The Robust Phylogeny of Korean Wild Boar (Sus scrofa coreanus) Using Partial D-Loop Sequence of mtDNA

  • Cho, In-Cheol (Jeju Sub-Station, National Institute of Animal Science, Rural Development Administration) ;
  • Han, Sang-Hyun (Jeju Sub-Station, National Institute of Animal Science, Rural Development Administration) ;
  • Fang, Meiying (College of Animal Science and Technology, China Agricultural University) ;
  • Lee, Sung-Soo (Jeju Sub-Station, National Institute of Animal Science, Rural Development Administration) ;
  • Ko, Moon-Suck (Jeju Sub-Station, National Institute of Animal Science, Rural Development Administration) ;
  • Lee, Hang (Conservation Genome Resource Bank for Korean Wildlife, Brain Korea 21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University) ;
  • Lim, Hyun-Tae (Division of Applied Life Science (Brain Korea 21 Program), Graduate School of Gyeongsang National University) ;
  • Yoo, Chae-Kyoung (Division of Applied Life Science (Brain Korea 21 Program), Graduate School of Gyeongsang National University) ;
  • Lee, Jun-Heon (Division of Animal Science and Resources, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Jeon, Jin-Tae (Division of Applied Life Science (Brain Korea 21 Program), Graduate School of Gyeongsang National University)
  • 투고 : 2009.06.17
  • 심사 : 2009.09.04
  • 발행 : 2009.11.30


In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.


연구 과제 주관 기관 : Rural Development Administration, Ministry of Education, Science and Technology


  1. Bandelt, H.J., Forster, P., and Rohl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37-48
  2. Birren, B., Green, E.D., Klapholz, S., Myers, R.M., and Roskams, J. (1997). Genome Analysis: A Laboratory Manual (USA: Cold Spring Harbor Laboratory Press)
  3. Bokonyi, S. (1974). History of domestic mammals in central and Eastern Europe. Academiai Kiado
  4. Brown, W.M., George, Jr. M., and Wilson, A.C. (1979). Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76, 1967-1971
  5. Choi, D.K. (2003). Understanding the Earth. Seoul National University press
  6. Dobson, M., and Yoshinari, K. (1998). Origin of the Japanese land mammal fauna: Allocation of extant species to historically-based categories. Daiyonki Kenkyu. 37, 385-395
  7. Epstein, H. (1984). Pig. In handbook of evolution of domesticated animals, I.L. Mason, eds. (London : Longman), pp. 145-162
  8. Excoffier, L. (2004). Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infiniteisland model. Mol. Ecol. 13, 853-864
  9. 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
  10. Fang, M., Hu, X., Jiang, T., Braunschweig, M., Hu, L., Du, Z., Feng, J., Zhang, Q., Wu, C., and Li, N. (2005). The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers. Anim. Genet. 36, 7-13
  11. Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925
  12. Giuffra, E., Kijas, J.M.H., Amarger, V., Carlborg, O., Jeon, J.T., and Andersson, L. (2000). The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785-1791
  13. Goudet, J., Raymond, M., Meeüs, T., and Rousset, F. (1996). Testing differentiation in diploid populations. Genetics 144, 1933-1940
  14. Hasegawa, M., Kishino, H., and Yano, T. (1985). Dating of the humanape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174
  15. Herre, W., and Rohrs, M. (1977). Zoological considerations on the origins of farming and domestication. In Handbook of Origins of Agriculture, C.A. Reed, eds. (Mouton : The Hague), pp. 245-279
  16. Hongo, H., Ishiguro, N., Watanobe, T., Shigehara, N., Anezaki, T., Long, V.T., Bihn, D.V., Tien, N.T., and Nam, N.H. (2002). Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian Domestic pigs and Ryukyu wild boars. Zool. Sci. 19, 1329-1335
  17. Huelsenbeck, J.P., and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754-755
  18. Kawamura, Y. (2007). Last glacial and Holocene land mammals of the Japanese islands : their fauna, extinction and immigration. The Quaternary Research 46, 171-177
  19. Kijas, J.M.H., and Andersson, L. (2001). A phylogenetic study of the domestic pig estimated from the near-complete mtDNA genome. J. Mol. Evol. 52, 302-308
  20. Kim, K.I., Lee, J.H., Li, K., Zhang, Y.P., Lee, S.S., Gongora, J., and Moran, C. (2002). Phylogenetic relationships of Asian and European pig breeds determinated by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet. 33, 19-25
  21. Larson, G., Dobney, K., Albarella, U., Fang, M., Matisoo-Smith, E., Robins, J., Lowden, S., Finlayson, H., Brand, T., Willerslev, E., et al. (2005). Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618-1621
  22. Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J.D., Edwards, C.J., Schlumbaum, A., Dinu, A., et al. (2007). Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc. Natl. Acad. Sci. USA 104, 15276-15281
  23. Li, S.J., Yang, S.H., Zhao, S.H., Fan, B., Yu, M., Wang, H.S., Li, M.H., Liu, B., Xiong, T.A., and Li, K. (2004). Genetic diversity analyses of 10 indigenous Chinese pig populations based on 20 microsatellites. J. Anim. Sci. 82, 368-374
  24. Lin, C.S., Sun, Y.L., and Liu, C.Y. (1999). Complete nucleotide sequence of pig (Sus scrofa) mitochondrial genome and dating evolutionary divergence within Artiodactyla. Gene 236, 107-114
  25. Naya, Y., Horiuchi, M., Ishiguro, N., and Shinagawa, M. (2003). Bacteriological and genetic assessment of game meat from Japanese wild boars. J. Agric. Food. Chem. 51, 345-349
  26. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press
  27. Norton, C.J. (2000). The current state of Korean paleoanthropology. J. Hum. Evol. 38, 803-825
  28. Okumura, N., Ishiguro, N., Nakano, M., Hirai, K., Matsui, A., and Sahara, M. (1996). Geographic population structure and sequence divergence in the mitochondrial DNA control region of the Japanese wild boar (Sus scrofa leucomystax), with reference to those of domestic pigs. Biochem. Genet. 34, 179-189
  29. Rogers, A. (1995). Genetic evidence for a Pleistocene population explosion. Evolution 49, 608-615
  30. Ronquist, F., and Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574
  31. Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X., and Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497
  32. Ruvinsky, A., and Rothschild, M.F. (1998). Systematics and evolution of the pig. In Handbook of The Genetics of the Pig, M.F. Rothschild, and A. Ruvinsky, eds. (Oxfordshire, CAB International), pp. 1-16
  33. Schneider, S., and Excoffier, L. (1999). Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152, 1079-1089
  34. Swofford, D.L. (2003). PAUP*. Phylogenetic analysis using parsimony (*and other methods), Version 4. Sinauer Associates
  35. Tavare, S. (1986). Some probabilistic and statisical problems on the analysis of DNA sequences. Lectures. Lect. Math. Life. Sci. 17, 57-86
  36. Thompson, J.D., Higgins, D.G., and Gibson, T.I. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680
  37. Watanobe, T., Ishiguro, N., and Nakano, M. (2003). Phylogeography and population structure of the Japanese wild boar Sus scrofa leucomystax: mitochondrial DNA variation. Zoolog. Sci. 20, 1477- 1489
  38. Watanobe, T., Ishiguro, N., Nakano, M., Matsui, A., Hongo, H., Yamazaki, K., and Takahashi, O. (2004) Prehistoric Sado Island populations of Sus scrofa distinguished from contemporary Japanese wild boar by ancient mitochondrial DNA. Zoolog. Sci. 21, 219-228
  39. Weir, B.S. (1996). Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates
  40. Xia, X., and Xie, Z. (2001). DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92, 371- 373
  41. Yang, J., Wang, J., Kijas, J., Liu, B., Han, H., Yu, M., Yang, H., Zhao, S., and Li, K. (2003). Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs. J. Hered. 94, 381-385