Analyzing the genetic structure of populations: individual assignment

We'll finish up with a few final observations about F-statistics before taking a new approach to analysis of population structure - individual assignment. Individual assignment groups individuals into "populations" based on genotypic similarity. The reason for the scare quotes around "populations" will become evident as we outline the logic behind the method implemented in Structure. We won't go into all of the gory mathematical details, but I'll do my best to give you a conceptual understanding of the approach. Structure is widely used and very powerful, but like any powerful tool, it must be used cautiously.

Project #2

• Project #2
• Protea repens data
  • CSV format
  • Structure format
• Scripts for Bayesian F-statistics
  • R script
  • JAGS code for full model
  • JAGS code for f=0 model
  • JAGS code for theta=0 model
• Prunier et al. on SNP variation in Protea repens (in press in American Journal of Botany, PDF format)

Online notes

Associated readings

Gopalan, P., W. Hao, D. M. Blei and J. D. Storey. 2016. Scaling probabilistic models of genetic variation to millions of humans. Nature Genetics 48:1587-1590. link

Pritchard, J. K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959 link