geographic structure

Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M & Bergelson J 2005 The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196.

  • we view both Structure and hierarchical clustering as tools for exploring the data
  • the results should not be taken literally
  • we do not believe that there are K = 8 random-mating populations in A. thaliana, as might be suggested by Figures 2 and 3
  • nor do we believe that populations are related in a tree-like manner, as might be suggested by Figure S1
  • we used a model-based clustering algorithm implemented in Structure v. 2.0
  • since A. thaliana is largely homozygous, we used a haploid setting
  • we used the "linkage model" with "correlated allele frequencies" in Structure
  • where genetic distances (calculated by fitting a third-order polynomial to the Lister and Dean recombinant inbred mapping data) were used to indicate locus proximity