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MBE Advance Access published online on December 17, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn289
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© 2008 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

Gene expression levels are a target of recent natural selection in the human genome

Sridhar Kudaravalli1, Jean-Baptiste Veyrieras1, Barbara E. Stranger2, Emmanouil T. Dermitzakis2 and Jonathan K. Pritchard1,3

1 Dept of Human Genetics, The University of Chicago, 920 E 58th St CLSC 507, Chicago IL 60637, USA
2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
3 Howard Hughes Medical Institute

Correspondence to skudarav{at}uchicago.edu, md4{at}sanger.ac.uk, pritch{at}uchicago.edu.

Received for publication August 16, 2008. Revision received December 9, 2008. Accepted for publication December 9, 2008.

Changes in gene expression may represent an important mode of human adaptation. However, to date, there are relatively few known examples in which selection has been shown to act directly on levels or patterns of gene expression. In order to test whether SNPs that affect gene expression in cis are frequently targets of positive natural selection in humans, we analyzed genome-wide SNP and expression data from cell lines associated with the International HapMap Project. Using a haplotype-based test for selection that was designed to detect incomplete selective sweeps, we found that SNPs showing signals of selection are more likely than random SNPs to be associated with gene expression levels in cis. This signal is significant in the Yoruba (which is the population that shows the strongest signals of selection overall), and shows a trend in the same direction in the other HapMap populations. Our results argue that selection on gene expression levels is an important type of human adaptation. Finally, our work provides an analytical framework for tackling a more general problem that will become increasingly important: namely, testing whether selection signals overlap significantly with SNPs that are associated with phenotypes of interest.

Key Words: Population Genetics • Recent Positive Selection • eQTL mapping • Humans • iHS


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