DOI: 10.5061/dryad.4902q
title: 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

description: 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.
description: 1_Aargenteus_D-loop_YSuzukiThe sequences of the mitochondrial control region of Apodemus argenteus used for the construction of the phylogenetic tree and network.2_Aargenteus_Cytb_YSuzukiThe mitochondrial cytochrome b gene sequences of Apodemus argenteus used for the construction of the phylogenetic tree and network.3_Aargenteus_Cytb+D-loop_YSuzukiThe 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_YSuzukiThe mitochondrial control region sequences of Apodemus specious used for the construction of the phylogenetic tree and network.5_Aspeciosus_Cytb_YSuzukiThe mitochondrial cytochrome b gene sequences of Apodemus specious used for the construction of the phylogenetic tree and network.6_Aspeciosus_Cytb+d-loop_YSuzukiThe 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_IThe 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-2The 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+IIThe 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_IIabcdThe 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+IIThe 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_IThe file is formatted for Arleqin and the sequences represent the clade I of the control region of Apodemus argenteus.13_Aargenteus_Cytb_Clade_Ia-1The 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-2The 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+IIThe 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_IIabcdThe 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+IIThe 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.nexThe sequences of the cytochrome b gene of Apodemus artenteus used for the BEAST analysis.19_Aspeciosus_Cytb_BEAST_YSuzuki.nexThe sequences of the cytochrome b gene of Apodemus specious used for the BEAST analysis.20_Aspeciosus_D-loop_Clade_I+IIThe file is formatted for Arleqin and the sequences represent clades I and II of the control region of Apodemus specious.21_Aspeciosus_D-loop_TotalThe 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+IIThe file is formatted for Arleqin and the sequences represent clades I and II of the cytochrome b gene of Apodemus specious.23_Aspeciosus_Cytb_TotalThe file is formatted for Arleqin and the sequences represent whole data set of the cytochrome b gene of Apodemus specious.24_Aspeciosus_Cytb_HokkaidoThe file is formatted for Arleqin and the data represent the cytochrome b gene sequences of Apodemus specious from Hokkaido.