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Open Access Research article

Evolutionary forces shaping genomic islands of population differentiation in humans

Tamara Hofer12*, Matthieu Foll12 and Laurent Excoffier12

Author Affiliations

1 Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland

2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

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BMC Genomics 2012, 13:107  doi:10.1186/1471-2164-13-107

Published: 22 March 2012

Additional files

Additional file 1:

Comparison of observed and simulated FST distributions. Q-Q plots of observed FST values and FST values simulated under the FIM and the HIM.

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Additional file 2:

The steps involved in the HMM approach to detect HDIs and LDIs. Illustration of the procedure used to identify islands with significant high and low population differentiation in the human genome.

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Additional file 3:

List of all detected HDIs and LDIs. The properties of all HDIs and LDIs detected under the hierarchical island model.

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Additional file 4:

Test of enrichment of SNP categories in SNP subsets. Fisher exact test for enrichment or depletion of SNPs with a given consequence to transcript (Ensembl) in genomic islands defined by the selection test or by the HMM approach.

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Additional file 5:

Island size and recombination rate. Plots illustrating the relationship between island size and local recombination rate in genic and non-genic HDIs and LDIs.

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Additional file 6:

List of non-synonymous SNPs located in HDIs or LDIs with a p-value ≤ 0.05. Candidate loci that might be affected by local adaptation or balancing selection, due to their effect on the transcript, significant level of population differentiation, and location within HDIs or LDIs, respectively.

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Additional file 7:

Overlap of HDIs and LDIs to candidate regions for selection identified in previous studies. Histogram of recombination rate of all genomic bins, bins overlapping to HDIs, and bins overlapping to LDIs.

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Additional file 8:

Overlap of HDIs and LDIs to candidate regions for selection identified in previous studies. Number of candidate regions for selection detected by previous studies that overlap with the 625 HDIs and 197 LDIs identified in this study [98,100-117].

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Additional file 9:

Estimated parameters for the HMM. Parameters of the HMM for each chromosome estimated by the Baum-Welch algorithm. (S8_HMM_parameters.xls can be viewed with Microsoft Excel or Excel Viewer).

Format: XLS Size: 70KB Download file

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