Bayesian Population Genetic Data Analysis

The notes and files provided here were used in Bayesian parts of the Population Genetic Data Analysis module in the Summer Institute in Statistical Genetics at North Carolina State University, 26-28 May 2004 and the European Institute in Statistical Genetics at the University of Algarve, Faro, Portugal, 19-21 July 2004.

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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Examples

Binomial sampling

Inbreeding at one locus with two alleles

Inbreeding with partial dominance (SMFO)

Estimating gametic disequilibrium

• Assuming random union of gametes

• Allowing all disequilibria to be non-zero

Population structure analysis

• Mosquito data

  • Two-alleles per locus (using WinBUGS)

  • Multiple alleles per locus (using Hickory; 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.

• 2002

• 2003

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

Kent Holsinger