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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.

bmc evolutionary biology

Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus