Signals of recent positive selection in a worldwide sample of human populations
- Joseph K. Pickrell1,13,
- Graham Coop1,1213,
- John Novembre1,2,
- Sridhar Kudaravalli1,
- Jun Z. Li3,
- Devin Absher4,
- Balaji S. Srinivasan5,6,7,8,
- Gregory S. Barsh9,
- Richard M. Myers4,
- Marcus W. Feldman10 and
- Jonathan K. Pritchard1,1113
- 1 Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA;
- 2 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA;
- 3 Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA;
- 4 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
- 5 Stanford Genome Technology Center, Stanford University, Stanford, California 94305, USA;
- 6 Program in Biomedical Informatics, Stanford University, Stanford, California 94305, USA;
- 7 Department of Computer Science, Stanford University, Stanford, California 94305, USA;
- 8 Department of Statistics, Stanford University, Stanford, California 94305, USA;
- 9 Department of Genetics, Stanford University, Stanford, California 94305, USA;
- 10 Department of Biological Sciences, Stanford University, Stanford, California 94305, USA;
- 11 Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
Abstract
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.
Footnotes
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↵12 Present address: Section of Evolution and Ecology, University of California, Davis, California 95616, USA.
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↵13 Corresponding authors.
E-mail pickrell{at}uchicago.edu; fax (773) 834-0508.
E-mail gmcoop{at}ucdavis.edu; fax (530) 752-1449.
E-mail pritch{at}uchicago.edu; fax (773) 834-0505.
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[Supplemental material is available online at www.genome.org. The data from this study is publicly available at http://hgdp.uchicago.edu/.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.087577.108.
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- Received October 1, 2008.
- Accepted January 13, 2009.
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Freely available online through the Genome Research Open Access option.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
