Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Isec2012 o hara

788 views

Published on

Published in: Technology
  • Be the first to comment

  • Be the first to like this

Isec2012 o hara

  1. 1. Fossil Mammals in Time (and Space) Bob OHara BiK-F, Frankfurt am Main, Germany http://blogs.nature.com/boboh/2012/07/04/ISEC2012
  2. 2. Kiitoksia..Mikael ForteliusJussi Eronen – University of Helsinki
  3. 3. I want to play with the fossil recordSome obvious statistical issues
  4. 4. The fossil record has holes Where are the missing lynx?
  5. 5. Theres a process here somewhereThe real distribution?
  6. 6. Extinction & Speciation in the fossil record• How do they vary? – can we blame climate change?• Who dies? – Related to traits?
  7. 7. Bad NewsI wont answer either question
  8. 8. Good NewsThere is some progress, and theremight be more before the next ISEC
  9. 9. Where I am Now
  10. 10. Where I am Now• Sundvollen © Andres Lopez-Sepzulcre
  11. 11. No, where the research has got to?• Got the simple model working• Starting to puzzle over the full model
  12. 12. The problems• Estimating dates of sites – many based on fossils, not external data• Estimating actual extinction and speciation times – mark recapture
  13. 13. The First Problem Getting some data
  14. 14. A database. Woooo!http://www.helsinki.fi/science/now/database.html
  15. 15. Data• 282 Species• 347 locations – Europe (not Russia)• Covers last 25m years
  16. 16. The Data Species Date Dating I II III IV MethodSite 1 1 0 1 0 12-14 CSite 2 1 1 0 0 12-15 CSite 3 0 0 0 1 1-3 MNSite 4 0 1 0 0 5-12 OISite 5 0 1 0 1 2-7 MN
  17. 17. Independent Dating• Paleaomagnetic Bloggy explanation: http://tinyurl.com/ctskvmx• Oxygen IsotopesWikipedia explains:http://en.wikipedia.org/wiki/Oxygen_isotope_ratio_cycle http://en.wikipedia.org/wiki/File:Phanerozoic_Climate_Change.png
  18. 18. The Model I: SpeciesNow 25 mya Extinction Speciation U(0, Speciation) U(Extinction, 25)
  19. 19. The Model II: Sites If dating uses Date independent data U(min, max)Now 25 mya Date U(0, 25) If dating uses fossil data
  20. 20. The Model III: ObservationsNow 25 myaPr(Observed|Extant) ~ Species + Site Logistic regression
  21. 21. Estimating extinction/speciaiotnNow 25 myaPr(Observed|Extant) ~ Species + Site Logistic regression
  22. 22. Model Fitting model {• OpenBUGS for(l in 1:NLocations) { for(s in 1:NSpecies) { Presences[l,s] ~ dbern(p[l,s]) – MCMC Age[l]) 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] ~ 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) }
  23. 23. Estimated Site DatesLooks OK Not good But no calibration Not good (& doesnt converge) Time (mya)
  24. 24. Speciation & Extinction Rates
  25. 25. What Next?• Calibration needs improvement? – also spatial effects• Extend the model to look at trait effects – frailty models
  26. 26. http://blogs.nature.com/boboh/2012/07/04/ISEC2012Credit: Dr. H.G of Cromer
  27. 27. http://blogs.nature.com/boboh/2012/07/04/ISEC2012 But Im an effing Bison!Credit: Dr. H.G of Cromer

×