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Fossil Mammals in Time (and Space)
Bob O'HaraBiK-F, Frankfurt am Main, Germany
http://blogs.nature.com/boboh/2012/07/04/ISEC2012
Kiitoksia..
Mikael ForteliusJussi Eronen
– University of Helsinki
I want to play with thefossil record
Some obvious statistical issues
The fossil record has holes
Where are the missing lynx?
There's a process here somewhere
The real distribution?
Extinction & Speciationin the fossil record
• How do they vary?– can we blame climate change?
• Who dies?– Related to traits?
Bad News
I won't answer either question
Good News
There is some progress, and there might be more before the next ISEC
Where I am Now
Where I am Now
• Sundvollen
© Andres Lopez-Sepzulcre
No, where the research has got to?
• Got the simple model working• Starting to puzzle over the full model
The problems
• Estimating dates of sites– many based on fossils, not external data
• Estimating actual extinction and speciation times– mark recapture
The First Problem
Getting some data
A database. Woooo!
http://www.helsinki.fi/science/now/database.html
Data
• 282 Species• 347 locations
– Europe (not Russia)
• Covers last 25m years
The DataSpecies Date Dating
MethodI II III IV
Site 1 1 0 1 0 12-14 C
Site 2 1 1 0 0 12-15 C
Site 3 0 0 0 1 1-3 MN
Site 4 0 1 0 0 5-12 OI
Site 5 0 1 0 1 2-7 MN
Independent Dating
• Paleaomagnetic
• Oxygen Isotopes
Bloggy explanation:http://tinyurl.com/ctskvmx
Wikipedia explains:http://en.wikipedia.org/wiki/Oxygen_isotope_ratio_cycle
http://en.wikipedia.org/wiki/File:Phanerozoic_Climate_Change.png
The Model I: Species
Now 25 mya
ExtinctionU(0, Speciation)
SpeciationU(Extinction, 25)
The Model II: Sites
Now 25 mya
DateU(min, max)
DateU(0, 25)
If dating uses independent data
If dating uses fossil data
The Model III: Observations
Pr(Observed|Extant) ~ Species + Site
Logistic regression
Now 25 mya
Estimating extinction/speciaiotn
Now 25 mya
Pr(Observed|Extant) ~ Species + Site
Logistic regression
Model Fitting
• OpenBUGS– MCMC
model { for(l in 1:NLocations) { for(s in 1:NSpecies) { Presences[l,s] ~ dbern(p[l,s]) logit(pSTAR[l,s]) <- mu + al.Loc[l] + al.Sp[s] p[l,s] <- pSTAR[l,s]*step(Age[l]-Extinct[s])*step(Speciate[s]-Age[l]) } Age[l] ~ dunif(MinAge[l], MaxAge[l]) al.Loc[l] ~ dnorm(muL,tauLoc) } for(s in 1:NSpecies) { Speciate[s] ~ dunif(Extinct[s], 25) Extinct[s] ~ dunif(0,Speciate[s]) al.Sp[s] ~ dnorm(muS,tauSp) }
sdLoc ~ dunif(0,10); tauLoc <- pow(sdLoc,-2) sdSp ~ dunif(0,10); tauSp <- pow(sdSp,-2)
mu ~ dnorm(0,2) muL ~ dnorm(0,2) muS ~ dnorm(0,2)}
Estimated Site DatesLooks OK
Not good(& doesn't converge)
Not goodBut no calibration
Time (mya)
Speciation & Extinction Rates
What Next?
• Calibration needs improvement?– also spatial effects
• Extend the model to look at trait effects– frailty models
http://blogs.nature.com/boboh/2012/07/04/ISEC2012
Credit: Dr. H.G of Cromer
But I'm an effing Bison!
http://blogs.nature.com/boboh/2012/07/04/ISEC2012
Credit: Dr. H.G of Cromer