A Map of Recent Positive Selection in the Human Genome

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
PLoS Biology (Impact Factor: 9.34). 04/2006; 4(3):e72. DOI: 10.1371/journal.pbio.0040072
Source: PubMed


The identification of signals of very recent positive selection provides information about the adaptation of modern humans to local conditions. We report here on a genome-wide scan for signals of very recent positive selection in favor of variants that have not yet reached fixation. We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap Project. In all three continental groups we find widespread signals of recent positive selection. Most signals are region-specific, though a significant excess are shared across groups. Contrary to some earlier low resolution studies that suggested a paucity of recent selection in sub-Saharan Africans, we find that by some measures our strongest signals of selection are from the Yoruba population. Finally, since these signals indicate the existence of genetic variants that have substantially different fitnesses, they must indicate loci that are the source of significant phenotypic variation. Though the relevant phenotypes are generally not known, such loci should be of particular interest in mapping studies of complex traits. For this purpose we have developed a set of SNPs that can be used to tag the strongest approximately 250 signals of recent selection in each population.

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    • "Identification of local adaptation may get even more complicated if selection varies over the entire geographical range but acts at a very local scale. For example, it seems that neither humans nor A. thaliana have experienced large-scale local adaptation across their geographic range, but rather local selection within different populations (Voight et al. 2006;Huber et al. 2014). C. bursa-pastoris is a young species (Douglas et al. 2015) that inhabits very diverse environments and may be exposed to different selective constrains in different regions as well. "
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    • "Weak selection requires more time to increase the frequency of a beneficial allele to intermediate frequencies, allowing variation around an advantageous site to be maintained by recombination (Slatkin, 2008). iHS signals also decay with time as diversity is reintroduced to the region via recombination , even if selection was relatively strong (Voight et al., 2006). The benefit gained by C282Y carriers is not sufficient for selection to act strongly. "
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    • "For a detailed description of each measurement please see Sabeti et al. (2002), van Voight et al. (2006), and Sabeti et al. (2007). The " extended haplotype structure approach " can also detect recent or on-going selective events (not older than ∼30,000 years–Oleksyk et al., 2010) using a single population (van Voight et al., 2006). Concerning the interpretation of the results, if you are " lucky, " you may find a selection pressure on an allele with known phenotypical associations by candidate gene studies or genome wide association studies (explained below), which would simplify the interpretation of your finding. "
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