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.
1_Aargenteus_D-loop_YSuzuki
The sequences of the mitochondrial control region of Apodemus argenteus used for the construction of the phylogenetic tree and network.
2_Aargenteus_Cytb_YSuzuki
The mitochondrial cytochrome b gene sequences of Apodemus argenteus used for the construction of the phylogenetic tree and network.
3_Aargenteus_Cytb+D-loop_YSuzuki
The concatenated sequences of the mitochondrial controla region and cytochrome b gene of Apodemus argenteus used for the construction of the phylogenetic tree and network.
4_Aspeciosus_D-loop_YSuzuki
The mitochondrial control region sequences of Apodemus specious used for the construction of the phylogenetic tree and network.
5_Aspeciosus_Cytb_YSuzuki
The mitochondrial cytochrome b gene sequences of Apodemus specious used for the construction of the phylogenetic tree and network.
6_Aspeciosus_Cytb+d-loop_YSuzuki
The concatenated sequences of the mitochondrial control region and cytochrome b gene of Apodemus specious used for the construction of the phylogenetic tree and network.
7_Aargenteus_D-loop_Clade_I
The file is formatted for Arleqin and the sequences represent clade I of the control region of Apodemus argenteus.
8_Aargenteus_D-loop_Clade_Ia-1+Ia-2
The file is formatted for Arleqin and the sequences represent clade Ia-1 and clade Ia-2 of the control region of Apodemus argenteus.
9_Aargenteus_D-loop_Clade_Ia+II
The file is formatted for Arleqin and the sequences represent clade Ia-1 and clade II of the control region of Apodemus argenteus.
10_Aspeciosus_D-loop_Clade_IIabcd
The file is formatted for Arleqin and the sequences represent the four subgroups of clade II of the control region of Apodemus specious.
11_Aargenteus_D-loop_I+II
The file is formatted for Arleqin and the sequences represent the clades I and II of the control region of Apodemus argenteus.
12_Aargenteus_Cytb_Clade_I
The file is formatted for Arleqin and the sequences represent the clade I of the control region of Apodemus argenteus.
13_Aargenteus_Cytb_Clade_Ia-1
The file is formatted for Arleqin and the sequences represent clade Ia-1 of the cytochrome b gene of Apodemus argenteus.
14_Aargenteus_Cytb_Clade_Ia-2
The file is formatted for Arleqin and the sequences represent clade Ia-2 of the cytochrome b gene of Apodemus argenteus.
15_Aargenteus_Cytb_Clade_Ia+II
The file is formatted for Arleqin and the sequences represent clade Ia and clade II of the cytochrome b gene of Apodemus argenteus.
16_Aspeciosus_Cytb_Clade_IIabcd
The file is formatted for Arleqin and the sequences represent clade II of the cytochrome b gene of Apodemus speciosus. The sequenc data set was used as an input file for Arlequin.
17_Aargenteus_Cytb_I+II
The file is formatted for Arleqin and the sequences represent clades I and II of the cytochrome b gene of Apodemus artenteus.
18_Aargenteus_Cytb_BEAST_YSuzuki.nex
The sequences of the cytochrome b gene of Apodemus artenteus used for the BEAST analysis.
19_Aspeciosus_Cytb_BEAST_YSuzuki.nex
The sequences of the cytochrome b gene of Apodemus specious used for the BEAST analysis.
20_Aspeciosus_D-loop_Clade_I+II
The file is formatted for Arleqin and the sequences represent clades I and II of the control region of Apodemus specious.
21_Aspeciosus_D-loop_Total
The file is formatted for Arleqin and the sequences represent the whole data set of the control region of Apodemus specious.
22_Aspeciosus_Cytb_Clade_I+II
The file is formatted for Arleqin and the sequences represent clades I and II of the cytochrome b gene of Apodemus specious.
23_Aspeciosus_Cytb_Total
The file is formatted for Arleqin and the sequences represent whole data set of the cytochrome b gene of Apodemus specious.
24_Aspeciosus_Cytb_Hokkaido
The file is formatted for Arleqin and the data represent the cytochrome b gene sequences of Apodemus specious from Hokkaido.