Molecular Genetic Analysis of Ancient Cattle Bones Excavated from Archaeological Sites in Jeju, Korea

  • Kim, Jae-Hwan (Department of Life Science, College of Natural Sciences, Cheju National University) ;
  • Oh, Ju-Hyung (Department of Life Science, College of Natural Sciences, Cheju National University) ;
  • Song, Ji-Hoon (Department of Life Science, College of Natural Sciences, Cheju National University) ;
  • Jeon, Jin-Tae (Division of Applied Life Science, Gyeongsang National University) ;
  • Han, Sang-Hyun (National Institute of Subtropical Agriculture, Rural Development Administration) ;
  • Jung, Yong-Hwan (Jeju Biodiversity Research Institute, Jeju HiDI) ;
  • Oh, Moon-You (Department of Life Science, College of Natural Sciences, Cheju National University)
  • Received : 2005.06.26
  • Accepted : 2005.08.24
  • Published : 2005.12.31

Abstract

Ancient cattle bones were excavated from archaeological sites in Jeju, Korea. We used molecular genetic techniques to identify the species and establish its relationship to extant cattle breeds. Ancient DNA was extracted from four sources: a humerus (Gonae site, A.D. 700-800), two fragments of radius, and a tooth (Kwakji site, A.D. 0-900). The mitochondrial DNA (mtDNA) D-loop regions were cloned, sequenced, and compared with previously reported sequences of various cattle breeds (9 Asian, 8 European, and 3 African). The results revealed that these bones were of the breed, Bos taurus, and a phylogenetic tree indicated that the four cattle bones formed a monophyletic group with Jeju native black cattle. However, the patterns of sequence variation and reports from archaeological sites suggest that a few wild cattle, with a different maternal lineage, may have existed on Jeju Island. Our results will contribute to further studies of the origin of Jeju native cattle and the possible existence of local wild cattle.

Keywords

Ancient;Archaeological Site;Bos taurus;D-Loop;Jeju Native Cattle;Monophyletic;Origin

Acknowledgement

Supported by : Korea Research Foundation

References

  1. Giles, R. E., Blanc, H., Cann, H. M., and Wallace, D. C. (1980) Maternal inheritance of human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 77, 6715-6719
  2. Hagelberg, E., Bell, L. S., Allen, T., Boyde, A., Jones, S. J., et al. (1991) Analysis of ancient bone DNA: techniques and applications. Philos. Trans. R. Pros. Soc. Lond. B 333, 399-407 https://doi.org/10.1098/rstb.1991.0090
  3. Hant, O., Krings, M., Ward, R. H., and Paabo, S. (1996) The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59, 368-376
  4. Kavar, T., Habe, F., Brem, G., and Dovc, P. (1999) Mitochondrial D-loop sequence variation among the 16 maternal lines of the Lipizzan horse breed. Anim. Genet. 30, 102-108 https://doi.org/10.1046/j.1365-2052.1999.00419.x
  5. Kim, K. I., Lee, J. H., Lee, S. S., and Yang, Y. H. (2003) Phylogenetic relationships of northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism. Biochem. Genet. 41, 91-98 https://doi.org/10.1023/A:1022021900205
  6. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., pp. 9.14?9.23, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
  7. Shin, T. K., Lee, C. K., Kim, S. H., Yang, K. C., Ko, C. H., et al. (1992) An anatomy study of animal bones excavated in the Kwakji archaeological site in Cheju Island. Go-Moon-Wha 40, 31-42
  8. Sohn, P. K. (1990) Paleolithic sites in Korea. Seoul: Korea Prehistory Institute (in Korea)
  9. Weinstock, J., Willerslev, E., Sher, A., Tong, W., Ho, S. Y. M., et al. (2005) Evolution, systematics, and phylogeography of Pleistocene horses in the new world: a molecular perspective. PLOS Biol. 3, e241 https://doi.org/10.1371/journal.pbio.0030241
  10. Anderson, S., De Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., et al. (1982) Complete sequence of bovine mitochondrial DNA. Conserved feature of the mammalian mitochondrial genome. J. Mol. Evol. 156, 683-717
  11. Avise, J. C. (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos. Trans. R. Soc. Lond. B 312, 325-342 https://doi.org/10.1098/rstb.1986.0011
  12. Cook, C. E., Wang, Y., and Sensabaugh, G. (1999) A mitochondrial control region and cytochrome b phylogeny of Sika Deer (Cervus Nippon) and report of Tandem repeats in the control region. Mol. Phylogenet. Evol. 12, 47-56 https://doi.org/10.1006/mpev.1998.0593
  13. Bae, K. D. (1992) Pleistocene environment and paleolithic stone industries of the Korean peninsula; in Pacific Northeast Asia in Prehistory, Aikens, C. M. and Rhee, S. N. (eds.), pp. 13?23, Pullman: Washington State University Press
  14. Higuchi, R., Bowman, B., Freiberger, M., Ryder, O. A., and Wilson, A. C. (1984) DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282-284 https://doi.org/10.1038/312282a0
  15. Ricaut, F. X., Keyser-Tracqui, C., Crubezy, E., and Ludes, B. (2005) STR-genotyping from human medieval tooth and bone samples. Forensic. Sci. Int. 151, 31-35 https://doi.org/10.1016/j.forsciint.2004.07.001
  16. Brown, W. M., George, M., and Wilson, A. C. (1979) Rapid evolution of animal mitocondrial DNA. Proc. Natl. Acad. Sci. USA 76, 1967-1971
  17. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (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 https://doi.org/10.1093/nar/22.22.4673
  18. Min, M. S., Okumura, H., Jo, D. J., An, J. H., Kim, K. S., et al. (2004) Molecular phylogenetic status of the Korean goral and Japanese serow based on partial sequences of the mitochondrial cytochrome b gene. Mol. Cells 17, 365-372
  19. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparable studies of nucleotide sequences. J. Mol. Evol. 16, 111-120 https://doi.org/10.1007/BF01731581
  20. Faerman, M., Bar-Gal, G. K., Filon, D., Greenblatt, C. L., Stager, L., et al. (1998) Determining the sex of infanticide victims from the late Roman era through ancient DNA analysis. J. Arch. Sci. 25, 861-865 https://doi.org/10.1006/jasc.1997.0231
  21. Jung, Y. H., Han, S. H., Shin, T. K., and Oh, M. Y. (2002) Genetic characterization of horse bone excavated from the Kwakji archaeological site, Jeju, Korea. Mol. Cells 14, 224-230
  22. Loftus, R. T., MacHugh, D. E., Ngere, L. O., Balain, D. S., Badi, A. M., et al. (1994) Mitochondrial genetic variation in European, African and Indian cattle populations. Anim. Genet. 25, 265-271 https://doi.org/10.1111/j.1365-2052.1994.tb00203.x
  23. Shin, T. K., Jin, J. K., and Lee, C. S. (1996) Archaeological study of animal bones excavated from Cheju Kimnyungri cave site. Korean J. Vet. Res. 36, 757-761
  24. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709-715 https://doi.org/10.1038/362709a0
  25. Chung, E. R., Kim, W. T., Kim, Y. S., and Han, S. K. (2000) DNA fingerprinting of Korean cattle using AFLP markers. J. Anim. Sci. Technol. (Kor.) 42, 391-406
  26. Aquadro, C. F. and Greenberg, B. D. (1982) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103, 287-312
  27. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) ver. 3.572, Computer program distributed by the author, Dept. of Genetics, University of Washington, Seattle, WA
  28. Kim, H. C., Jung, K. S., Lee, K. H., Kang, C. H., Ahn, M. J., et al. (2002a) Comparative anatomical study of animal bones excavated from the Konaeli archaeological site on Jeju Island. Subtropical Agri. Biotech., Cheju Nat'l Univ. 18, 129-141
  29. Paabo, S. (1985) Molecular cloning of ancient Egyptian mummy DNA. Nature 314, 644-645 https://doi.org/10.1038/314644a0
  30. Kim, H. L., Kang, C. H., and Shin, T. K. (2002b) Comparative anatomical study on animal bones excavated from the Jongdal- Ri Shell Mound archaeological site IV on Jeju Island. Korean J. Vet. Res. 42, 309-320
  31. Chung, E. R., Kim, W. T., Kim, Y. S., Lee, J. K., and Han, S. K. (2002) Sequence and genetic variation of mitochondrial DNA D-loop region in Korean catle. J. Anim. Sci. Technol. (Kor.) 44, 181-190 https://doi.org/10.5187/JAST.2002.44.2.181
  32. Hoss, M., Jaruga, P., Zastawny, T, H., Dizdaroglu, M., and Paabo, S. (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304-1307 https://doi.org/10.1093/nar/24.7.1304
  33. Norton, C. J. (2000) The current state of Korean paleoanthropology. J. Hum. Evol. 38, 803-825 https://doi.org/10.1006/jhev.1999.0390
  34. Oh, M. Y., Ko, M. H., Kim, G. O., Oh, Y. S., Kim, S. J., et al. (1994) Phylogenetic relationship of Cheju native horses by mitochondrial DNA analysis. Mol. Cells 4, 13-20
  35. Cann, R. L., Brown, W. M., and Wilson, A. C. (1984) Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics 325, 31-36
  36. MacHugh, D. E., Shriver, M. D., Loftus, R. T., Cunningham, P., and Bradley, D. G. (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146, 1071-1086
  37. Phillips, W. (1961) World distribution of the major types of cattle. J. Hered. 52, 207-213
  38. Cheju National University Museum (1997) Jeju Jongdalri Shell- Mount, pp. 101-108, Bukjeju County, Jeju, Korea
  39. Graham, D. E. (1978) The isolation of high molecular weight DNA from whole organisms or large tissue masses. Analyt. Biochem. 85, 609v613 https://doi.org/10.1016/0003-2697(78)90262-2
  40. Wilson, A. C., Cann, L., Carr, S. M., George, M., and Gyllensten, U. B. (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol. J. Linn. Soc. 26, 375-400 https://doi.org/10.1111/j.1095-8312.1985.tb02048.x
  41. Melo-Ferreira, J., Boursot, P., Suchentrunk, F., Ferrand, N., and Alves, P. C. (2005) Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Mol. Ecol. 14, 2459-2464 https://doi.org/10.1111/j.1365-294X.2005.02599.x
  42. Maniatis, T., Frisch, E. F., and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, Cold spring Harbor University Press
  43. Mannen, H., Tsuji, S., Loftus, R. T., and Bradley, D. G. (1998) Mitochondrial DNA variation and evolution of Japanese black cattle (Bos taurus). Genetics 150, 1169-1175