蓝海人类学在线 Ryan WEI's Forum of Anthropology

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族群相关SNP研究:Population-specific common SNPs reflect demographic histories

发表于 2016-8-1 15:25 | 显示全部楼层 |阅读模式
Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance
Background                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.
                Results                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.
                Conclusions                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.
 楼主| 发表于 2016-8-1 15:34 | 显示全部楼层
本帖最后由 一统浆糊 于 2016-8-1 15:36 编辑

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FIN,IBS 是欧洲人,中间是中国跟日本人,后两个是非洲人。
发表于 2016-8-1 16:45 | 显示全部楼层
 楼主| 发表于 2016-8-2 02:10 | 显示全部楼层
除非:1。出非洲人群占相当一部分。OR 2。大量基因回流非洲。OR 3。非洲的多样性被消灭了。
发表于 2016-8-2 10:06 | 显示全部楼层
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