Dept. Ecology, Evolution, & Organismal Biology
Iowa State University
I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record.
Time at MBL
Monday July 24 - Sunday July 30
Morning lecture slides and example scripts
- Hierarchical models and integrative Bayesian analysis (slides)
- Bayesian divergence-time estimation (slides)
- Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. (doi: 10.1093/sysbio/syu039).
- Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. (PDF)
- Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF)
- BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html)
- Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html
- also see references in divergence-time tutorial
- More tutorials on divergence time estimation in RevBayes and BEAST2 (link)
- Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics (link)