Kondo R, Horai S, Satta Y, Takahata N
National Institute of Genetics, Graduate University for Advanced Studies, Mishima, Japan.
J Mol Evol. 1993 Jun;36(6):517-31. doi: 10.1007/BF00556356.
Focusing on the synonymous substitution rate, we carried out detailed sequence analyses of hominoid mitochondrial (mt) DNAs of ca. 5-kb length. Owing to the outnumbered transitions and strong biases in the base compositions, synonymous substitutions in mtDNA reach rapidly a rather low saturation level. The extent of the compositional biases differs from gene to gene. Such changes in base compositions, even if small, can bring about considerable variation in observed synonymous differences and may result in the region-dependent estimate of the synonymous substitution rate. We demonstrate that such a region dependency is due to a failure to take proper account of heterogeneous compositional biases from gene to gene but that the actual synonymous substitution rate is rather uniform. The synonymous substitution rate thus estimated is 2.37 +/- 0.11 x 10(-8) per site per year and comparable to the overall rate for the noncoding region. On the other hand, the rate of nonsynonymous substitutions differs considerably from gene to gene, as expected under the neutral theory of molecular evolution. The lowest rate is 0.8 x 10(-9) per site per year for COI and the highest rate is 4.5 x 10(-9) for ATPase 8, the degree of functional constraints (measured by the ratio of the nonsynonymous to the synonymous substitution rate) being 0.03 and 0.19, respectively. Transfer RNA (tRNA) genes also show variability in the base contents and thus in the nucleotide differences. The average rate for 11 tRNAs contained in the 5-kb region is 3.9 x 10(-9) per site per year. The nucleotide substitutions in the genome suggest that the transition rate is about 17 times faster than the transversion rate.
聚焦于同义替换率，我们对长度约为5kb的类人猿线粒体（mt）DNA进行了详细的序列分析。由于转换数量众多且碱基组成存在强烈偏差，mtDNA中的同义替换迅速达到相当低的饱和水平。组成偏差的程度因基因而异。即使碱基组成的变化很小，也可能导致观察到的同义差异出现相当大的变化，并可能导致同义替换率的区域依赖性估计。我们证明，这种区域依赖性是由于未能适当考虑基因间组成偏差的异质性，但实际的同义替换率相当均匀。由此估计的同义替换率为每年每个位点2.37 +/- 0.11 x 10(-8)，与非编码区的总体速率相当。另一方面，非同义替换率因基因而异，这正如分子进化中性理论所预期的那样。最低速率是COI基因每年每个位点0.8 x 10(-9)，最高速率是ATPase 8基因的4.5 x 10(-9)，功能限制程度（通过非同义替换率与同义替换率的比值衡量）分别为0.03和0.19。转运RNA（tRNA）基因在碱基含量上也存在变异性，因此在核苷酸差异上也存在变异性。5kb区域中包含的11个tRNA的平均速率为每年每个位点3.9 x 10(-9)。基因组中的核苷酸替换表明，转换速率比颠换速率快约17倍。
