通過分子鐘估算分歧時間是進化生物學研究中的常用手段,。在實際運用中，分子標記的替換飽和常因得不到充分的模型擬合而誤導結(jié)果,。鑒于線粒體基因組的高演化速率,，其在分子鐘運用中的局限性已為眾多研究者所警覺。但由于不同生物類群的演化時間跨度,、可用化石標定,、線粒體基因組演化速率各異，該分子標記的局限性不能一概而論,。
中國科學院成都生物研究所兩棲爬行動物研究室曾曉茂研究員課題組以有尾兩棲動物為例,，通過對比分別基于線粒體基因組和核基因外顯子估算的分歧時間，評估了在特定類群中線粒體基因高演化速率對時間估算的誤導模式,。結(jié)果表明，由于有尾類起源古老（2-3億年）且缺乏涉及近期分歧事件的有效化石標定,，基于線粒體基因的分子鐘分析嚴重高估了分歧事件發(fā)生的時間,。特別是較年輕的事件，可能被高估3-10倍,。如類似評估在其他生物類群開展,，將有利于分子鐘分析的標記選擇以及對其結(jié)果的理解和運用。
該研究結(jié)果近期發(fā)表在國際刊物《分子生物學與進化》（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.
