Thursday, March 29, 2007

Another one on signatures of selection, but for fixed alleles

New paper on evidence from HapMap SNPs on population specific selective sweeps...(via p-ter at GNXP).Unlike other tests of selection, their test looks for alleles that have reached fixation. They find evidence for selection sweeps for pigmentation genes, earwax type related genes, malaria resistance, skeletal development, fertility related genes (they always seem to find signatures of selection for reproduction related genes, for some reason??)

A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation

Ryosuke Kimura, Akihiro Fujimoto, Katsushi Tokunaga, Jun Ohashi

PLoS ONE 2(3): e286

Abstract: Phenotypic divergences between modern human populations have developed as a result of genetic adaptation to local environments over the past 100,000 years. To identify genes involved in population-specific phenotypes, it is necessary to detect signatures of recent positive selection in the human genome. Although detection of elongated linkage disequilibrium (LD) has been a powerful tool in the field of evolutionary genetics, current LD-based approaches are not applicable to already fixed loci. Here, we report a method of scanning for population-specific strong selective sweeps that have reached fixation. In this method, genome-wide SNP data is used to analyze differences in the haplotype frequency, nucleotide diversity, and LD between populations, using the ratio of haplotype homozygosity between populations. To estimate the detection power of the statistics used in this study, we performed computer simulations and found that these tests are relatively robust against the density of typed SNPs and demographic parameters if the advantageous allele has reached fixation. Therefore, we could determine the threshold for maintaining high detection power, regardless of SNP density and demographic history. When this method was applied to the HapMap data, it was able to identify the candidates of population-specific strong selective sweeps more efficiently than the outlier approach that depends on the empirical distribution. This study, confirming strong positive selection on genes previously reported to be associated with specific phenotypes, also identifies other candidates that are likely to contribute to phenotypic differences between human populations.

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