- Email: [email protected]
Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea
GENE-40760; No. of pages: 6; 4C: Gene xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Short communication
Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea Hye Ri Kim, Yung Chul Park ⁎ College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
a r t i c l e
i n f o
Article history: Received 26 March 2015 Received in revised form 15 July 2015 Accepted 7 August 2015 Available online xxxx Keywords: Apodemus agrarius coreae Striped field mouse Population expansion Haplotype diversity Median joining network
a b s t r a c t The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd = 0.967) and low levels of nucleotide diversity (π = 0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. © 2015 Published by Elsevier B.V.
1. Introduction The striped field mouse Apodemus agrarius is distributed from Eastern Europe to the Russian Far East, including Korean Peninsula and China (Thomas, 1906; Corbet, 1978; Musser and Carleton, 1993). This species inhabits open habitats of temperate forests and is the most common rodent in woodlands and forests of the Korean Peninsula (Jones and Johnson, 1965). In the Korean Peninsula, four subspecies of A. agrarius have been recognized traditionally (Jones and Johnson, 1965), including Apodemus agrarius manchuricus in the extreme northern part of the peninsula, Apodemus agrarius pallescens in the coastal lowlands of the southern part of the peninsula, Apodemus agrarius coreae throughout the major portion of the peninsula, and Apodemus agrarius chejuensis on Jeju Island, off the southern coast of the Peninsula. Several studies (Koh, 1986, 1987, 1991; Koh and Yoo, 1992; Koh et al., 2000), however, have suggested that A. a. pallescens is a synonym of A. a. coreae and that only two subspecies, A. a. coreae and A. a. chejuensis, are distributed in the southern region of the Korean Peninsula based on morphological characteristics and restriction fragment length polymorphisms (RFLPs)
Abbreviations: Hd, haplotype diversity; Π, nucleotide diversity; K, average number of nucleotide differences; H, number of haplotypes; S, number of variable sites; Cyt b, cytochrome b; AMOVA, analysis of molecular variance; Fst, pairwise fixation index; MJN, median joining network. ⁎ Corresponding author. E-mail address: [email protected] (Y.C. Park).
of mitochondrial DNA. Based on the first half (213 bp) of the mitochondrial DNA control region and 12S rRNA gene sequences, Koh et al. (2000) showed that only the subspecies A. a. coreae is distributed widely throughout South Korea. However, the study of genetic divergence that have been conducted to date on Korean population of A. agrarius included only very short mitochondrial DNA sequences from a small set of samples from a few locations (Koh et al., 2000; Sakka et al., 2010). In the present study, we analyzed mitochondrial cyt b sequences from A. agrarius populations that were collected from various sites of Korean mainland, in addition to most of the locations in South Korea that were sampled in previous studies (Koh et al., 2000; Sakka et al., 2010). The aim of this study was to reveal the genetic diversity and genetic structure of A. a. coreae population in Korea. 2. Materials and methods 2.1. Sample collection Mitochondrial cytochrome b (cyt b) sequences were collected from 54 individuals of A. a. coreae from 2012 to 2014 in the northwestern, northeastern, central, and southwestern regions of South Korea (Fig. 1), and additional five cyt b sequences of Korean A. a. coreae (YS, GS, and Kan) were obtained from GenBank (Supplementary Table 1). Korean individuals of A. a. coreae were grouped into four populations (NWS, NES, CTS, and SWS) depending on their geographic distributions (Fig. 1). To infer haplotype relationship between populations from Korea and its neighboring regions, we have included previously
http://dx.doi.org/10.1016/j.gene.2015.08.014 0378-1119/© 2015 Published by Elsevier B.V.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
2
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Fig. 1. Collection sites of the Korean populations of Apodemus agrarius. Apodemus a. coreae and A. a. chejuensis are distributed in the Korean mainland and Jeju Island, respectively. A. a. coreae populations from other collection sites except that for Yangsan (YS) were partitioned geographically into four groups: the northwestern (NWS), northeastern (NES), central (CTS), and southwestern Korea (SWS). The haplotypes and abbreviations of their collection sites are indicated in each box. Detailed information on the haplotypes and their localities is shown in Supplementary Table 1.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
published cyt b sequences of A. agrarius specimens collected from its neighboring regions (Supplementary Table 1 and Supplementary Fig. 1). Apodemus chevrieri (HQ896709) and Apodemus peninsulae (AB073809) were used as outgroup. 2.2. DNA extraction, PCR, and sequencing Total genomic DNA was extracted from the ear punch tissue of specimens using an AccuPrep® Genomic DNA Extraction Kit (Bioneer Corporation, Daejeon, Korea) according to manufacturer's protocol. Fragments of mitochondrial cyt b were amplified by polymerase chain reaction (PCR) using primers L7 and H6 (Kocher et al., 1989). PCR amplification was carried out using a GeneAmp® PCR system 9700 (Applied Biosystems, Foster City, CA, USA) in 20 μL reaction mixtures, containing 1 μL genomic DNA as template, 10 pmol each primer, 250 μM dNTPs, 2.5 mM MgCl2, and 1 U Taq Polymerase (Promega, Madison, WI, USA). The temperature profile for PCR amplification was as follows: denaturation at 95 °C for 5 min, followed by 35 cycles at 95 °C for 1 min, 55 °C for 1 min, and 72 °C for 1 min, and a final extension at 72 °C for 5 min. PCR products were electrophoresed on 1% agarose gel and purified with a Cleanmix DNA Purification Kit (Talent Srl, Trieste, Italy). Sequencing of the purified products was performed using an ABI Prism® Big Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) and a Gene Amp PCR system 9700 (Applied Biosystems). Sequences were determined by automated sequencing on a 3730 DNA Sequencer (Applied Biosystems) on 8% polyacrylamide gels. 2.3. Data analysis 2.3.1. Genetic diversity and gene flow Genetic diversity and gene flow were analyzed in populations with sample size of three or more individuals. Haplotype diversity (Hd) and nucleotide diversity (π) were calculated using DnaSP.5.10 (Librado and Rozas, 2009). Partitioning of genetic variation within and among populations was calculated using the analysis of molecular variance (AMOVA) implemented in Arlequin v. 3.5 (Excoffier and Lischer, 2010), by computing conventional F-statistics from haplotypes with 1000 permutations. Genetic differentiation between populations was calculated from the pairwise fixation index (Fst) using Arlequin v. 3.5. The significance of each Fst value was tested with 1000 random permutations (Slatkin, 1991). 2.3.2. Demographic history Past population expansion was estimated based on the neutrality tests of Tajima's D (Tajima, 1989) and Fu's Fs (Fu, 1997) using Arlequin 3.5, and p-values were generated using 1000 simulations with a model of selective neutrality. 2.3.3. Genetic structure Mitochondrial cyt b sequences were aligned using Clustal X 1.8 (Thompson et al., 1997) and manually adjusted in Se–Al v2.0 alignment editor (available at http://evolve.zoo.ox.ac.uk/). Phylogenetic tree was constructed using Bayesian inference (BI) procedures implemented in MrBayes 3.2.2 (Ronquist et al., 2012). For the BI analysis, TrN+I + G was selected as the best substitution model under the Akaike Information Criterion (AIC) using Modeltest 3.7 (Posada and Crandall, 1998). We applied separate partitions for the 1st, 2nd, and 3rd codon positions and unlinked base composition, transition matrices, proportions of invariant sites, and gamma shapes. The BI analysis was performed using two independent runs of four incrementally heated Markov chains (one cold chain and three hot chains) which were simultaneously run for 2 million generations, with sampling conducted every 500 generations. Stationarity was checked by plotting log likelihood values against generation number and the first 25% of generated trees from each run
3
Table 1 Genetic diversity of Apodemus agrarius coreae in Korea. Population
NWS NES CTS SWS Total populations
N
8 25 5 20 58
H
7 13 5 13 35
S
20 28 9 35 64
Genetic diversity
K
Hd
π
0.964 ± 0.077 0.903 ± 0.043 1.000 ± 0.126 0.953 ± 0.028 0.967 ± 0.012
0.00866 ± 0.00122 0.00673 ± 0.00103 0.00432 ± 0.00116 0.00626 ± 0.00084 0.00683 ± 0.00065
7.214 5.610 3.600 5.211 5.691
N; number of sequences, H; number of haplotypes, S; number of variable sites, Hd; haplotype diversity, π; nucleotide diversity, K; average number of nucleotide differences.
were discarded as burn-in. The pairwise genetic distances between haplogroups were calculated based on the K2P model (Kimura, 1980). The median joining network (MJN) was constructed to reveal the relationships between the Korean and its neighboring haplotypes using NETWORK v. 4.613 (Bandelt et al., 1999). 3. Results 3.1. Genetic diversity, gene flow and demographic history We identified 64 polymorphic sites in the entire data set of 833 bp, comprising 35 haplotypes from 59 individuals in the four Korean populations of A. a. coreae (NWS, NES, CTS, and SWS). There were 7 haplotypes from NWS, 13 haplotypes from NES, 5 haplotypes from CTS, and 13 haplotypes from SWS (Table 1). The analyses of genetic diversity revealed high levels of haplotype diversity (Hd = 0.967) and low nucleotide diversity (π = 0.00683) in A. a. coreae. The AMOVA of A. a. coreae populations indicated that most of the haplotype diversity was found within populations (94.5%), but an appreciable amount was still present between the populations (5.5%) (Supplementary Table 2). Significant fixation indices (Fst) were observed between NWS and NES as well as between NWS and SWS, while a low level of genetic differentiation was observed between SWS and NES (Table 2). Neutrality tests of Korean A. a. coreae produced significantly negative values in both Tajima's D (− 2.029, p = 0.006) and Fu's Fs (−22.101, p = 0.000). 3.2. Genetic structure The BI analysis resolved the mainland A. a. coreae haplotypes into four clades, among which Haplogroups 2 and 3 received low bootstrap supports of 56% and 78%, respectively (Fig. 2). Most of the Korean haplotypes were included in Haplogroup 1. Short branches and unresolved nodes, which are present within each clade of the BI tree, are probably caused by the low number of mutations between the haplotypes. In the MJN (Fig. 3), haplotypes of A. a. chejuensis were well separated from those of other Korean A. a. coreae. Haplogroups 2 and 3 were more closely related to each other than to the other Korean haplogroups. The pairwise genetic distance also showed close relationship between Haplogroups 2 and 3 (0.005) compared with the distances between the other Korean haplogroups (Table 3). The genetic distances between haplogroups of the A. a. coreae were lower than those between haplogroups of the two subspecies A. a. coreae and A. a. chejuensis (Table 3). Table 2 Pairwise fixation index (Fst) between four local populations of Korean Apodemus agrarius coreae. Populations
NES
NWS
CTS
SWS
NES NWS CTS SWS
– 0.094⁎ 0.013 0.029
– 0.016 0.137⁎
– −0.006
–
⁎ p b 0.05.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
4
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Fig. 2. Phylogenetic relationships of the Korean populations of Apodemus agrarius coreae inferred from the Bayesian inference analysis. Numbers on the nodes indicate posterior probabilities. The representative four clades are indicated as Haplogroups (Haplogroups 1, 2, 3, and 4) and compared with those of the median joining network (Fig. 3). Abbreviations for collection sites of the haplotypes are indicated within the parentheses. For abbreviations see Fig. 1.
Fig. 3. The median joining network of Apodemus agrarius haplotypes from Korea and its neighboring regions. Haplotypes are shown in different colors according to their geographical location. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
5
Table 3 Pairwise genetic distance between Korean haplogroups of Apodemus agrarius. Korean haplogroups used for pairwise comparisons are shown in Figs. 2 and 3. Values below or along the diagonal line are genetic distances between or within haplogroups, respectively. Species
A. a. coreae
A. a. chejuensis
Lineages
Haplogroup 1 Haplogroup 2 Haplogroup 3 Haplogroup 4
No. haplotypes
Mainland (n = 27) Mainland (n = 4) Mainland (n = 2) Mainland (n = 2) Jeju Island (n = 6)
A. a. coreae
A. a. chejuensis
Haplogroup 1
Haplogroup 2
Haplogroup 3
Haplogroup 4
0.005 ± 0.003 0.009 ± 0.002 0.009 ± 0.002 0.015 ± 0.002 0.021 ± 0.002
0.003 ± 0.001 0.005 ± 0.001 0.011 ± 0.001 0.017 ± 0.001
0.002 0.014 ± 0.002 0.019 ± 0.002
0.006 ± 0.004 0.021 ± 0.001
Most of Korean haplotypes were included within Haplogroup 1, which was congruent with the BI tree topology. H14 of Haplogroup 1, which is the most common haplotype whose many adjacent single haplotypes were connected by one or two mutations, was shared among three populations (NES, CTS, and SWS), H1 and H22 were shared between two populations, and the remaining haplotypes were specific to their collection sites. Some of Korean haplotypes, particularly those in northern South Korea (Haplogroups 2 and 4), clustered with haplotypes of the Russian Far East, while Haplogroup 1 formed its own clade, which was separated from haplotypes of the neighboring countries of the Korean Peninsula as well as other Korean haplogroups (Fig. 3). 4. Discussion The Korean A. a. coreae is characterized by high haplotype diversity but low nucleotide diversity, which indicates only small differences between the haplotypes. This is also evident from the MJN, which shows mostly single nucleotide differences between the haplotypes. Similar genetic diversity pattern was observed in various species of the genus Apodemus, which might have experienced historical isolation and adaptive radiation under various environmental conditions present at their refuges during the Quaternary climate change (Serizawa et al., 2000; Sakka et al., 2010). As in the cases of the Siberian chipmunk (Eutamias sibiricus) and the Chinese black-spotted frog (Pelophylax nigromaculatus) (Lee et al., 2008; Zhang et al., 2008), the Korean Peninsula under the subtropical climate during the Quaternary (Liu and Li, 1996; Lee, 1999; Park and Kong, 2001) may have played an important role as refuge for A. a. coreae, which might have experienced population expansion and genetic isolation. According to the AMOVA and the fixation indices (Fst), geographical barriers for gene flow within South Korea might occur between the populations of NWS and NES as well as those of NWS and SWS. Despite long geographic distance that separates the SWS and NES populations, significant differentiation was not observed between the two populations, probably because their habitats are connected through the Baekdudaegan mountain range, which stretches through most of the length of the Korean Peninsula, from the northern region to southern and southwestern regions (Fig. 1). The MJN, which included haplotypes from the neighboring regions of the Korean Peninsula, resolved the relationship between the Korean and its neighboring haplotypes as well as within the Korean haplotypes (Fig. 3). In the MJN, four haplogroups were recognized in A. a. coreae. According to a previous study (Sakka et al., 2010), a Korean haplotype from Kanghwado Island, an island off the western coast of the Korean Peninsula, was separated by three mutation steps from the haplotypes of the Russian Far East (Askold Island, Reineke Island, and Russky Island). Our MJN also confirms close connection between some Korean haplotypes (those in Haplogroups 2, 3 and 4) and haplotypes of the Russian Far East. Haplogroup 2 is closely related to the haplotypes H68, H70, and H71 from the Russian Far East. H27 in Haplogroup 2, which is distributed in central South Korea, is separated by only two mutation steps from a haplotype H68 from the Russian Far East (Khorolsky District) and acts as a stepping-stone between Russian haplotypes and other Korean haplotypes (H3, H23, and H24) within the Haplogroup 2. In MJN, Haplogroup 3 is closely related to Haplogroup
0.005 ± 0.005
2, as indicated by the pairwise genetic distance (Table 3). Haplogroup 4 is more closely related to other haplotypes (H52 and H69) from the Russian Far East than to the other Korean haplogroups. Haplogroup 1, which includes most Korean haplotypes, is well isolated from the other Korean haplogroups (Haplogroups 2, 3, and 4) as well as haplotypes from the neighboring regions of the Korean Peninsula. Traditionally it has been known that only a subspecies A. a. coreae is present in the mainland of South Korea. However, our current findings confirmed the presence of other genetic lineages, as well as the Korean endemic Haplogroup 1, that are closely related to haplotypes from the Russian Far East. Thus, further investigation on the validity of the subspecies status of A. a. coreae are required by implementing additional morphological samples as well as genetic data from the populations in the Korean Peninsula and its neighboring countries. Haplogroup 1 forms a star-like structure in the MJN, which indicates relatively low levels of sequence divergence and high frequency of unique mutations (only a few mutations are shared in most of the haplotype nodes) and thus corroborates the results of the genetic diversity analysis (Table 1). The demographic expansion corresponds well to the widely observed patterns of population expansion in organisms across taxa following the last glacial period (Serizawa et al., 2000; Michaux et al., 2004; Sakka et al., 2010; de Jong et al., 2011). Thus, the haplotypes of Haplogroup 1 appear to have experienced population expansion since their migration into Korea, which is congruent with the results of the two neutrality tests. These results indicate that the Korean Peninsula might have played an important role as a refuge during the Quaternary glaciations, as suggested in previous studies (Serizawa et al., 2000; Sakka et al., 2010). 5. Conclusions Korean population of A. a. coreae is characterized by high haplotype diversity and low nucleotide diversity. There are four haplogroups recognized in A. a. coreae. Haplotypes of the other haplogroups, with the exception of the Korean endemic Haplogroup 1, are closely related to those from the Russian Far East. These findings show that further investigations should be conducted to confirm the validity of subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations in the Korean Peninsula and its neighboring countries. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.gene.2015.08.014. Acknowledgments This work was supported by a grant from Kangwon Green Environment Center (KWGEC) in 2014. The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the quality of the paper. References Bandelt, H.J., Forster, P., Röhl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
6
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Corbet, G.B., 1978. The Mammals of the Palaearctic Region: a Taxonomic Review. British Museum (Natural History) and Cornell University Press, London and Ithaca, NY. de Jong, M.A., Wahlberg, N., van Eijk, M., Brakefield, P.M., Zwaan, B.J., 2011. Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia. PLoS ONE 6, e21385. Excoffier, L., Lischer, H., 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567. Fu, Y.X., 1997. Statistical tests of neutrality against population growth, hitch hiking and background selection. Genetics 147, 915–925. Jones, J.K., Johnson, D.H., 1965. Synopsis of the lagomorphs and rodents of Korea. Univ. Kans. Publ. Mus. Nat. Hist. 16, 357–407. Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. U. S. A. 86, 6196–6200. Koh, H.S., 1986. Geographic variation of morphometric characters among three subspecies of striped field mice, Apodemus agrarius Pallas (Muridae, Rodentia) from Korea. Korean J. Syst. Zool. 29, 272–282. Koh, H.S., 1987. Systematic studies of Korean rodents: III. Morphometric and chromosomal analyses of striped field mice, Apodemus agrarius chejuensis Jones and Johnson, from Cheju-Do. Korean J. Syst. Zool. 3, 24–40. Koh, H.S., 1991. Multivariate analysis with morphometric characters of samples representing eight subspecies of striped field mice, Apodemus agrarius Pallas (Rodentia, Mammalia), in Asia: the taxonomic status of subspecies chejuensis at Cheju Island, Korea. Korean J. Syst. Zool. 7, 179–188. Koh, H.S., Yoo, B.S., 1992. Variation of mitochondrial DNA in two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis from Korea. Korean J. Syst. Zool. 35, 332–338. Koh, H.S., Lee, W.J., Kocher, T.D., 2000. The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis. Heredity 85, 30–36. Lee, J.H., 1999. Geology of Korea, Geological Society of Korea. Sigma Press, Seoul. Lee, M.Y., Lissovsky, A.A., Park, S.K., Obolenskaya, E.V., Dokuchaev, N.E., Zhang, Y.P., et al., 2008. Mitochondrial cytochrome b sequence variations and population structure of
Siberian chipmunk (Tamias sibiricus) in northeastern Asia and population substructure in South Korea. Mol. Cells 26, 566–575. Librado, P., Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452. Liu, D.S., Li, Z.G., 1996. Geography of Asia. Commercial Press, Beijing. Michaux, J.R., Libois, R., Paradis, E., Filippucci, M.G., 2004. Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East. Mol. Phylogenet. Evol. 32, 788–798. Musser, G.G., Carleton, M.D., 1993. Family Muridae. In: Wilson, D.E., Reeder, D.A. (Eds.), Mammal Species of the World, seconded. Smithsonian Institution Press, Washington, D.C., pp. 501–755. Park, Y.A., Kong, W.S., 2001. The Quaternary Environment of Korea. Seoul National University Press (in Korean). Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817–818. Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542. Sakka, H., Quere, J.P., Kartavtseva, I., Marina, P.K., Chelomina, G., Atopkin, D., Bogdanov, A., Michaux, J.H., 2010. Comparative phylogeography of four Apodemus species (Mammalia: Rodentia) in the Asian Far East: evidence of Quaternary climatic changes in their genetic structure. Biol. J. Linn. Soc. 100, 797–821. Serizawa, K., Suzuki, H., Tsuchiya, K., 2000. A phylogenetic view on species radiation in Apodemus inferred from variation of nuclear and mitochondrial genes. Biochem. Genet. 38, 27–40. Slatkin, M., 1991. Inbreeding coefficients and coalescence times. Genet. Res. 58, 167–175. Tajima, F., 1989. The effect of change in population size on DNA polymorphism. Genetics 123, 597–601. Thomas, O., 1906. The Duke of Bedford's zoological exploration in eastern Asia: II. List of small mammals from Korea and Quelpart. Proc. Zool. Soc. London 18, 858–865. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The clustal x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882. Zhang, H., Yan, J., Zhang, G., Zhou, K., 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol. Biol. 8, 21.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Short communication
Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea Hye Ri Kim, Yung Chul Park ⁎ College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
a r t i c l e
i n f o
Article history: Received 26 March 2015 Received in revised form 15 July 2015 Accepted 7 August 2015 Available online xxxx Keywords: Apodemus agrarius coreae Striped field mouse Population expansion Haplotype diversity Median joining network
a b s t r a c t The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd = 0.967) and low levels of nucleotide diversity (π = 0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. © 2015 Published by Elsevier B.V.
1. Introduction The striped field mouse Apodemus agrarius is distributed from Eastern Europe to the Russian Far East, including Korean Peninsula and China (Thomas, 1906; Corbet, 1978; Musser and Carleton, 1993). This species inhabits open habitats of temperate forests and is the most common rodent in woodlands and forests of the Korean Peninsula (Jones and Johnson, 1965). In the Korean Peninsula, four subspecies of A. agrarius have been recognized traditionally (Jones and Johnson, 1965), including Apodemus agrarius manchuricus in the extreme northern part of the peninsula, Apodemus agrarius pallescens in the coastal lowlands of the southern part of the peninsula, Apodemus agrarius coreae throughout the major portion of the peninsula, and Apodemus agrarius chejuensis on Jeju Island, off the southern coast of the Peninsula. Several studies (Koh, 1986, 1987, 1991; Koh and Yoo, 1992; Koh et al., 2000), however, have suggested that A. a. pallescens is a synonym of A. a. coreae and that only two subspecies, A. a. coreae and A. a. chejuensis, are distributed in the southern region of the Korean Peninsula based on morphological characteristics and restriction fragment length polymorphisms (RFLPs)
Abbreviations: Hd, haplotype diversity; Π, nucleotide diversity; K, average number of nucleotide differences; H, number of haplotypes; S, number of variable sites; Cyt b, cytochrome b; AMOVA, analysis of molecular variance; Fst, pairwise fixation index; MJN, median joining network. ⁎ Corresponding author. E-mail address: [email protected] (Y.C. Park).
of mitochondrial DNA. Based on the first half (213 bp) of the mitochondrial DNA control region and 12S rRNA gene sequences, Koh et al. (2000) showed that only the subspecies A. a. coreae is distributed widely throughout South Korea. However, the study of genetic divergence that have been conducted to date on Korean population of A. agrarius included only very short mitochondrial DNA sequences from a small set of samples from a few locations (Koh et al., 2000; Sakka et al., 2010). In the present study, we analyzed mitochondrial cyt b sequences from A. agrarius populations that were collected from various sites of Korean mainland, in addition to most of the locations in South Korea that were sampled in previous studies (Koh et al., 2000; Sakka et al., 2010). The aim of this study was to reveal the genetic diversity and genetic structure of A. a. coreae population in Korea. 2. Materials and methods 2.1. Sample collection Mitochondrial cytochrome b (cyt b) sequences were collected from 54 individuals of A. a. coreae from 2012 to 2014 in the northwestern, northeastern, central, and southwestern regions of South Korea (Fig. 1), and additional five cyt b sequences of Korean A. a. coreae (YS, GS, and Kan) were obtained from GenBank (Supplementary Table 1). Korean individuals of A. a. coreae were grouped into four populations (NWS, NES, CTS, and SWS) depending on their geographic distributions (Fig. 1). To infer haplotype relationship between populations from Korea and its neighboring regions, we have included previously
http://dx.doi.org/10.1016/j.gene.2015.08.014 0378-1119/© 2015 Published by Elsevier B.V.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
2
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Fig. 1. Collection sites of the Korean populations of Apodemus agrarius. Apodemus a. coreae and A. a. chejuensis are distributed in the Korean mainland and Jeju Island, respectively. A. a. coreae populations from other collection sites except that for Yangsan (YS) were partitioned geographically into four groups: the northwestern (NWS), northeastern (NES), central (CTS), and southwestern Korea (SWS). The haplotypes and abbreviations of their collection sites are indicated in each box. Detailed information on the haplotypes and their localities is shown in Supplementary Table 1.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
published cyt b sequences of A. agrarius specimens collected from its neighboring regions (Supplementary Table 1 and Supplementary Fig. 1). Apodemus chevrieri (HQ896709) and Apodemus peninsulae (AB073809) were used as outgroup. 2.2. DNA extraction, PCR, and sequencing Total genomic DNA was extracted from the ear punch tissue of specimens using an AccuPrep® Genomic DNA Extraction Kit (Bioneer Corporation, Daejeon, Korea) according to manufacturer's protocol. Fragments of mitochondrial cyt b were amplified by polymerase chain reaction (PCR) using primers L7 and H6 (Kocher et al., 1989). PCR amplification was carried out using a GeneAmp® PCR system 9700 (Applied Biosystems, Foster City, CA, USA) in 20 μL reaction mixtures, containing 1 μL genomic DNA as template, 10 pmol each primer, 250 μM dNTPs, 2.5 mM MgCl2, and 1 U Taq Polymerase (Promega, Madison, WI, USA). The temperature profile for PCR amplification was as follows: denaturation at 95 °C for 5 min, followed by 35 cycles at 95 °C for 1 min, 55 °C for 1 min, and 72 °C for 1 min, and a final extension at 72 °C for 5 min. PCR products were electrophoresed on 1% agarose gel and purified with a Cleanmix DNA Purification Kit (Talent Srl, Trieste, Italy). Sequencing of the purified products was performed using an ABI Prism® Big Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) and a Gene Amp PCR system 9700 (Applied Biosystems). Sequences were determined by automated sequencing on a 3730 DNA Sequencer (Applied Biosystems) on 8% polyacrylamide gels. 2.3. Data analysis 2.3.1. Genetic diversity and gene flow Genetic diversity and gene flow were analyzed in populations with sample size of three or more individuals. Haplotype diversity (Hd) and nucleotide diversity (π) were calculated using DnaSP.5.10 (Librado and Rozas, 2009). Partitioning of genetic variation within and among populations was calculated using the analysis of molecular variance (AMOVA) implemented in Arlequin v. 3.5 (Excoffier and Lischer, 2010), by computing conventional F-statistics from haplotypes with 1000 permutations. Genetic differentiation between populations was calculated from the pairwise fixation index (Fst) using Arlequin v. 3.5. The significance of each Fst value was tested with 1000 random permutations (Slatkin, 1991). 2.3.2. Demographic history Past population expansion was estimated based on the neutrality tests of Tajima's D (Tajima, 1989) and Fu's Fs (Fu, 1997) using Arlequin 3.5, and p-values were generated using 1000 simulations with a model of selective neutrality. 2.3.3. Genetic structure Mitochondrial cyt b sequences were aligned using Clustal X 1.8 (Thompson et al., 1997) and manually adjusted in Se–Al v2.0 alignment editor (available at http://evolve.zoo.ox.ac.uk/). Phylogenetic tree was constructed using Bayesian inference (BI) procedures implemented in MrBayes 3.2.2 (Ronquist et al., 2012). For the BI analysis, TrN+I + G was selected as the best substitution model under the Akaike Information Criterion (AIC) using Modeltest 3.7 (Posada and Crandall, 1998). We applied separate partitions for the 1st, 2nd, and 3rd codon positions and unlinked base composition, transition matrices, proportions of invariant sites, and gamma shapes. The BI analysis was performed using two independent runs of four incrementally heated Markov chains (one cold chain and three hot chains) which were simultaneously run for 2 million generations, with sampling conducted every 500 generations. Stationarity was checked by plotting log likelihood values against generation number and the first 25% of generated trees from each run
3
Table 1 Genetic diversity of Apodemus agrarius coreae in Korea. Population
NWS NES CTS SWS Total populations
N
8 25 5 20 58
H
7 13 5 13 35
S
20 28 9 35 64
Genetic diversity
K
Hd
π
0.964 ± 0.077 0.903 ± 0.043 1.000 ± 0.126 0.953 ± 0.028 0.967 ± 0.012
0.00866 ± 0.00122 0.00673 ± 0.00103 0.00432 ± 0.00116 0.00626 ± 0.00084 0.00683 ± 0.00065
7.214 5.610 3.600 5.211 5.691
N; number of sequences, H; number of haplotypes, S; number of variable sites, Hd; haplotype diversity, π; nucleotide diversity, K; average number of nucleotide differences.
were discarded as burn-in. The pairwise genetic distances between haplogroups were calculated based on the K2P model (Kimura, 1980). The median joining network (MJN) was constructed to reveal the relationships between the Korean and its neighboring haplotypes using NETWORK v. 4.613 (Bandelt et al., 1999). 3. Results 3.1. Genetic diversity, gene flow and demographic history We identified 64 polymorphic sites in the entire data set of 833 bp, comprising 35 haplotypes from 59 individuals in the four Korean populations of A. a. coreae (NWS, NES, CTS, and SWS). There were 7 haplotypes from NWS, 13 haplotypes from NES, 5 haplotypes from CTS, and 13 haplotypes from SWS (Table 1). The analyses of genetic diversity revealed high levels of haplotype diversity (Hd = 0.967) and low nucleotide diversity (π = 0.00683) in A. a. coreae. The AMOVA of A. a. coreae populations indicated that most of the haplotype diversity was found within populations (94.5%), but an appreciable amount was still present between the populations (5.5%) (Supplementary Table 2). Significant fixation indices (Fst) were observed between NWS and NES as well as between NWS and SWS, while a low level of genetic differentiation was observed between SWS and NES (Table 2). Neutrality tests of Korean A. a. coreae produced significantly negative values in both Tajima's D (− 2.029, p = 0.006) and Fu's Fs (−22.101, p = 0.000). 3.2. Genetic structure The BI analysis resolved the mainland A. a. coreae haplotypes into four clades, among which Haplogroups 2 and 3 received low bootstrap supports of 56% and 78%, respectively (Fig. 2). Most of the Korean haplotypes were included in Haplogroup 1. Short branches and unresolved nodes, which are present within each clade of the BI tree, are probably caused by the low number of mutations between the haplotypes. In the MJN (Fig. 3), haplotypes of A. a. chejuensis were well separated from those of other Korean A. a. coreae. Haplogroups 2 and 3 were more closely related to each other than to the other Korean haplogroups. The pairwise genetic distance also showed close relationship between Haplogroups 2 and 3 (0.005) compared with the distances between the other Korean haplogroups (Table 3). The genetic distances between haplogroups of the A. a. coreae were lower than those between haplogroups of the two subspecies A. a. coreae and A. a. chejuensis (Table 3). Table 2 Pairwise fixation index (Fst) between four local populations of Korean Apodemus agrarius coreae. Populations
NES
NWS
CTS
SWS
NES NWS CTS SWS
– 0.094⁎ 0.013 0.029
– 0.016 0.137⁎
– −0.006
–
⁎ p b 0.05.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
4
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Fig. 2. Phylogenetic relationships of the Korean populations of Apodemus agrarius coreae inferred from the Bayesian inference analysis. Numbers on the nodes indicate posterior probabilities. The representative four clades are indicated as Haplogroups (Haplogroups 1, 2, 3, and 4) and compared with those of the median joining network (Fig. 3). Abbreviations for collection sites of the haplotypes are indicated within the parentheses. For abbreviations see Fig. 1.
Fig. 3. The median joining network of Apodemus agrarius haplotypes from Korea and its neighboring regions. Haplotypes are shown in different colors according to their geographical location. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
5
Table 3 Pairwise genetic distance between Korean haplogroups of Apodemus agrarius. Korean haplogroups used for pairwise comparisons are shown in Figs. 2 and 3. Values below or along the diagonal line are genetic distances between or within haplogroups, respectively. Species
A. a. coreae
A. a. chejuensis
Lineages
Haplogroup 1 Haplogroup 2 Haplogroup 3 Haplogroup 4
No. haplotypes
Mainland (n = 27) Mainland (n = 4) Mainland (n = 2) Mainland (n = 2) Jeju Island (n = 6)
A. a. coreae
A. a. chejuensis
Haplogroup 1
Haplogroup 2
Haplogroup 3
Haplogroup 4
0.005 ± 0.003 0.009 ± 0.002 0.009 ± 0.002 0.015 ± 0.002 0.021 ± 0.002
0.003 ± 0.001 0.005 ± 0.001 0.011 ± 0.001 0.017 ± 0.001
0.002 0.014 ± 0.002 0.019 ± 0.002
0.006 ± 0.004 0.021 ± 0.001
Most of Korean haplotypes were included within Haplogroup 1, which was congruent with the BI tree topology. H14 of Haplogroup 1, which is the most common haplotype whose many adjacent single haplotypes were connected by one or two mutations, was shared among three populations (NES, CTS, and SWS), H1 and H22 were shared between two populations, and the remaining haplotypes were specific to their collection sites. Some of Korean haplotypes, particularly those in northern South Korea (Haplogroups 2 and 4), clustered with haplotypes of the Russian Far East, while Haplogroup 1 formed its own clade, which was separated from haplotypes of the neighboring countries of the Korean Peninsula as well as other Korean haplogroups (Fig. 3). 4. Discussion The Korean A. a. coreae is characterized by high haplotype diversity but low nucleotide diversity, which indicates only small differences between the haplotypes. This is also evident from the MJN, which shows mostly single nucleotide differences between the haplotypes. Similar genetic diversity pattern was observed in various species of the genus Apodemus, which might have experienced historical isolation and adaptive radiation under various environmental conditions present at their refuges during the Quaternary climate change (Serizawa et al., 2000; Sakka et al., 2010). As in the cases of the Siberian chipmunk (Eutamias sibiricus) and the Chinese black-spotted frog (Pelophylax nigromaculatus) (Lee et al., 2008; Zhang et al., 2008), the Korean Peninsula under the subtropical climate during the Quaternary (Liu and Li, 1996; Lee, 1999; Park and Kong, 2001) may have played an important role as refuge for A. a. coreae, which might have experienced population expansion and genetic isolation. According to the AMOVA and the fixation indices (Fst), geographical barriers for gene flow within South Korea might occur between the populations of NWS and NES as well as those of NWS and SWS. Despite long geographic distance that separates the SWS and NES populations, significant differentiation was not observed between the two populations, probably because their habitats are connected through the Baekdudaegan mountain range, which stretches through most of the length of the Korean Peninsula, from the northern region to southern and southwestern regions (Fig. 1). The MJN, which included haplotypes from the neighboring regions of the Korean Peninsula, resolved the relationship between the Korean and its neighboring haplotypes as well as within the Korean haplotypes (Fig. 3). In the MJN, four haplogroups were recognized in A. a. coreae. According to a previous study (Sakka et al., 2010), a Korean haplotype from Kanghwado Island, an island off the western coast of the Korean Peninsula, was separated by three mutation steps from the haplotypes of the Russian Far East (Askold Island, Reineke Island, and Russky Island). Our MJN also confirms close connection between some Korean haplotypes (those in Haplogroups 2, 3 and 4) and haplotypes of the Russian Far East. Haplogroup 2 is closely related to the haplotypes H68, H70, and H71 from the Russian Far East. H27 in Haplogroup 2, which is distributed in central South Korea, is separated by only two mutation steps from a haplotype H68 from the Russian Far East (Khorolsky District) and acts as a stepping-stone between Russian haplotypes and other Korean haplotypes (H3, H23, and H24) within the Haplogroup 2. In MJN, Haplogroup 3 is closely related to Haplogroup
0.005 ± 0.005
2, as indicated by the pairwise genetic distance (Table 3). Haplogroup 4 is more closely related to other haplotypes (H52 and H69) from the Russian Far East than to the other Korean haplogroups. Haplogroup 1, which includes most Korean haplotypes, is well isolated from the other Korean haplogroups (Haplogroups 2, 3, and 4) as well as haplotypes from the neighboring regions of the Korean Peninsula. Traditionally it has been known that only a subspecies A. a. coreae is present in the mainland of South Korea. However, our current findings confirmed the presence of other genetic lineages, as well as the Korean endemic Haplogroup 1, that are closely related to haplotypes from the Russian Far East. Thus, further investigation on the validity of the subspecies status of A. a. coreae are required by implementing additional morphological samples as well as genetic data from the populations in the Korean Peninsula and its neighboring countries. Haplogroup 1 forms a star-like structure in the MJN, which indicates relatively low levels of sequence divergence and high frequency of unique mutations (only a few mutations are shared in most of the haplotype nodes) and thus corroborates the results of the genetic diversity analysis (Table 1). The demographic expansion corresponds well to the widely observed patterns of population expansion in organisms across taxa following the last glacial period (Serizawa et al., 2000; Michaux et al., 2004; Sakka et al., 2010; de Jong et al., 2011). Thus, the haplotypes of Haplogroup 1 appear to have experienced population expansion since their migration into Korea, which is congruent with the results of the two neutrality tests. These results indicate that the Korean Peninsula might have played an important role as a refuge during the Quaternary glaciations, as suggested in previous studies (Serizawa et al., 2000; Sakka et al., 2010). 5. Conclusions Korean population of A. a. coreae is characterized by high haplotype diversity and low nucleotide diversity. There are four haplogroups recognized in A. a. coreae. Haplotypes of the other haplogroups, with the exception of the Korean endemic Haplogroup 1, are closely related to those from the Russian Far East. These findings show that further investigations should be conducted to confirm the validity of subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations in the Korean Peninsula and its neighboring countries. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.gene.2015.08.014. Acknowledgments This work was supported by a grant from Kangwon Green Environment Center (KWGEC) in 2014. The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the quality of the paper. References Bandelt, H.J., Forster, P., Röhl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014
6
H.R. Kim, Y.C. Park / Gene xxx (2015) xxx–xxx
Corbet, G.B., 1978. The Mammals of the Palaearctic Region: a Taxonomic Review. British Museum (Natural History) and Cornell University Press, London and Ithaca, NY. de Jong, M.A., Wahlberg, N., van Eijk, M., Brakefield, P.M., Zwaan, B.J., 2011. Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia. PLoS ONE 6, e21385. Excoffier, L., Lischer, H., 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567. Fu, Y.X., 1997. Statistical tests of neutrality against population growth, hitch hiking and background selection. Genetics 147, 915–925. Jones, J.K., Johnson, D.H., 1965. Synopsis of the lagomorphs and rodents of Korea. Univ. Kans. Publ. Mus. Nat. Hist. 16, 357–407. Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. U. S. A. 86, 6196–6200. Koh, H.S., 1986. Geographic variation of morphometric characters among three subspecies of striped field mice, Apodemus agrarius Pallas (Muridae, Rodentia) from Korea. Korean J. Syst. Zool. 29, 272–282. Koh, H.S., 1987. Systematic studies of Korean rodents: III. Morphometric and chromosomal analyses of striped field mice, Apodemus agrarius chejuensis Jones and Johnson, from Cheju-Do. Korean J. Syst. Zool. 3, 24–40. Koh, H.S., 1991. Multivariate analysis with morphometric characters of samples representing eight subspecies of striped field mice, Apodemus agrarius Pallas (Rodentia, Mammalia), in Asia: the taxonomic status of subspecies chejuensis at Cheju Island, Korea. Korean J. Syst. Zool. 7, 179–188. Koh, H.S., Yoo, B.S., 1992. Variation of mitochondrial DNA in two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis from Korea. Korean J. Syst. Zool. 35, 332–338. Koh, H.S., Lee, W.J., Kocher, T.D., 2000. The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis. Heredity 85, 30–36. Lee, J.H., 1999. Geology of Korea, Geological Society of Korea. Sigma Press, Seoul. Lee, M.Y., Lissovsky, A.A., Park, S.K., Obolenskaya, E.V., Dokuchaev, N.E., Zhang, Y.P., et al., 2008. Mitochondrial cytochrome b sequence variations and population structure of
Siberian chipmunk (Tamias sibiricus) in northeastern Asia and population substructure in South Korea. Mol. Cells 26, 566–575. Librado, P., Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452. Liu, D.S., Li, Z.G., 1996. Geography of Asia. Commercial Press, Beijing. Michaux, J.R., Libois, R., Paradis, E., Filippucci, M.G., 2004. Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East. Mol. Phylogenet. Evol. 32, 788–798. Musser, G.G., Carleton, M.D., 1993. Family Muridae. In: Wilson, D.E., Reeder, D.A. (Eds.), Mammal Species of the World, seconded. Smithsonian Institution Press, Washington, D.C., pp. 501–755. Park, Y.A., Kong, W.S., 2001. The Quaternary Environment of Korea. Seoul National University Press (in Korean). Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817–818. Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542. Sakka, H., Quere, J.P., Kartavtseva, I., Marina, P.K., Chelomina, G., Atopkin, D., Bogdanov, A., Michaux, J.H., 2010. Comparative phylogeography of four Apodemus species (Mammalia: Rodentia) in the Asian Far East: evidence of Quaternary climatic changes in their genetic structure. Biol. J. Linn. Soc. 100, 797–821. Serizawa, K., Suzuki, H., Tsuchiya, K., 2000. A phylogenetic view on species radiation in Apodemus inferred from variation of nuclear and mitochondrial genes. Biochem. Genet. 38, 27–40. Slatkin, M., 1991. Inbreeding coefficients and coalescence times. Genet. Res. 58, 167–175. Tajima, F., 1989. The effect of change in population size on DNA polymorphism. Genetics 123, 597–601. Thomas, O., 1906. The Duke of Bedford's zoological exploration in eastern Asia: II. List of small mammals from Korea and Quelpart. Proc. Zool. Soc. London 18, 858–865. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The clustal x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882. Zhang, H., Yan, J., Zhang, G., Zhou, K., 2008. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol. Biol. 8, 21.
Please cite this article as: Kim, H.R., Park, Y.C., Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea, Gene (2015), http://dx.doi.org/10.1016/j.gene.2015.08.014