Abstract. The symmetric island model with D demes and equal migration rates is often chosen for the investigation of the consequences of population subdivision. Here we show that a stepping stone model has a more pronounced effect on the genealogy of a sample. For samples from a small geographical region commonly used in genetic studies of humans and Drosophila, there is a shift of the frequency spectrum that decreases the number of low frequency derived alleles, and skews the distribution of statistics of Tajima, Fu and Li, and Fay and Wu. Stepping stone spatial structure also changes the two locus sampling distribution, increases both linkage disequilibrium and the probability that two sites are perfectly correlated. 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.
Preprint as PDF * Genetics 176 (2007), 969-981