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Genetics. 2007 Jun;176(2):969-81. Epub 2007 Apr 3.

Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum.

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1
Department of Statistics, Cornell University, Ithaca, New York 14853, USA.

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 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.

PMID:
17409067
PMCID:
PMC1894623
DOI:
10.1534/genetics.107.071464
[Indexed for MEDLINE]
Free PMC Article
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