Population differentiation as a test for selective sweeps.

By Hua Chen, Nick Patterson, David Reich. Genome Research, 2010

785 citations recorded by the source corpus.

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 have not been highlighted by previous scans for selection.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/538c45a7fdb90e23df486ccbd45c7be6ea7de4b4

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In Genetics

1. Bin Han
2. Xuehui Huang
3. S. Tishkoff
4. Caixia Gao

Citations in the corpus

• Genetic adaptation to high altitude in the Ethiopian highlands (2012, methodology): “We additionally performed the XP-CLR test, which is more robust to selection from standing variation and to SNP ascertainment bias [26].”
• Natural variations and genome-wide association studies in crop plants. (2014, background): “, simple diversity ratio, cross-population composite likelihood ratio, and cross-population extended haplotype homozygosity) (13, 79).”