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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • De, A; Durrett, R

Published Date

  • June 2007

Published In

Volume / Issue

  • 176 / 2

Start / End Page

  • 969 - 981

PubMed ID

  • 17409067

Pubmed Central ID

  • PMC1894623

Electronic International Standard Serial Number (EISSN)

  • 1943-2631

International Standard Serial Number (ISSN)

  • 0016-6731

Digital Object Identifier (DOI)

  • 10.1534/genetics.107.071464


  • eng