Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
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Mitochondrial Cytochrome b Sequence Variations and Population Structure of Siberian Chipmunk (Tamias sibiricus) in Northeastern Asia and Population Substructure in South Korea

  • Lee, Mu-Yeong (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University) ;
  • Lissovsky, Andrey A. (Zoological Museum of Moscow State University) ;
  • Park, Sun-Kyung (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University) ;
  • Obolenskaya, Ekaterina V. (Zoological Museum of Moscow State University) ;
  • Dokuchaev, Nikolay E. (Institute of Biological Problems of the North FEB RAS) ;
  • Zhang, Ya-Ping (Laboratory for Conservation and Utilization of Bio-resource, Yunnan University) ;
  • Yu, Li (Laboratory for Conservation and Utilization of Bio-resource, Yunnan University) ;
  • Kim, Young-Jun (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University) ;
  • Voloshina, Inna (Lazovsky State Nature Reserve) ;
  • Myslenkov, Alexander (Lazovsky State Nature Reserve) ;
  • Choi, Tae-Young (National Institute of Environmental Research, Environmental Research Complex) ;
  • Min, Mi-Sook (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University) ;
  • Lee, Hang (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University)
  • Received : 2008.06.18
  • Accepted : 2008.10.09
  • Published : 2008.12.31
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Abstract

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

Keywords

Acknowledgement

Supported by : Korea Research Foundation

References

  1. Allendorf, FW., and Luikart, G. (2007). Conservation and the genetics of populations. (Blackwell Publishing)
  2. Andersen, B.G., and Borns, HW. (1997). The ice age world: An introduction to quatemary history and research with emphasis on North America and Northern Europe during the last 2.5 million years (Oslo, Scandinavian University Press)
  3. Arbogast, B.S., Browne, RA, and Weigl, P.O. (2001). Evolutionary genetics and pleistocene biogeography of North American tree squirrels (Tamiasciurus). J. Mammal. 82, 302-319 https://doi.org/10.1644/1545-1542(2001)082<0302:EGAPBO>2.0.CO;2
  4. Avise, J.C., Walker, D., and Johns, G.C. (1998). Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc. BioI. Sci. 265,1707-1712
  5. Banbury, J.L., and Spicer, G.S. (2007). Molecular systematics of chipmunks (Neotamias) inferred by mitochondrial control regions sequences. J. Mammal. Evol. 14,149-162 https://doi.org/10.1007/s10914-006-9035-1
  6. Bandelt, H.J., Forster, P., and R6hl, A. (1999). Median-joining networks inferring intraspecific phylogenies. Mol. BioI. Evol. 16,37-48 https://doi.org/10.1093/oxfordjournals.molbev.a026036
  7. Bradley, RD., and Baker, R.J. (2001). A test of the genetic species concept: cytochrome-b sequences and mammals. J. Mammal. 82, 960-973 https://doi.org/10.1644/1545-1542(2001)082<0960:ATOTGS>2.0.CO;2
  8. Brunhoff, C., Galbreath, E., Fedorov, B., Cook. A., and Jaarola, M. (2003). Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quatemary biogeography of high latitudes. Mol. Ecol. 12,957-968 https://doi.org/10.1046/j.1365-294X.2003.01796.x
  9. Cassens, I., Waerebeek, K.V., Best, P.B., Crespo, EA, Reyes, J., and Milinkovitch, M.C. (2003). The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures. Mol. Ecol. 12, 1781-1792 https://doi.org/10.1046/j.1365-294X.2003.01876.x
  10. Cheng, H.D. (1991). Systematic studies on three species of the family sciuridae from Manchuria and Korea: morphometric and chromosomal analyses. (Chungbuk National University)
  11. Cho, E.S., Jung, C.G., Sohn, S.G., Kim, CW., and Han, S.J. (2007). Population genetic structure of the ark shell Scapharca broughionli Schrenck from Korea, China, and Russia based on COl gene sequences. Mar. Biotechnol. 9, 203-216 https://doi.org/10.1007/s10126-006-6057-x
  12. Demboski, J.R., and Sullivan, J. (2003). Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America. Mol. Phylogenet. Evol. 26, 389-408 https://doi.org/10.1016/S1055-7903(02)00363-9
  13. Donnelly, R., Tavare, S., Balding, D.J., and Griffiths, R.C., (1996). Estimating the age of the common ancestor of men from the ZFY intron. Science 272,1357-1359 https://doi.org/10.1126/science.272.5266.1357
  14. Eddingsaas, AA, Jacobsen, BK, Lessa, E.P., and Cook, JA (2004). Evolutionary history of the arctic ground squirrel (Sper mophilus parryiJ) in Nearctic Beringlia. J. Mammal. 85, 601-610 https://doi.org/10.1644/BRB-204
  15. Excoffier, L., Laval, G., and Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50
  16. Fedorov, V.B., and Stenseth, N.C. (2001). Glacial survival of the Norwegian lemming (Lemmus femmus) in Scandinavia: inference from mitochondrial DNA variation. Proc. BioI. Sci. 268, 809-814
  17. Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 36, 331-336
  18. Good, J.M., and Sullivan, J. (2001). Phylogeography of the redtailed chipmunk, a northern rocky mountain endemic. Mol. Ecol. 10, 2683-2695 https://doi.org/10.1046/j.0962-1083.2001.01397.x
  19. Good, J.M., Oemboski, J.R., Nagorsen, OW., and Sullivan, J. (2003). Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution 57,1900-1916 https://doi.org/10.1111/j.0014-3820.2003.tb00597.x
  20. Gunduz, i., Jaarola, M., Tez, C., Yeniyurt, C., Polly, P.O., and Searle, J.B. (2007). Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species. Mol. Phylogenet. Evol. 43, 916-935 https://doi.org/10.1016/j.ympev.2007.02.021
  21. Hall, TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/N1. Nucleic Acids Symp. Ser. 41, 95-98
  22. Hewitt, G.M. (2000). The genetic legacy of the Quaternary ice ages. Natures 405, 907-913 https://doi.org/10.1038/35016000
  23. Irwin, O.M., Kocher, 1.0., and Wilson, AC. (1991). Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144 https://doi.org/10.1007/BF02515385
  24. Jones, J.K., and Johnson, O.H. (1965). Synopsis of the lagomorphs and rodents of Korea. University of Kansas Publications, Museum of Natural History 16,357-407
  25. Kang, TW., Lee, E.H., Kim, M.S., Paik, S.G., Kim, S.S., and Kim, C.B. (2005). Molecular phylogeny and geography of Korean Medaka Fish (Oryzias fat/pes). Mol. Cells 20,151-156
  26. Kocher, 1.0., Thomas, W.K, Meyer, A, Edwards, S.V., Paabo, S., Villablanca, F'x', and Wilson, AC. (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86, 6196-6200
  27. Koh, H.S., Lee, W.J., and Kocher, T'o. (2000). The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius cneiuensis. Heredity 85,30-36 https://doi.org/10.1046/j.1365-2540.2000.00723.x
  28. Kumar, S. (1995). PHYLTEST: Phylogeny hypothesis testing. Penn State University, University Park, PA 16801
  29. Lissovosky, AA, Obolenskaya, EV., and Emelyanova, L.G. (2006). The structure of voice signals of Siberian chipmunk (Tamias sibuicus Laxmann 1769; Rodentia: Sciuridae). Russian J. Theriol. 5,93-98
  30. Markov, KK, Lazukov, G.I., and Nikolayv, VA (1965). The Quaternary period (Glacial period - Antropogen period). Vol. 1. (The territory of the USSR). (In Russian)
  31. Miranda, G.B., Andrades-Miranda, J., Oliveira, L.F., Langguth, A, and Mattevi, M.S. (2007). Geographic patterns of genetic variation and conservation consequences in three South American rodents. Biochem. Genet. 45, 839-856 https://doi.org/10.1007/s10528-007-9122-x
  32. Ognev, S.1. (1940). The mammals of USSR and adjacent countries. (Moscow and Leningrad 4). (in Russian) (A translation: Ognev, S.1. 1966. Mammals of the USSR and adjacent countries: rodents. Israel Program for Scientific Translations, Jerusalem 4)
  33. Ohdachi, S.D., Abe, H., and Han, S.H. (2003). Phylogenetical positions of Sorex sp. (Insectivora, Mammalia) from Cheju Island and S. caecutiens from the Korean peninsula, inferred from mitochondrial cytochrome b gene sequences. Zool. Sci. 20, 91-95 https://doi.org/10.2108/zsj.20.91
  34. Oshida, T., Masuda, R., and Yoshida, M.C. (1996). Phylogenetic relationships among Japanese species of the family Sciuridae (Mammalia, Rodentia), inferred 12S ribosomal RNA genes. Zool. Sci. 13,615-620 https://doi.org/10.2108/zsj.13.615
  35. Oshida, T., Abramov, A, Yanagawa, H., and Masuda, R. (2005) Phylogeography of the Russian flying squirrel (Pteromys volans): implication of refugia theory in arboreal small mammal of Eurasia. Mol. Ecol. 14, 1191-1196 https://doi.org/10.1111/j.1365-294X.2005.02475.x
  36. Park, J.K., Choe, B.L., and Eom, K.S. (2004a). Two mitochondrial lineages in Korean freshwater Corb/cula (Corbiculidae: Bivalvia). Mol. Cells 3, 410-414
  37. Park, Y.C., Maekawa, K., Matsumoto, T., Santoni, R., and Choe, J.C. (2004b). Molecular phylogeny and biogeography of the Korean wood roaches Cryptocercus spp. Mol. Phylogenet. Evol. 30, 450-464 https://doi.org/10.1016/S1055-7903(03)00220-3
  38. Piaggio, AJ., and Spicer, G.S. (2001). Molecular phylogeny of the chipmunks inferred from mitochondrial cytochrome b and cytochrome oxidase II gene sequences. Mol. Phylogenet. Evol. 20, 335-350 https://doi.org/10.1006/mpev.2001.0975
  39. Posada, D., and Crandall, K.A (1998). MODEL TEST: Testing the model of DNA substitution. Bioinformatics 14, 817-818 https://doi.org/10.1093/bioinformatics/14.9.817
  40. Reich, DE., and Goldstein, D.B. (1998). Genetic evidence for a Paleolithic human population expansion in Africa. Proc. AntI. Acad. Sci. USA 96. 8119-8123
  41. Rozas, J., Sanchez-Del Barrio, J.C., Messeguer, X., and Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19,2496-2497 https://doi.org/10.1093/bioinformatics/btg359
  42. Schulte-Hostedde, AI., Gibbs, H.L., and Millar, J.S. (2001). Microgeographic genetic structure in the yellow-pine chipmunk (Tam/asamoenus). Mol. Ecol. 10,1625-1631 https://doi.org/10.1046/j.1365-294X.2001.01298.x
  43. Spradling, TA, Hafner, M.S., and Demastes, J.w. (2001). Differences in rate of cytochrome-b evolution among species of rodents. J. of Mammal. 82, 65-80 https://doi.org/10.1644/1545-1542(2001)082<0065:DIROCB>2.0.CO;2
  44. Steppan, S.J., Storz, B.L., and Hoffmann, R.S. (2004). Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Mol. Phylogenet. Evol. 30, 703-719 https://doi.org/10.1016/S1055-7903(03)00204-5
  45. Suzuki, H., Sato, Y., Ohba, N., Bae, J.S., Jin, B.R., Sohn, H.D., and Kim, SE. (2004). Phylogeographic analysis of the firefly, Luciole lateralis, in Japan and Korea based on mitochondrial cytochrome oxidase II gene sequences (Coleoptera: Lampyr/dae). Biochem. Genet. 42, 287-300 https://doi.org/10.1023/B:BIGI.0000039805.75118.8f
  46. Swofford, D.L. (2001). PAUP*. Phylogenetic analysis using parsimony (*and Other Methods). Version 4.0b8 (Sunderland, Massachusetts, Sinauer Associates)
  47. Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. BioI. Evol. 24,1596-1599 https://doi.org/10.1093/molbev/msm092
  48. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 https://doi.org/10.1093/nar/25.24.4876
  49. Won, C.M., and Smith, K.G. (1999). History and current status of mammals of the Korean Peninsula. Mammal Rev. 29, 3-33 https://doi.org/10.1046/j.1365-2907.1999.00034.x