Bayesian Population Genetic Data Analysis

The notes and files provided here were used in Bayesian parts of the Evolutionary Population Genetic Data module in the Summer Institute in Statistical Genetics at North Carolina State University, 25-27 May 2005.

A paper providing evidence that athletes use Bayesian learning (instinctively) in experiments designed to simulate tennis appeared in the 15 January 2004 issue of Nature.

Notes

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LaTeX source

Examples

Binomial sampling

Genotype sampling

• Assuming no inbreeding (f = 0)

• Allowing inbreeding (estimating f)

• Inbreeding with partial dominance (SMFO)

Population structure analysis

• Mosquito data

  • Multiple alleles per locus (NEXUS)

• Platanthera leucophaea

  • RAPD data (NEXUS)

  • Allozyme data (NEXUS)

Software used or mentioned during the module

WinBUGS

Hickory

R -- 'GNU S', a freely available language and environment for statistical computing and graphics

BOA -- Bayesian Output analysis, routines for convergence diagnostics in R and S-Plus

Earlier versions of the notes

If for some reason you are interested in versions of the notes from earlier years, they are also available here.

• 2004

• 2003

• 2002

Notes and materials provided here are provided under a Creative Commons License.

Kent Holsinger