Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.
Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.
复制标题
密码子偏倚选择强度随时间的变化导致果蝇碱基组成进化模式的对比。
DOI：
10.1093/gbe/evw291
复制
发表时间：
2017-01-01
影响因子：
3.3
通讯作者：
Zeng K
中科院分区：
文献类型：
--
作者：
Jackson BC;Campos JL;Haddrill PR;Charlesworth B;Zeng K
四重简并编码位点构成了基因组的主要组成部分，并且经常被用来推断选择和人口统计学，因此理解它们的进化是重要的。尽管以前的努力，许多问题的原因，在这些网站在果蝇的碱基组成的变化仍然没有答案。为了进一步阐明这一问题，我们从D. simulans。我们分析了来自D. simulans，以及现有的多态性数据集，从非洲人口的D。黑腹菌利用D. yakuba作为一个外群，我们发现了明确的证据，选择4倍网站沿着这两个谱系在一个相当长的时间，与GC含量增加的选择强度。基于一个明确的模型的碱基组成的演变，我们认为，在这两个谱系中观察到的AT偏向的取代模式可能是由于祖先减少选择强度，是不太可能的结果，增加突变偏向AT单独。通过使用两种基于多态性的方法来估计不同时间尺度上的选择系数，我们发现，密码子使用的选择强度在D. simulans在最近的过去，但在D.黑腹果蝇的基因组DNA含量比短期的高得多，表明选择强度持续下降，以至于短期估计表明选择仅在基因组中GC最丰富的部分活跃。最后，我们提供的证据复杂的进化模式的puppet中性短内含子，这是不能解释的标准GC偏向基因转换模型。这些结果揭示了一个动态的图片基地组成的演变。
Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.