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MBE Advance Access published online on July 3, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp134
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Interrogating eleven fast-evolving genes for signatures of recent positive selection in worldwide human populations

Andrés Moreno-Estrada1, Kun Tang2,3, Martin Sikora1, Tomàs Marquès-Bonet1,4, Ferran Casals5, Arcadi Navarro1,6, Francesc Calafell1,7, Jaume Bertranpetit1,7, Mark Stoneking3 and Elena Bosch1,7

1 Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
2 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
3 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
4 Department of Genome Sciences, University of Washington, Seattle, USA
5 Ste Justine Hospital Research Centre, Department of Pediatric, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1C5, Canada
6 Institució Catalana de Recerca i Estudis Avançats (ICREA) i UPF
7 Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain

Corresponding author: Elena Bosch, Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003 Barcelona, Spain. Tel. +34 93 316 0841, Fax. +34 93 316 0901, E-mail: elena.bosch{at}upf.edu

Received for publication January 30, 2009. Revision received June 18, 2009. Accepted for publication June 25, 2009.

Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs in chimpanzee, mouse, rat and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes were then further explored for signatures of recent positive selection using SNP data. We genotyped 223 SNPs in 39 worldwide populations from the HGDP Diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each gene. After exploring the allele frequency spectrum, population differentiation and the maintainance of long unbroken haplotypes, we found signals of recent adaptative phenomena in only one of the 11 candidate gene regions. However, the signal of recent selection in this region may come from a different, neighbouring gene (CD5) rather than from the candidate gene itself (VPS37C). For this set of positively-selected genes in the human lineage, we find no indication that these genes maintained their rapid evolutionary pace among human populations. Based on these data, it therefore appears that adaptation for human-specific and for population-specific traits may have involved different genes.

Key Words: Accelerated Evolution • Recent Positive Selection • SNP Data • Extended Haplotype Homozygosity • Population Differentiation • Human Genome Diversity Panel


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