Bielawski Joseph P, Yang Ziheng
Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom.
J Struct Funct Genomics. 2003;3(1-4):201-12.
The rapid accumulation of genomic sequences in public databases will finally allow large scale studies of gene family evolution, including evaluation of the role of positive Darwinian selection following a duplication event. This will be possible because recent statistical methods of comparing synonymous and nonsynonymous substitution rates permit reliable detection of positive selection at individual amino acid sites and along evolutionary lineages. Here, we summarize maximum-likelihood based methods, and present a framework for their application to analysis of gene families. Using these methods, we investigated the role of positive Darwinian selection in the ECP-EDN gene family of primates and the Troponin C gene family of vertebrates. We also comment on the limitations of these methods and discuss directions for further improvements.
公共数据库中基因组序列的快速积累最终将使基因家族进化的大规模研究成为可能，包括评估复制事件后正向达尔文选择的作用。这之所以成为可能，是因为最近比较同义替换率和非同义替换率的统计方法能够可靠地检测单个氨基酸位点以及沿进化谱系的正向选择。在这里，我们总结基于最大似然法的方法，并提出一个将其应用于基因家族分析的框架。使用这些方法，我们研究了正向达尔文选择在灵长类动物的嗜酸性粒细胞阳离子蛋白-嗜酸性粒细胞衍生神经毒素（ECP-EDN）基因家族和脊椎动物的肌钙蛋白C基因家族中的作用。我们还评论了这些方法的局限性，并讨论了进一步改进的方向。
