Lightning talk presented at SSB Standalone Meetings in Baton Rouge, Louisiana, on 10 January 2017.

1. Generalizing phylogenetics to infer shared evolutionary
events
Jamie R. Oaks1
1Department of Biological Sciences, Auburn University
January 10, 2017
Shared divergences Jamie Oaks – phyletica.org 1/12

2. Assumption: All processes of
diversification affect each lineage
independently and only cause
bifurcating divergences.
Shared divergences Jamie Oaks – phyletica.org 2/12

3. Shared divergences Jamie Oaks – phyletica.org 3/12

4. Shared divergences Jamie Oaks – phyletica.org 3/12

5. Shared divergences Jamie Oaks – phyletica.org 3/12

6. Why account for shared divergences?
1. Improve inference
Shared divergences Jamie Oaks – phyletica.org 4/12

7. Why account for shared divergences?
1. Improve inference
2. Provide a framework for studying processes of co-diversification
Shared divergences Jamie Oaks – phyletica.org 4/12

8. τ1
Shared divergences Jamie Oaks – phyletica.org 5/12

9. τ1
Shared divergences Jamie Oaks – phyletica.org 5/12

10. m1 m2 m3 m4 m5
τ1 τ2 τ1 τ1τ2 τ1τ2 τ3 τ1τ2
Shared divergences Jamie Oaks – phyletica.org 6/12

11. m1 m2 m3 m4 m5
τ1 τ2 τ1 τ1τ2 τ1τ2 τ3 τ1τ2
We want to infer the model and divergence times given variable characters
(SNPs, AFLPs, indels) from across the genome
Shared divergences Jamie Oaks – phyletica.org 6/12

12. Ecoevolity: Estimating evolutionary coevality
CTMC model of characters evolving along genealogies
Coalescent model of genealogies branching within populations
Dirichlet-process or uniform prior across divergence models
Gibbs sampling1 and reversible-jump MCMC2 to numerically sample
models
Analytically integrate over genealogies3
1
R. M. Neal (2000). Journal of Computational and Graphical Statistics 9: 249–265
2
P. J. Green (1995). Biometrika 82: 711–732
3
D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932
Shared divergences Jamie Oaks – phyletica.org 7/12

13. Ecoevolity: Estimating evolutionary coevality
CTMC model of characters evolving along genealogies
Coalescent model of genealogies branching within populations
Dirichlet-process or uniform prior across divergence models
Gibbs sampling1 and reversible-jump MCMC2 to numerically sample
models
Analytically integrate over genealogies3
Fast, full-likelihood Bayesian method to infer patterns of
co-diversification from genome-scale data
1
R. M. Neal (2000). Journal of Computational and Graphical Statistics 9: 249–265
2
P. J. Green (1995). Biometrika 82: 711–732
3
D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932
Shared divergences Jamie Oaks – phyletica.org 7/12

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0.00 0.02 0.04 0.06 0.08
0.000.020.040.06
True divergence time
Estimateddivergencetime
The true model is in the 95% credible set 97% of the time
Shared divergences Jamie Oaks – phyletica.org 8/12

15. Everything is on GitHub. . .
Software:
Ecoevolity: https://github.com/phyletica/ecoevolity
Open-Science Notebook:
https://github.com/phyletica/ecoevolity-experiments
Shared divergences Jamie Oaks – phyletica.org 9/12

16. Next step: A general framework
Generalize Bayesian
phylogenetics to incorporate
shared divergences
Sample models numerically via
reversible-jump MCMC
Benefits:
Improve phylogenetic inference
Framework for studying
processes of co-diversification τ1τ2τ3
Shared divergences Jamie Oaks – phyletica.org 10/12

17. Acknowledgments
Ideas and feedback:
Leach´e Lab
Minin Lab
Mark Holder
Tracy Heath
Michael Landis
Computation:
Funding:
Photo credits:
PhyloPic!
Shared divergences Jamie Oaks – phyletica.org 11/12

18. Questions?
joaks@auburn.edu
c 2007 Boris Kulikov boris-kulikov.blogspot.com
Shared divergences Jamie Oaks – phyletica.org 12/12

19. Solution:
Accommodate shared
divergence models
Advantage:
More data to estimate
shared parameters
True history
τ1τ2τ3
Problem:
Current methods
only consider
general model
Consequence:
Unnecessary
parameters
introduce error
Current tree model
τ1 τ2 τ3τ4 τ5 τ6 τ7 τ8
Shared divergences Jamie Oaks – phyletica.org 12/12