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Originally published as Genetics Published Articles Ahead of Print on April 3, 2007.

Genetics, Vol. 176, 969-981, June 2007, Copyright © 2007
doi:10.1534/genetics.107.071464

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Stepping-Stone Spatial Structure Causes Slow Decay of Linkage Disequilibrium and Shifts the Site Frequency Spectrum

Arkendra De* and Richard Durrett{dagger},1

* Department of Statistics and {dagger} Department of Mathematics, Cornell University, Ithaca, New York 14853

1 Corresponding author: 523 Malott Hall, Cornell University, Ithaca, NY 14853.
E-mail: rtd1{at}cornell.edu

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.




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