A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism
A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism
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DOI：
10.1534/genetics.104.033795
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发表时间：
2005-03-01
期刊：
影响因子：
3.3
通讯作者：
Mitchell-Olds, T
中科院分区：
文献类型：
--
作者：
Schmid, KJ;Ramos-Onsins, S;Mitchell-Olds, T
同时分析多个基因组位点是研究种群历史和自然选择对物种遗传变异模式影响的有力手段。通过调查随机分布在12个拟南芥基因组区域的334个核苷酸序列多态性，我们研究了核苷酸序列多态性的标准中性模型是否与观察到的数据一致。总位点的平均核苷酸多样性为0.0071，沉默位点的平均核苷酸多样性为0.0083。虽然基因座之间的多样性水平是可变的，没有观察到与局部重组率的相关性，但多态性水平与物理连锁的基因座（< 250 kb）相关。我们发现，Tajima的D-和D/Dmin-和Fu和Li的D-，D*-和F-，F*-统计量的观察分布与标准中性模型下的预期分布显著不同，这是由于稀有多态性和高方差过多。观察到的和预期的分布费和吴的H是没有不同的，这表明人口统计过程，而不是选择在多个位点是负责偏离一个中立的模型。最大似然比较的替代人口模型，如逻辑人口增长，冰川避难所，或过去的瓶颈没有产生参数估计，更符合观察到的模式。然而，排除高度多态性的“离群位点”导致符合逻辑增长模型。各种中性测试揭示了一组可能在选择下进化的候选基因座。
The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (< 250 kb). We found that observed distributions of Tajima's D- and D/Dmin- and of Fu and Li's D-, D*- and F-, F*-statistics differed significantly from the expected distributions under a standard neutral model due to an excess of rare polymorphisms and high variances. Observed and expected distributions of Fay and Wu's H were not different, suggesting that demographic processes and not selection at multiple loci are responsible for the deviation from a neutral model. Maximum-likelihood comparisons of alternative demographic models like logistic population growth, glacial refugia, or past bottlenecks did not produce parameter estimates that were more consistent with observed patterns. However, exclusion of highly polymorphic "outlier loci" resulted in a fit to the logistic growth model. Various tests of neutrality revealed a set of candidate loci that may evolve under selection.