A Map of Recent Positive Selection in the Human Genome

By Benjamin F. Voight, S. Kudaravalli, Xiaoquan Wen, J. K. Pritchard. PLoS Biology, 2006

2,880 citations recorded by the source corpus.

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 ∼250 signals of recent selection in each population.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/fec772a7cf60fea25932ce04439e71e492d684c0

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In Genetics

Citations in the corpus

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation (2010, positive): “These include signals of partial sweeps [20], reduced diversity at putatively neutral sites [28,29] and an excess of SNPs with extreme population differentiation (high FST) within genes (Figure 1A) [30].”
Genomics and the future of conservation genetics (2010, background): “In this context, a landscape genomics approach allows the mapping of associations between adaptive genome region”
Whole-genome sequencing of multiple Arabidopsis thaliana populations (2011, methodology): “We have also developed a modified version of the integrated haplotype score (iH”
Genome-Wide Inference of Ancestral Recombination Graphs (2013, methodology): “Panel (B) is based on 271 100-kb regions predicted to have undergone partial selective sweeps in the YRI population based on the iHS statistic [72].”
Exercise is the real polypill. (2013, background): “Despite recent strong selection pressure (495), our genetic makeup is largely shaped to support the physical activity (PA) patterns of hunter-gatherer societies living in the Paleolithic era, for which food/fluid procurement (and thus survival) was obligatorily linked to PA (71, 347).”
Widespread Genomic Signatures of Natural Selection in Hominid Evolution (2009, background): “However, whole genome scans have identified relatively few regions with convincing evidence of positive selection [15,16], an important role for background selection has generally been discounted [5,17,18], and it has been suggested that the association with recombination may reflect a mutagenic eff”
Fast and flexible simulation of DNA sequence data. (2008, background): “In particular, there is no guarantee that these methods are accu-rate—patterns of linkage disequilibrium (LD) at longer distances cannot necessarily be extrapolated from patterns of LD at shorter distances (Wall 2004).”