 Site frequency spectra from genomic SNP surveysGaneshkumar Ganapathy and Marcy K. Uyenoyama Theoretical Population Biology, 2009, vol. 75, issue 4, 346-354 Abstract: 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 (θ). 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. Keywords: Site frequency spectrum; Single nucleotide polymorphism; Ewens’ sampling formula; Infinite-sites model; Standard neutral model (search for similar items in EconPapers) Downloads: (external link) Related works: Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:75:y:2009:i:4:p:346-354 DOI: 10.1016/j.tpb.2009.04.003 Access Statistics for this article Theoretical Population Biology is currently edited by Jeremy Van Cleve More articles in Theoretical Population Biology from Elsevier |
Is your work missing from RePEc? Here is how to contribute.
Questions or problems? Check the EconPapers FAQ or send mail to .
EconPapers is hosted by the
School of Business at Örebro University.