Influence of stepping stone spatial structure on common population genetic statistics

The island model with D colonies and equal migration rates is often chosen for the investigation of the consequences of population migration. Here we show that the stepping stone model has a more pronounced effect on the genealogy of a sample. For local sampling scenarios, there is a shift of the frequency spectrum that decreases the percentage of low number derived alleles. The skew in frequency spectrum changes the distribution of statistics based on the site frequency spectrum. Stepping stone spatial structure also changes the two locus sampling distribution, increases linkage disequilibrium, and changes the distribution of r 2. This may cause a false prediction of cold spots of recombination and may confuse haplotype tests which compute probabilities based on a homogeneously mixing population.