Email updates

Keep up to date with the latest news and content from BMC Genetics and BioMed Central.

Open Access Highly Accessed Methodology article

A general linear model-based approach for inferring selection to climate

Srilakshmi M Raj12, Luca Pagani1, Irene Gallego Romero3, Toomas Kivisild1 and William Amos4*

Author Affiliations

1 Department of Biological Anthropology, Henry Wellcome Building, University of Cambridge, Fitzwilliam Street, Cambridge, UK

2 Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

3 Department of Human Genetics, University of Chicago, Chicago, IL, USA

4 Department of Zoology, University of Cambridge, Cambridge, UK

For all author emails, please log on.

BMC Genetics 2013, 14:87  doi:10.1186/1471-2156-14-87

Published: 22 September 2013

Abstract

Background

Many efforts have been made to detect signatures of positive selection in the human genome, especially those associated with expansion from Africa and subsequent colonization of all other continents. However, most approaches have not directly probed the relationship between the environment and patterns of variation among humans. We have designed a method to identify regions of the genome under selection based on Mantel tests conducted within a general linear model framework, which we call MAntel-GLM to Infer Clinal Selection (MAGICS). MAGICS explicitly incorporates population-specific and genome-wide patterns of background variation as well as information from environmental values to provide an improved picture of selection and its underlying causes in human populations.

Results

Our results significantly overlap with those obtained by other published methodologies, but MAGICS has several advantages. These include improvements that: limit false positives by reducing the number of independent tests conducted and by correcting for geographic distance, which we found to be a major contributor to selection signals; yield absolute rather than relative estimates of significance; identify specific geographic regions linked most strongly to particular signals of selection; and detect recent balancing as well as directional selection.

Conclusions

We find evidence of selection associated with climate (P < 10-5) in 354 genes, and among these observe a highly significant enrichment for directional positive selection. Two of our strongest 'hits’, however, ADRA2A and ADRA2C, implicated in vasoconstriction in response to cold and pain stimuli, show evidence of balancing selection. Our results clearly demonstrate evidence of climate-related signals of directional and balancing selection.

Keywords:
Climate; Adaptation; Human evolution; Natural selection; Environmental adaptation; Population genetics