Open Access Research article

Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

Ananyo Choudhury12, Scott Hazelhurst13, Ayton Meintjes4, Ovokeraye Achinike-Oduaran12, Shaun Aron1, Junaid Gamieldien5, Mahjoubeh Jalali Sefid Dashti5, Nicola Mulder4, Nicki Tiffin5 and Michèle Ramsay12*

Author Affiliations

1 Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa

2 Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

3 School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa

4 Department Clinical Laboratory Sciences, Computational Biology Group, IDM, University of Cape Town, Cape Town, South Africa

5 South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa

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BMC Genomics 2014, 15:437  doi:10.1186/1471-2164-15-437

Published: 6 June 2014



Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data.


The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones.


Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease.