Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus

Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.

研究背景：借助系统发育推断（phylogenetic inference）阐释历史演化事件，确定分子标记的可靠进化速率至关重要。尽管新兴研究证据表明种内遗传变异（intraspecific genetic variation）具有较高的进化速率，但由于鲜有可用的近期校准节点（calibration point），这类高进化速率的持续时长仍不明确。除利用化石证据外，还可依托已被广泛证实的第四纪冰期旋回（Quaternary glacial cycles）时间框架估算进化速率——该框架大概率推动了种群快速扩张与岛间扩散两类事件的发生。
研究结果：本研究对两种温带起源的日本姬鼠属物种*Apodemus argenteus*与*A. speciosus*的线粒体细胞色素b（cytochrome b, Cytb）基因及控制区（control region, CR）序列开展分析，发现来自日本北部岛屿北海道的种群存在快速扩张的信号。假设末次冰期后距今7~10千年（kyr BP）的全球变暖与此次扩张相关，则*A. argenteus*的Cytb与CR基因的进化速率（单位：每百万年位点置换率，myr）分别为11%~16%与22%~32%；*A. speciosus*的对应速率则分别为12%~17%与17%~24%。此外，对来自其余南部主岛（本州、四国与九州）的*A. speciosus*线粒体DNA（mtDNA）序列的分析，也检测到了显著的快速扩张信号；若假设此次冰期后种群扩张事件发生在距今约130 kyr BP的远古时期，则可估算出Cytb基因的进化速率为3.1%/位点/百万年。采用Cytb基因11%~17%/位点/百万年的较高进化速率进行贝叶斯分析（Bayesian analyses），结果支持与末次冰盛期（Last Glacial Maximum）相关的近期种群动态或分化事件。而3.1%/位点/百万年的较慢进化速率，则更适配距今130 kyr BP以上的古老冰期相关的多次分化事件。
研究结论：在鼠科啮齿类的系统发育推断中，Cytb基因的快、慢两类进化速率可分别对应末次冰盛期与更早冰盛期相关的物种分化事件。这类升高的进化速率似乎在10万年以内便出现了衰减。