通过分子钟估算分歧时间是进化生物学研究中的常用手段。在实际运用中，分子标记的替换饱和常因得不到充分的模型拟合而误导结果。鉴于线粒体基因组的高演化速率，其在分子钟运用中的局限性已为众多研究者所警觉。但由于不同生物类群的演化时间跨度、可用化石标定、线粒体基因组演化速率各异，该分子标记的局限性不能一概而论。
中国科学院成都生物研究所两栖爬行动物研究室曾晓茂研究员课题组以有尾两栖动物为例，通过对比分别基于线粒体基因组和核基因外显子估算的分歧时间，评估了在特定类群中线粒体基因高演化速率对时间估算的误导模式。结果表明，由于有尾类起源古老（2-3亿年）且缺乏涉及近期分歧事件的有效化石标定，基于线粒体基因的分子钟分析严重高估了分歧事件发生的时间。特别是较年轻的事件，可能被高估3-10倍。如类似评估在其他生物类群开展，将有利于分子钟分析的标记选择以及对其结果的理解和运用。
该研究结果近期发表在国际刊物《分子生物学与进化》（Molecular Biology and Evolution）上。(生物谷 Bioon.com)
doi:10.1093/molbev/msr072
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Exploring Patterns and Extent of Bias in Estimating Divergence Time from Mitochondrial DNA Sequence Data in a Particular Lineage: A Case Study of Salamanders (Order Caudata)
Yuchi Zheng, Rui Peng, Masaki Kuro-o and Xiaomao Zeng
In the practice of molecular dating, substitution saturation will bias the results if not properly modeled. Date estimates based on commonly used mitochondrial DNA sequences likely suffer from this problem because of their high substitution rate. Nevertheless, the patterns and extent of such expected bias remain unknown for many major evolutionary lineages, which often differ in ages, available calibrations, and substitution rates of their mitochondrial genome. In this case study of salamanders, we used estimates based on multiple nuclear exons to assess the effects of saturation on dating divergences using mitochondrial genome sequences on a timescale of ∼200–300 My. The results indicated that, due to saturation for older divergences and in the absence of younger effective calibration points, dates derived from the mitochondrial data were considerably overestimated and systematically biased toward the calibration point for the ingroup root. The overestimate might be as great as 3–10 times (about 20 My) older than actual divergence dates for recent splitting events and 40 My older for events that are more ancient. For deep divergences, dates estimated were strongly compressed together. Furthermore, excluding the third codon positions of protein-coding genes or only using the RNA genes or second codon positions did not considerably improve the performance. In the order Caudata, slowly evolving markers such as nuclear exons are preferred for dating a phylogeny covering a relatively wide time span. Dates estimated from these markers can be used as secondary calibrations for dating recent events based on rapidly evolving markers for which mitochondrial DNA sequences are attractive candidates due to their short coalescent time. In other groups, similar evaluation should be performed to facilitate the choice of markers for molecular dating and making inferences from the results.
