DOI QR코드

DOI QR Code

Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area

  • Hong, Jong Ha (Institute of Korean Archaeology and Ancient History, Kyung Hee University) ;
  • Oh, Chang Seok (Department of Mortuary Science, College of Bio-Convergence, Eulji University) ;
  • Kim, Sun (Research Institute of Buddhist Cultural Heritage) ;
  • Kang, In Uk (Institute of Korean Archaeology and Ancient History, Kyung Hee University) ;
  • Shin, Dong Hoon (Comparative Anatomy Lab, Institute of Forensic and Anthropological Science, Seoul National University College of Medicine)
  • Received : 2021.11.10
  • Accepted : 2022.01.28
  • Published : 2022.08.01

Abstract

Objective: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea. Methods: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software. Results: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia. Conclusion: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

Keywords

Acknowledgement

This work was supported by the Ministry of Education of the Republic of Korea and the National Research Foundation of Korea (NRF-2019S1A5C2A01083578; 2020R1I1A1A01073501).

References

  1. Lin M, Miracle P, Baker G. Towards the identification of the exploitation of cattle labour from distal metapodials. J Archaeol Sci 2016;66:44-56. https://doi.org/10.1016/j.jas.2015.12.006
  2. Hong JH, Oh CS, Cho CW, Shin YM, Cho TS, Shin DH. Mitochondrial DNA analysis of Bos taurus bone collected from ruins of the Joseon Period in a tributary of the Cheonggyecheon creek, South Korea. J Archaeol Sci Rep 2018;17:785-92. https://doi.org/10.1016/j.jasrep.2017.10.019
  3. Hong JH, Kang IU, Shin DH, Kim JE. Origin and diffusion of Equus caballus from the archaeological and genetic perspectives. Anat Biol Anthropol 2020;33:57-68. https://doi.org/10.11637/aba.2020.33.2.57
  4. Lippold S, Knapp M, Kuznetsova T, et al. Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat Commun 2011;2:450. https://doi.org/10.1038/ncomms1447
  5. Librado P, Fages A, Gaunitz C, et al. The evolutionary origin and genetic makeup of domestic horses. Genetics 2016;204:423-34. https://doi.org/10.1534/genetics.116.194860
  6. Clutton-Brock J. A natural history of domesticated mammals. London, UK: Cambridge University Press; 1999.
  7. Outram AK, Stear NA, Bendrey R, et al. The earliest horse harnessing and milking. Science 2009;323:1332-5. https://doi.org/10.1126/science.1168594
  8. Vila C, Leonard JA, Gotherstrom A, et al. Widespread origins of domestic horse lineages. Science 2001;291:474-7. https://doi.org/10.1126/science.291.5503.474
  9. Jansen T, Forster P, Levine MA, et al. Mitochondrial DNA and the origins of the domestic horse. Proc Natl Acad Sci USA 2002;99:10905-10. https://doi.org/10.1073/pnas.152330099
  10. McGahern AM, Edwards CJ, Bower MA, et al. Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses. Anim Genet 2006;37:498-502. https://doi.org/10.1111/j.1365-2052.2006.01506.x
  11. Lei CZ, Su R, Bower MA, et al. Multiple maternal origins of native modern and ancient horse population in China. Anim Genet 2009;40:933-44. https://doi.org/10.1111/j.1365-2052.2009.01950.x
  12. Lira J, Linderholm A, Olaria C, et al. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Mol Ecol 2010;19:64-78. https://doi.org/10.1111/j.1365-294X.2009.04430.x
  13. Achilli A, Olivieri A, Soares P, et al. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci USA 2012;109:2449-54. https://doi.org/10.1073/pnas.1111637109
  14. Gaunitz C, Fages A, Hanghoj K, et al. Ancient genomes revisit the ancestry of domestic and Przewalski's horses. Science 2018;360:111-4. https://doi.org/10.1126/science.aao3297
  15. Yang L, Kong X, Yang S, et al. Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse. PLoS One 2018;13:e0201564. https://doi.org/10.1371/journal.pone.0201564
  16. Xu X, Arnason U. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. Gene 1994;148:357-62. https://doi.org/10.1016/0378-1119(94)90713-7
  17. Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N. Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse. J Mol Evol 1995;41:180-8. https://doi.org/10.1007/BF00170671
  18. Kim KI, Yang YH, Lee SS, et al. Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Anim Genet 1999;30:102-8. https://doi.org/10.1046/j.1365-2052.1999.00419.x
  19. Oakenfull EA, Lim HN, Ryder OA. A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus. Conserv Genet 2000;1:341-55. https://doi.org/10.1023/A:1011559200897
  20. Aberle KS, Distl O. Domestication of the horse: results based on microsatellite and mitochondrial DNA markers. Arch Anim Breed 2004;47:517-35. https://doi.org/10.5194/aab-47-517-2004
  21. Royo LJ, Alvarez I, Beja-Pereira A, et al. The origins of Iberian horses assessed via mitochondrial DNA. J Hered 2005;96:663-9. https://doi.org/10.1093/jhered/esi116
  22. Cai DW, Han L, Xie CZ, Li SN, Zhou H, Zhu H. Mitochondrial DNA analysis of Bronze Age horses recovered from Chifeng region, Inner Mongolia, China. Prog Nat Sci 2007;17:544-50. https://doi.org/10.1080/10020070708541034
  23. Cieslak M, Pruvost M, Benecke N, et al. Origin and history of mitochondrial DNA lineages in domestic horses. PLoS One 2010;5:e15311. https://doi.org/10.1371/journal.pone.0015311
  24. Kim S, Hong JH, Shin DH. Animal bones found at Gongpyeong-dong archaeological site, the capital area of Joseon Dynasty period. Anat Biol Anthropol 2020;33:99-105. https://doi.org/10.11637/aba.2020.33.2.99
  25. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nat Rev Genet 2001;2:353-9. https://doi.org/10.1038/35072071
  26. Ho SYW, Gilbert MTP. Ancient mitogenomics. Mitochondrion 2010;10:1-11. https://doi.org/10.1016/j.mito.2009.09.005
  27. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-4. https://doi.org/10.1093/molbev/msw054
  28. Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park K-D, Kim H. Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: phylogenomic and bayesian coalescent perspectives. PLoS One 2018;e0203917. https://doi.org/10.1371/journal.pone.0203917
  29. Ning T, Ling Y, Hu S, et al. Local origin or external input: modern horse origin in East Asia. BMC Evol Biol 2019;19:217. https://doi.org/10.1186/s12862-019-1532-y
  30. Cho GJ. Genetic Relationship among the Korean Native and Alien Horses Estimated by Microsatellite Polymorphism. Asian-Australas J Anim Sci 2006;19:784-8. https://doi.org/10.5713/ajas.2006.784
  31. Kusliy MA, Vorobieva NV, Tishkin AA, et al. Traces of late bronze and early iron age mongolian horse mitochondrial lineages in modern populations. Genes 2021;12:412. https://doi.org/10.3390/genes12030412
  32. Ma H, Wu Y, Xiang H, et al. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences. PeerJ 2018;6:e4896. https://doi.org/10.7717/peerj.4896
  33. Vershinina AO, Kapp JD, Baryshnikov GF, Shapiro B. The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections. Mol Ecol Reseour 2020;20:1182-90. https://doi.org/10.1111/1755-0998.13130
  34. Vorobiera NV, Makunin AI, Druzhkova AS, et al. High genetic diversity of ancient horses from the Ukok Plateau. PLoS One 2020;15:e0241997. https://doi.org/10.1371/journal.pone.0241997
  35. Der Sarkissian C, Ermini L, Schubert M, et al. Evolutionary genomics and conservation of the endangered Przewalski's horse. Curr Biol 2015;25:2577-83. https://doi.org/10.1016/j.cub.2015.08.032
  36. Goto H, Ryder OA, Fisher AR, et al. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biol Evol 2011;3:1096-106. https://doi.org/10.1093/gbe/evr067