The Role of Geography in Human Adaptation
Graham Coop1#¤a*, Joseph K. Pickrell1#*, John Novembre1¤b, Sridhar Kudaravalli1, Jun Li2, Devin Absher3,Richard M. Myers3, Luigi Luca Cavalli-Sforza4, Marcus W. Feldman5, Jonathan K. Pritchard1,6*
1 Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America, 2 Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America, 3 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America, 4Department of Genetics, Stanford University, Stanford, California, United States of America, 5 Department of Biological Sciences, Stanford University, Stanford, California, United States of America, 6 Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
Abstract
Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme FST values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.
Author Summary
Since the beginning of the study of evolution, people have been fascinated by recent human evolution and adaptation. Despite great progress in our understanding of human history, we still know relatively little about the selection pressures and historical factors that have been important over the past 100,000 years. In that time human populations have spread around the world and adapted in a wide variety of ways to the new environments they have encountered. Here, we investigate the genomic signal of these adaptations using a large set of geographically diverse human populations typed at thousands of genetic markers across the genome. We find that patterns at selected loci are predictable from the patterns found at all markers genome-wide. On the basis of this, we argue that selection has been strongly constrained by the historical relationships and gene flow between populations.
Citation: Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, et al. (2009) The Role of Geography in Human Adaptation. PLoS Genet 5(6): e1000500. doi:10.1371/journal.pgen.1000500
Editor: Mikkel H. Schierup, University of Aarhus, Denmark
Received: November 12, 2008; Accepted: May 4, 2009; Published: June 5, 2009
Copyright: © 2009 Coop et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by a Packard Foundation grant to J. Pritchard. J. Pickrell was supported by a National Institutes of Health training grant to the University of Chicago. G. Coop was also supported by funds from UC Davis. J. Novembre was supported by a US National Science Foundation postdoctoral research fellowship in bioinformatics. M. Feldman was supported by grant GM28016. J. Pritchard is an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: gmcoop@ucdavis.edu (GC); pickrell@uchicago.edu (JKP); pritch@uchicago.edu (JKP)
# These authors contributed equally to this work.
¤a Current address: Section of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, United States of America
¤b Current address: Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
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