Data from: Time dependency of molecular evolutionary rates? Yes and no

Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, whereas a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. Although the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9–15 times higher than that estimated using the human–chimpanzee pair, in contrast, the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous to synonymous sites estimated using intra- and interspecific comparisons vary up to nine times, which corroborates our results independent of calibration times.

既往多项研究表明，基于分子序列（molecular sequences）推断的进化速率会因测算时长的不同而存在显著差异，另有诸多研究对此观点提出了反驳。本研究通过对处于不同选择约束水平的灵长类线粒体基因组（primate mitochondrial genomes）位点进行分组，对这一争议议题展开了系统性探究。研究结果显示，受约束位点（包括非同义位点（nonsynonymous sites）、D环（D-loop）及RNA位点）的进化速率存在一个数量级的差异，而同义位点（synonymous sites）的进化速率则几乎完全一致，且与测算时长无关。尽管基于欧洲人（H1单倍群）线粒体基因组得到的非同义位点进化速率，较人-黑猩猩比对所得结果高出9至15倍，但两类比对下的同义位点进化速率却极为相近。本研究还发现，基于种内与种间比对得到的非同义位点与同义位点的分化速率比最高可达9倍，这一结果不受校准时间的影响，进一步佐证了本研究的结论。