Abstract
BackgroundPopulation 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.ResultsThe 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.ConclusionsCommon 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-437) contains supplementary material, which is available to authorized users.
Highlights
Population differentiation is the result of demographic and evolutionary forces
These studies were based on a fixed number of single nucleotide polymorphisms (SNPs) which had clear ascertainment bias, it was difficult to reliably assess the nature and extent of genomic diversity that exists among different populations from these studies [15]
We have used the most recent version (October 2012) of the 1000 Genomes data to identify SNPs which are observed to be unique to each of the individual study populations [18]. These SNPs were categorized into common population-specific (CPS) SNPs and rare population-specific (RPS) SNPs based on a minor allele frequencies (MAF) cut-off of 0.05
Summary
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. The genotype data from these studies have been subjected to various computational techniques to derive estimates of population sizes and divergence times for the major demographic events in human history, which in many cases have been found to be in agreement with evidence from existing historical accounts and archaeological records [13,14] These studies were based on a fixed number of single nucleotide polymorphisms (SNPs) which had clear ascertainment bias (the SNPs included in the genotyping platforms were selected on the basis of their occurrence and frequencies primarily in European populations), it was difficult to reliably assess the nature and extent of genomic diversity that exists among different populations from these studies [15]. Two coding non-synonymous SNPs were detected in the UPK3B gene which plays an important role in AUM-cytoskeleton interaction in terminally differentiated urothelial cells
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