Site frequency spectra from genomic SNP surveys.


Journal Article

Genomic survey data now permit an unprecedented level of sensitivity in the detection of departures from canonical evolutionary models, including expansions in population size and selective sweeps. Here, we examine the effects of seemingly subtle differences among sampling distributions on goodness of fit analyses of site frequency spectra constructed from single nucleotide polymorphisms. Conditioning on the observation of exactly two alleles in a random sample results in a site frequency spectrum that is independent of the scaled rate of neutral substitution (theta). Other sampling distributions, including conditioning on a single mutational event in the sample genealogy or randomly selecting a single mutation from a genealogy with multiple mutations, have distinct site frequency spectra that show highly significant departures from the predictions of the biallelic model. Some aspects of data filtering may contribute to significant departures of site frequency spectra from expectation, apart from any violation of the standard neutral model.

Full Text

Duke Authors

Cited Authors

  • Ganapathy, G; Uyenoyama, MK

Published Date

  • June 2009

Published In

Volume / Issue

  • 75 / 4

Start / End Page

  • 346 - 354

PubMed ID

  • 19371756

Pubmed Central ID

  • 19371756

Electronic International Standard Serial Number (EISSN)

  • 1096-0325

International Standard Serial Number (ISSN)

  • 0040-5809

Digital Object Identifier (DOI)

  • 10.1016/j.tpb.2009.04.003


  • eng