction Early Warning Conclusions Acknowledgements
ddtE(xi) = 2
√r(t)(
√r(t) + θ − xi) (1)
ddtV (xi) = −2
√r(t)V (xi) + σ2(
√r(t) + θ) (2)
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 36/45
Introduction Early Warning Conclusions Acknowledgements
Carver
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 37/45
Introduction Early Warning Conclusions Acknowledgements
Boettiger et al. 2012, PRSICarl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 38/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 39/45
Introduction Early Warning Conclusions Acknowledgements
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 40/45
Introduction Early Warning Conclusions Acknowledgements
Unifying challenges in regime shifts
Weak signals
Uncertainty quantificationComputationally intensiveStatistical power is data limited
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 41/45
Introduction Early Warning Conclusions Acknowledgements
Unifying challenges in regime shifts
Weak signalsUncertainty quantification
Computationally intensiveStatistical power is data limited
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 41/45
Introduction Early Warning Conclusions Acknowledgements
Unifying challenges in regime shifts
Weak signalsUncertainty quantificationComputationally intensive
Statistical power is data limited
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 41/45
Introduction Early Warning Conclusions Acknowledgements
Unifying challenges in regime shifts
Weak signalsUncertainty quantificationComputationally intensiveStatistical power is data limited
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 41/45
Introduction Early Warning Conclusions Acknowledgements
Why Open Source?
Reproduceresearch
Find & fix bugs
Extend into newsoftware
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 42/45
Introduction Early Warning Conclusions Acknowledgements
Code
Literature
Discussions
Lab Notebook
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 43/45
Introduction Early Warning Conclusions Acknowledgements
The Open Lab Notebook
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 44/45
Introduction Early Warning Conclusions Acknowledgements
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/
Carl Boettiger, UC Davis [email protected] Regime shifts in ecology and evolution 45/45