Ochman H, Wilson A C
Department of Biochemistry, University of California, Berkeley 94720.
J Mol Evol. 1987;26(1-2):74-86. doi: 10.1007/BF02111283.
This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago. The median extent of divergence between S. typhimurium and E. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes. For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S. typhimurium and E. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.
本文通过将地质历史上已知时间发生的生态事件与真细菌、线粒体和叶绿体的16S核糖体RNA谱系树中的特定分支点联系起来，构建了一个细菌进化的时间尺度。这样就得到了时间与细菌RNA分歧之间的关系，可用于估计细菌树中其他分支之间的分歧时间。根据这种方法，鼠伤寒沙门氏菌和大肠杆菌在1.2亿至1.6亿年前发生了分歧，这一日期与证据相符，即这两种肠道菌目前主要占据的栖息地早在那个时候就已出现。鼠伤寒沙门氏菌和大肠杆菌在21千碱基蛋白质编码DNA的同义位点上的分歧中值为100%。这意味着沉默替代率为0.7 - 0.8%/百万年——这一速率与在哺乳动物、无脊椎动物和开花植物的核基因中观察到的速率非常相似。真核生物和原核生物在替代率上的相似性并不局限于蛋白质编码区域的沉默替代。真细菌中16S rRNA的平均替代率约为1%/50百万年，与脊椎动物和开花植物中18S rRNA的平均速率相似。同样，我们估计真细菌和真核生物中5S rRNA的平均速率约为1%/25百万年。对于这些肠道细菌的一些蛋白质编码基因，自鼠伤寒沙门氏菌和大肠杆菌分歧以来，沉默替代的程度远低于100%，这是由于同义密码子使用的极端偏差。此外，在这些细菌中，氨基酸替代率平均比沉默率低约20倍。相比之下，对于迄今为止研究的哺乳动物基因，平均替代率仅比沉默替代率低四至五倍。
