Demography-adjusted tests of neutrality based on genome-wide SNP data

DOI10.1016/J.TPB.2014.05.002MaRDI QIDQ744615zbMATH OpenOpenAlexWikidataFDO

Authors D. Kharzeev

Publication date 26 September 2014

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1307.0337

zbMATH Keywords

bottleneckcoalescent approximationinfinite-sites modelsingle nucleotide polymorphismsite frequency spectrum (SFS)

Mathematics Subject Classification ID

Mathematical geography and demography (91D20) Genetics and epigenetics (92D10)

Abstract: Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. A key ingredient is to specify the first two moments of the frequency spectrum. We show that these moments can be determined analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's $D$, Fay & Wu's $H$, and Zeng's $E$. The adjusted test statistics facilitate the direct comparison between populations and they show that most of the differences among populations seen in the original tests can be explained by demography. We carried out whole genome screens for deviation from neutrality and identified candidate regions of recent positive selection. We provide track files with values of the adjusted and original tests for upload to the UCSC genome browser.

Recommendations

• The third moments of the site frequency spectrum
• Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models
• An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties
• Site frequency spectra from genomic SNP surveys
• The neutral frequency spectrum of linked sites

Cites work

• Can one learn history from the allelic spectrum?
• Statistical properties of segregating sites
• The coalescent

Cited in

(6)

• The third moments of the site frequency spectrum
• An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties
• Cross-validated SNP density estimates
• Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models
• Modifying the chi-square and the CMH test for population genetic inference: adapting to overdispersion
• The neutral frequency spectrum of linked sites

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