Signals of recent positive selection in a worldwide sample of human populations.

By Joseph K. Pickrell, Graham Coop, John Novembre, S. Kudaravalli, Jun Z. Li, D. Absher, Balaji S. Srinivasan, G. Barsh, Richard M. Myers, Michal Feldman and 1 more. 2009

768 citations recorded by the source corpus.

Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel. We refine the geographic distributions of known selective sweeps, and find extensive overlap between these distributions for populations in the same continental region but limited overlap between populations outside these groupings. We present several examples of previously unrecognized candidate targets of selection, including signals at a number of genes in the NRG-ERBB4 developmental pathway in non-African populations. Analysis of recently identified genes involved in complex diseases suggests that there has been selection on loci involved in susceptibility to type II diabetes. Finally, we search for local adaptation between geographically close populations, and highlight several examples.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Inference of Population Structure using Dense Haplotype Data (2012, methodology): “Complete inferred-phase haplotypes ([21,44]) were downloaded from http://hgdp.”
Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics (2011, background): “Recent genome scans for signals of positive natural selection based on long haplotypes and population differentiation, found enrichment of T2D risk loci (Pickrell et al. 2009; Chen et al. 2010), which may reflect its correlation with energy metabolism (Neel 1962).”
Robust Identification of Local Adaptation from Allele Frequencies (2012, methodology): “Plots of geographic distributions were downloaded from the HGDP selection browser (Pickrell et al., 2009).”
selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection (2014, methodology): “In addition, we compare performance on these statistics with the programs ihs (Voight et al. , 2006) and xpehh (Pickrell et al. , 2009) (both available for download at http://hgdp.uchicago.edu/Software/ ).”
The UCSC Genome Browser database: update 2010 (2009, background): “The browser shows per-population allele frequencies plotted on a world map on the details page for each HGDP SNP.”
Ancestry informative markers for fine-scale individual assignment to worldwide populations (2010, positive): “[54] have recently pointed out, even though one would expect patterns of loci that are under natural selection to be distinct from neutral variation (with demography operating on the whole genome rather than on a few loci), it is often the case that putatively selected loci conform to the geographic”
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars (2013, result): “Because FST and PHS scans tend to identify loci at different stages of selection (15), partial (20%) but nonetheless substantial overlap in the loci identified by the two approaches was consistent with previous studies in Arabidopsis (15) and humans (43), which have demonstrated the dependence of ge”