Evolution 2017: NA functional composition

Talk by Peter Smits at Evolution Meetings 2017 in Portland, OR.

Follow along with my talk at https://youtu.be/JThsvvBrJ1s

Transcript

1. The changing functional composition of the North American species pool modeling species origination-extinction as a function of functional group and environmental context Peter D Smits Committee on Evolutionary Biology, University of Chicago
2. Question When are certain ecologies, ecotypes, or functional groups enriched or depleted in a species pool?
3. Species pool concept (Mittelbach and Schemske, 2015, TREE)
4. Functional groups (Bambach et al. 2007 Palaeontology)
5. Structured data in biology; the fourth-corner problem (Ovaskainen et al. 2017 Ecology Letters)
6. Age of Mammals
7. Differences in extinction risk relative expected species duration short long arboreal ground dwelling scansorial insectivore herbivore carnivore omnivore locomotor diet (Smits 2015 PNAS)
8. Covariates of interest individual-level (species i at time unit t) effect of locomotor type arboreal, digitigrade, plantigrade, unguligrade, fossorial, scansorial effect of dietary type carnivore, herbivore, insectivore, omnivore effect body size (rescaled log body mass) group-level (2 My time unit t) temperature record based on Mg/Ca estimates mean and range (rescaled log degrees) plant community phase following Graham 2011
9. Paleo-fourth corner model
10. Model and sampling statement definition yi,t ∼ Bernoulli(pi,t zi,t ) pi,t = logit−1(α0 + α1mi + rt ) rt ∼ N(0, σ) α0 ∼ N(0, 1) α1 ∼ N(1, 1) σ ∼ N+(1) zi,1 ∼ Bernoulli(φi,1) zi,t ∼ Bernoulli zi,t−1πi,t + t x=1 (1 − zi,x )φi,t φi,t = logit−1(aφ t,j[i] + bφ 1 mi + bφ 2 m2 i ) πi,t = logit−1(aπ t,j[i] + bπ 1 mi + bπ 2 m2 i ) aφ ∼ MVN(Uγφ, Σφ) aπ ∼ MVN(Uγπ, Σπ) Σφ = diag(τφ)Ωφdiag(τφ) Σπ = diag(τπ)Ωπdiag(τπ) ρ ∼ U(0, 1) bφ 1 ∼ N(0, 1) bπ 1 ∼ N(0, 1) bφ 2 ∼ N(−1, 1) bπ 2 ∼ N(−1, 1) γφ ∼ N(0, 1) γπ ∼ N(0, 1) τφ ∼ N+(1) τπ ∼ N+(1) Ωφ ∼ LKJ(2) Ωπ ∼ LKJ(2).
11. Bayesian inference and statistics flexible, expressive, intuitive regularize, partial pooling, external information Stan probabilistic programming language Hamiltonian Monte Carlo Automatic Differentiation Variational Inference
12. Probability of ecotype origination
13. Probability of ecotype survival
14. Group-level effects (plant phase, climate) on origination
15. Group-level effects (plant phase, climate) on survival
16. Ecotype-specific diversity
17. Relative ecotype diversity
18. Summary of results changes to ecotype composition driven by origination, not extinction specific ecotypes source of most variation in overall origination arboreal taxa decrease through Paleogene, all but absent by Neogene digitigrade and unguligrade herbivores only groups with sustained increase environmental covariates virtually always affect origination, not survival
19. Acknowledgements Advising Kenneth D. Angielczyk, Michael J. Foote, P. David Polly, Richard H. Ree, Graham Slater Angielczyk Lab David Grossnickle, Dallas Krentzel, Jackie Lungmus Foote lab Marites Villarosa Garcia, Nadia Pierrehumbert @PeterDSmits