Journal
GENETICS
Volume 176, Issue 2, Pages 969-981Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.107.071464
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The symmetric island model with D denies 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 front 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 and 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 that compute probabilities on the basis of a homogeneously mixing population.
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