Jan 21, 2010

Population differentiation as a test for selective sweeps

Genome Research
Hua ChenDavid E Reich

Abstract

Selective sweeps can increase genetic differentiation among populations and cause allele frequency spectra to depart from the expectation under neutrality. We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than methods based on the allele frequency spectrum. We apply this method to compare continentally diverse populations, as well as Northern and Southern Europeans. Our analysis identifies a list of loci as candidate targets of selection, including well-known selected loci and new regions that h...Continue Reading

  • References29
  • Citations153

References

Mentioned in this Paper

Genetic Drift
Establishment and Maintenance of Localization
Cell Differentiation Process
Genetic Equilibrium
Tribes
Probability
Alleles
Single Nucleotide Polymorphism
Scanning

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