Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum.
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 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.
De
Arkendra
A
Department of Statistics, Cornell University, Ithaca, New York 14853, USA.
Durrett
Richard
R
D002875:Chromosomes / Q000235:genetics; D004641:Emigration and Immigration / Q000639:trends; D005787:Gene Frequency; D005828:Genetics, Population; D007700:Kinetics; D015810:Linkage Disequilibrium / Q000502:physiology*; D008957:Models, Genetic; D011156:Population Density; D011336:Probability