Rand D M, Kann L M
Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
Genetica. 1998;102-103(1-6):393-407.
Two patterns are presented that illustrate the interaction of mutation and selection in the evolution of animal mtDNA: 1) variation among taxa in the ratio of polymorphism to divergence (rpd) at silent and replacement sites in protein-coding genes, and 2) strand-differences in polymorphism and divergence at 'silent' sites that suggest a mutation-selection balance in the evolution of codon usage. Cytochrome b data from GenBank show that about half of the species pairs tested have a significant excess of amino acid polymorphism, relative to divergence. The remaining half of species pairs do not depart from neutrality, but generally do show an excess of amino acid polymorphism. Sequences from Drosophila pseudoobscura displaying a signature of an expanding population show a slight, but non-significant, deficiency of amino acid polymorphism suggestive of recently intensified selection on mildly deleterious mutations. Genes whose reading frames lie on the major coding strand of Drosophila mtDNA show a preponderance of T- > C substitutions, while genes encoded on the minor strand experience more A- > G than T- > C substitutions between species at both silent and replacement sites. However, silent mutations at third codon positions are introduced into the population in proportions opposite to those observed as fixed differences between species (e.g., an excess of T- > C polymorphisms are found at the ND5 gene on the minor coding strand). The high A + T content of insect mtDNAs imposes strong codon usage bias favoring A-ending and T-ending codons resulting in a distinct mutation-selection balance for genes encoded on opposites strands. Thus, at both replacement and silent sites, mutations that appear to be constrained in terms of divergence between species are in excess within species. The data suggest that mildly deleterious mutations are common in mitochondrial genes. A test of this, and a competing, hypothesis is proposed that requires additional sequence surveys of polymorphism and divergence. An important challenge is to tease apart the impact of mutation and selection on levels of polymorphism versus divergence in a genome that does not generally recombine.
本文展示了两种模式，用以说明动物线粒体DNA（mtDNA）进化过程中突变与选择的相互作用：1）蛋白质编码基因中沉默位点和替换位点的多态性与分歧率（rpd）在不同分类群间的差异；2）“沉默”位点上多态性和分歧的链差异，这表明密码子使用进化过程中存在突变 - 选择平衡。来自GenBank的细胞色素b数据显示，约一半测试的物种对具有显著过量的氨基酸多态性，相对于分歧而言。其余一半的物种对未偏离中性，但通常也显示出过量的氨基酸多态性。显示种群扩张特征的拟暗果蝇序列表现出轻微但不显著的氨基酸多态性不足，这暗示了近期对轻度有害突变的选择加剧。果蝇mtDNA主要编码链上的阅读框基因显示T->C替换占优势，而次要链上编码的基因在物种间的沉默位点和替换位点都经历了更多的A->G替换而非T->C替换。然而，第三密码子位置的沉默突变在群体中的引入比例与作为物种间固定差异观察到的比例相反（例如，在次要编码链上的ND5基因发现过量的T->C多态性）。昆虫mtDNA的高A + T含量导致强烈的密码子使用偏好，有利于以A结尾和以T结尾的密码子，从而在相反链上编码的基因产生明显的突变 - 选择平衡。因此，在替换位点和沉默位点，在物种间分歧方面似乎受到限制的突变在物种内过量。数据表明轻度有害突变在线粒体基因中很常见。本文提出了对此及一个竞争性假设的检验，这需要对多态性和分歧进行额外的序列调查。一个重要的挑战是在一个通常不发生重组的基因组中，区分突变和选择对多态性水平与分歧的影响。
