Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster

We considered genome-wide four-fold degenerate sites from an African Drosophila melanogaster population and compared them to short introns. To include divergence and to polarize the data, we used its close relatives Drosophila simulans, Drosophila sechellia, Drosophila erecta and Drosophila yakuba as outgroups. In D. melanogaster, the GC content at four-fold degenerate sites is higher than in short introns; compared to its relatives, more AT than GC is fixed. The former has been explained by codon usage bias (CUB) favouring GC; the latter by decreased intensity of directional selection or by increased mutation bias towards AT. With a biallelic equilibrium model, evidence for directional selection comes mostly from the GC-rich ancestral base composition. Together with a slight mutation bias, it leads to an asymmetry of the unpolarized allele frequency spectrum, from which directional selection is inferred. Using a quasi-equilibrium model and polarized spectra, however, only purifying and...

本研究选取非洲黑腹果蝇（Drosophila melanogaster）种群的全基因组范围四折简并位点（four-fold degenerate sites），并将其与短内含子（short introns）进行对比分析。为纳入序列分化信息并实现数据极化，我们选用其近缘物种拟暗果蝇（Drosophila simulans）、塞谢拉果蝇（Drosophila sechellia）、直立果蝇（Drosophila erecta）以及亚暗果蝇（Drosophila yakuba）作为外类群（outgroups）。在黑腹果蝇中，四折简并位点的GC含量高于短内含子；相较于其近缘物种，该物种中固定的AT等位基因数量多于GC等位基因。前者可由偏好GC的密码子使用偏好性（codon usage bias, CUB）解释，后者则归因于定向选择强度减弱或向AT的突变偏好增强。基于双等位基因平衡模型（biallelic equilibrium model），定向选择的证据主要来源于高GC含量的祖先碱基组成。结合轻微的突变偏好，该特征会导致非极化等位基因频率谱（unpolarized allele frequency spectrum）出现不对称性，据此可推断定向选择的存在。然而，若采用准平衡模型（quasi-equilibrium model）与极化的频率谱，则仅能检测到纯化选择（purifying selection）以及……