Pesole G, Gissi C, De Chirico A, Saccone C
Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy.
J Mol Evol. 1999 Apr;48(4):427-34. doi: 10.1007/pl00006487.
We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some important "genomic laws." The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome, whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes. (2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide substitution rates are also provided.
我们首次在此展示一项基于对亲缘关系密切的生物体进行分析的综合性研究，以准确测定哺乳动物线粒体基因组中的核苷酸替换率。本研究基于现有数据尽可能精确地考察了不同功能性线粒体DNA区域的进化模式，揭示了一些重要的“基因组规律”。主要结论可总结如下：（1）发现线粒体DNA进化动态中存在高度的基因组内变异性。替换率强烈依赖于所考虑的区域，可以识别出进化缓慢和快速的区域。非同义位点、D环中央结构域以及tRNA和rRNA基因的进化比同义位点以及D环区域的两个外围结构域要慢得多。同义率在整个基因组中相当均匀，而非同义位点的速率取决于功能限制，因此在基因之间差异很大。（2）普遍接受的线粒体DNA比核DNA进化更快这一说法仅在某些区域成立，因此应针对特定的线粒体组成部分而言。特别是，非同义位点在线粒体基因和核基因中的速率相当；同义位点和小rRNA在线粒体中的进化速度比在其核对应物中快约20倍，tRNA则快约100倍。（3）物种特异性进化在D环区域尤为明显。由于所考虑的生物体对的分歧时间已知足够准确，因此也提供了绝对核苷酸替换率。
