Statistical Inference in Phylogeography

BIOL 79303     Statistical Inference in Phylogeography         Hickerson
CUNY Graduate Center (NEW room 3309)        Tu, 9:30 am-12:30 pm
Hands-on applications and analysis course where practitioners learn the tools that use phylogeographic data to estimate historical demographic parameters and test population or species histories. In recent years, this has become a statistically rigorous and computationally intensive endeavor that uses likelihood-based models that are explicitly built from coalescent theory. The course will cover these methods with a particular emphasis on simulation-based methods for testing complex demographic models and estimating relevant parameters under various models. The course will consist of lectures, literature review, and individual research projects that will involve conducting and presenting a simulation-based or likelihood-baed analysis. Students will use their own laptops.

Topics: hypothesis testing, probability, likelihood, coalescent models, estimating parameters (e.g. gene flow, population sizes and divergence times), power analyses, species delimitation, testing for biogeographic congruence across taxa, population structure, demographic model choice, basics inUNIX command line and R programming.

Recommended Text: Practical Computing for Biologists by Steven Haddock and Casey Dunn

Week 1 – Sept 2nd
Introductions with brief project descriptions and goals for the course

Readings for week 2

Hickerson_et al. 2010

Haddock and Dunn  – Chapter  4 (only skim 4)

in preparation for week 2

Haddock and Dunn  – Appendix 1

Windows people: install linux or Cygwin option (for tips go to Haddock and Dunn or Naoki’s help-page)
install PuTTY

Mac people: install Xcode (from your install disk, if you haven’t already done it. Naoki’s page is also useful for this)

Week 2 – Sept 9th

Unix/Command Line (terminals, command lines, remote servers, data simulation)

Discuss readings

Readings for week 3

Haddock and Dunn – Chapters 5

Stephenson, N. 1999. “In the beginning … was the command line”. Perennial reprinting 2003.
(available free – here)


Week 3 Sept 16

Unix/Command Line 2 (terminals, command lines, remote servers, data simulation)

Discuss readings

Readings for week 4
Edwards 2009

preparation for week 4
Install R

Week 4 Sept 30th

Using R

Download Sample Data

Paper presentation

Readings for week 5

Nielsen and Beaumont 2009

Week 5 Oct 7

Likelihood and Bayesian statistics for model-based phylogeography

Paper presentation

Readings for week 6

Csilléry et al. 2010

Week 6 Oct 14

“Home-brew ABC”

Paper presentation

Readings for week 7: see email

Week 7 Oct 21

ABC rejection and cross- validation

Project proposal (outline or abstract) Due

short Paper presentations

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