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：借助系统发育推断阐释演化历史事件，可靠的分子标记进化速率测算至关重要。尽管现有新兴研究证据表明种内遗传变异存在较高的进化速率，但由于鲜有可用的近期校准节点，这类高进化速率的持续时长仍不明确。除利用化石证据外，还可依托已被广泛验证的成熟可靠的第四纪冰期（Quaternary glacial cycles）时间框架来估算进化速率，该框架大概率推动了快速种群扩张与岛屿间扩散两类事件的发生。

研究结果：我们对两种温带起源的日本林鼠——阿氏林鼠（Apodemus argenteus）与日本林鼠（Apodemus speciosus）的线粒体细胞色素b（Cytb）和控制区（CR）基因序列展开分析，在日本北部岛屿北海道的种群中发现了快速扩张的信号。假设末次冰期后7~10千年前（kyr BP）的全球变暖与此次种群扩张相关，那么阿氏林鼠的Cytb与CR进化速率（单位：每个位点每百万年，myr）分别估算为11%~16%与22%~32%；日本林鼠的对应速率则分别为12%~17%与17%~24%。此外，对日本本州、四国与九州这其余南部主岛的日本林鼠线粒体DNA（mtDNA）序列检测发现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于约130千年前（kyr BP），则可估算得到Cytb的进化速率为3.1%/位点/百万年。采用Cytb 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）相关的近期种群历史或分化事件；而若针对130千年前以上的冰期相关分化事件，则采用3.1%/位点/百万年的较低进化速率更为合理。

研究结论：在鼠科啮齿类的系统发育推断中，Cytb的高、低进化速率可分别对应末次冰盛期与更早冰期的物种分化事件。这类升高的进化速率似乎在10万年内便出现了衰减。