Ashworth Laboratories, School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
J Mol Evol. 2010 Jan;70(1):116-28. doi: 10.1007/s00239-009-9314-6. Epub 2009 Dec 30.
Most previous studies of the evolution of codon usage bias (CUB) and intronic GC content (iGC) in Drosophila melanogaster were based on between-species comparisons, reflecting long-term evolutionary events. However, a complete picture of the evolution of CUB and iGC cannot be drawn without knowledge of their more recent evolutionary history. Here, we used a polymorphism dataset collected from Zimbabwe to study patterns of the recent evolution of CUB and iGC. Analyzing coding and intronic data jointly with a model which can simultaneously estimate selection, mutational, and demographic parameters, we have found that: (1) natural selection is probably acting on synonymous codons; (2) a constant population size model seems to be sufficient to explain most of the observed synonymous polymorphism patterns; (3) GC is favored over AT in introns. In agreement with the long-term evolutionary patterns, ongoing selection acting on X-linked synonymous codons is stronger than that acting on autosomal codons. The selective differences between preferred and unpreferred codons tend to be greater than the differences between GC and AT in introns, suggesting that natural selection, not just biased gene conversion, may have influenced the evolution of CUB. Interestingly, evidence for non-equilibrium evolution comes exclusively from the intronic data. However, three different models, an equilibrium model with two classes of selected sites and two non-equilibrium models with changes in either population size or mutational parameters, fit the intronic data equally well. These results show that using inadequate selection (or demographic) models can result in incorrect estimates of demographic (or selection) parameters.
大多数先前关于果蝇中密码子使用偏性（CUB）和内含子 GC 含量（iGC）进化的研究都是基于种间比较，反映了长期的进化事件。然而，如果不了解它们最近的进化历史，就无法描绘出 CUB 和 iGC 进化的全貌。在这里，我们使用来自津巴布韦的多态性数据集来研究 CUB 和 iGC 近期进化的模式。通过联合分析编码和内含子数据，并使用能够同时估计选择、突变和人口参数的模型，我们发现：（1）自然选择可能作用于同义密码子；（2）一个恒定的种群大小模型似乎足以解释大多数观察到的同义多态性模式；（3）GC 在内含子中比 AT 更受青睐。与长期进化模式一致，作用于 X 连锁同义密码子的持续选择比作用于常染色体密码子的选择更强。偏好密码子和非偏好密码子之间的选择差异往往大于内含子中 GC 和 AT 之间的差异，这表明自然选择，而不仅仅是偏向性基因转换，可能影响了 CUB 的进化。有趣的是，非平衡进化的证据仅来自内含子数据。然而，三个不同的模型，一个具有两类选择位点的平衡模型和两个具有种群大小或突变参数变化的非平衡模型，都同样适合同位素数据。这些结果表明，使用不适当的选择（或人口）模型可能会导致对人口（或选择）参数的错误估计。
