The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations.
The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations.
复制标题
DOI：
10.1038/hdy.2014.80
复制
发表时间：
2015-02
期刊：
影响因子：
3.8
通讯作者：
Zeng, K.
中科院分区：
文献类型：
--
作者：
Jackson, B. C.;Campos, J. L.;Zeng, K.
利用果蝇种群基因组学计划提供的数据，我们研究了影响卢旺达和法国果蝇种群遗传分化的因素。黑腹菌通过研究群体内多态性，我们发现长内含子（特别是那些>2000 bp的）中的位点比短内含子具有显著更低的π（核苷酸多样性）和更多的低频变体（通过Tajima's D，次要等位基因频率和两个群体中的一个特有的变体的患病率来测量），这表明内含子长度和选择性约束之间存在正相关关系。类似的蛋白质编码多态性分析表明，0倍（简并）的网站在更保守的基因比那些保守性较低的基因更强的纯化选择。有有限的证据表明，密码子偏好的选择对4倍（简并）位点的分化（如FST所测量的）有影响，4倍位点和短内含子的8-30 bp中的位点具有可比的FST值。与纯化选择的预期效果一致，长内含子中的位点和保守基因中的0倍位点分别比短内含子和不太保守的基因中的位点分化更少。非交换区域（例如第四条染色体）的基因在0倍和4倍简并位点处具有非常高的FST值，这可能是因为许多选择位点之间的紧密连锁导致群体内多样性的大幅减少。我们的分析还揭示了FST的微妙的统计特性，当来自多个单核苷酸多态性的信息结合在一起时会出现这种特性，并可能导致选择的重要信号被掩盖。
Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by FST) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable FST values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high FST values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of FST, which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection.
登录
查看更多内容
影响因子：
10.7
作者：
Arguello, J. Roman;Zhang, Yue;Long, Manyuan
通讯作者：
Long, Manyuan
影响因子：
10.7
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
4.5
作者：
Comeron JM;Ratnappan R;Bailin S
通讯作者：
Bailin S
影响因子：
10.7
作者：
Casillas, Sonia;Barbadilla, Antonio;Bergman, Casey M.
通讯作者：
Bergman, Casey M.
影响因子：
10.7
作者：
Campos JL;Halligan DL;Haddrill PR;Charlesworth B
通讯作者：
Charlesworth B