Anatomy & Biological Anthropology (해부∙생물인류학)

Korean Association of Physical Anthropologists (대한체질인류학회)
권호 표지
DOI QR코드

DOI QR Code

Principles of Archaeogenetics and the Current Trends of Ancient Genome Studies

고고유전학의 분석 원리와 최근 고유전체 연구 동향

  • Kim, Taeho (Biological Anthropology Laboratory, Department of Anthropology, College of Social Sciences, Seoul National University) ;
  • Woo, Eun Jin (Department of History, College of Liberal Arts, Sejong University) ;
  • Pak, Sunyoung (Biological Anthropology Laboratory, Department of Anthropology, College of Social Sciences, Seoul National University)
  • 김태호 (서울대학교 사회과학대학 인류학과 생물인류학 실험실) ;
  • 우은진 (세종대학교 인문과학대학 역사학과) ;
  • 박순영 (서울대학교 사회과학대학 인류학과 생물인류학 실험실)
  • Received : 2018.11.01
  • Accepted : 2018.12.05
  • Published : 2018.12.31
⟨ Previous Next ⟩

Abstract

Archaeogenetics is an academic discipline that aims to establish scientific facts of human history by integrating ancient DNA analyses with archaeological and anthropological evidence. After ancient DNA research was initiated about 30 years ago, it has been innovated so rapidly that the range of analysis has been extended toward the whole genome sequence of ancient genomes in recent 10 years. By this development, researchers have been able to study in detail the origins and migration patterns of hominin species and ancient human populations by approaches of evolutionary genetics. This study has reviewed main principles of the archaeogenetic analysis and the current trends of ancient genome studies with recent achievements. While sampling techniques and statistical analyses have been improved, typical research methods have been established by the findings on hominins and ancient western Eurasia populations. Recently, archaeogenecists have been applying the methods to studying those in other geographical areas. Nonetheless, there is still the lack of ancient genome research about populations in Eastern Asia including the Korean peninsula. This review ultimately aims to predict possibilities and promise of future ancient genome studies of ancient Korean populations.

고고유전학은 고DNA에 대한 분석을 고고학 및 인류학적 증거와 교차검증함으로써 인류사에 대한 과학적인 사실을 정립하고자 하는 학문이다. 30여 년 전 시작된 고DNA 연구는 급격하게 발전하여 최근 10년간은 전장유전체의 염기서열을 분석하는 고유전체 연구로 그 범위를 확장하였다. 이를 통해 고인류 종들과 현생 인류 고대 집단들의 기원 및 이주 패턴들을 진화유전학적으로 엄밀하게 연구하는 것이 가능해졌다. 본 연구에서는 고고유전학의 전반적인 분석 원리와 최근의 고유전체 연구 성과 및 경향을 검토하였다. 시료 채취 기술 및 통계 분석 방법의 발전, 고인류 및 서유라시아 고대 집단들의 고유전체 연구들을 통해 정립된 연구 방법들은 현재 다른 지역들에도 활발하게 적용되고 있는 추세다. 그러나 한반도를 포함한 동아시아 고유전체 연구는 아직 부진한 실정이다. 본 연구를 통해 아직 수행된 바 없는 한반도 고유전체 연구가 진행될 시 어떠한 사실들을 밝힐 수 있는지 그 가능성을 전망하고자 한다.

Keywords

References

  1. Paabo S. Molecular cloning of ancient Egyptian mummy DNA. Nature. 1985; 314:644-5. https://doi.org/10.1038/314644a0
  2. Hoss M, Paabo S. DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res. 1993; 21:3913-4. https://doi.org/10.1093/nar/21.16.3913
  3. Jobling M, Hollox E, Hurles M, Kivisild T, Tyler-Smith C. Finding and assaying genome diversity. In: Jobling M, Hollox E, Hurles M, Kivisild T, Tyler-Smith C. Human evolutionary genetics. New York: Garland Science; 2014. p. 95-6, 98-101, 123-8.
  4. Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature. 1987; 325:31-6. https://doi.org/10.1038/325031a0
  5. Reich D. Humanity's ghosts. In: Reich D. Who we are and how we got here. New York: Pantheon Books; 2018. p. 77-86, 94.
  6. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, et al. Classic selective sweeps were rare in recent human evolution. Science. 2011; 331:920-4. https://doi.org/10.1126/science.1198878
  7. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, et al. The Simons genome diversity project: 300 genomes from 142 diverse populations. Nature. 2016; 538:201-6. https://doi.org/10.1038/nature18964
  8. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A draft sequence of the Neandertal genome. Science. 2010; 328:710-22. https://doi.org/10.1126/science.1188021
  9. Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014; 505:43-9. https://doi.org/10.1038/nature12886
  10. Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan- Roodenberg S, et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PloS One. 2015; 10:e0129102. DOI:10.1371/journal.pone.0129102.
  11. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci U S A. 2013; 110:2223-7. https://doi.org/10.1073/pnas.1221359110
  12. Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Paabo S, Krause J, et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci U S A. 2014; 111:2229-34. https://doi.org/10.1073/pnas.1318934111
  13. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010; 468:1053-60. https://doi.org/10.1038/nature09710
  14. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012; 338:222-6.
  15. Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature. 2014; 514:445-9. https://doi.org/10.1038/nature13810
  16. Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc Natl Acad Sci U S A. 2016; 113:5652-7. https://doi.org/10.1073/pnas.1514696113
  17. Sankararaman S, Mallick S, Patterson N, Reich D. The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Curr Biol. 2016; 26:1241-7. https://doi.org/10.1016/j.cub.2016.03.037
  18. Meyer M, Arsuaga JL, de Filippo C, Nagel S, Aximu-Petri A, Nickel B, et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature. 2016; 531:504-7. https://doi.org/10.1038/nature17405
  19. Slon V, Mafessoni F, Vernot B, de Filippo C, Grote S, Viola B, et al. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature. 2018; 561:113-6. https://doi.org/10.1038/s41586-018-0455-x
  20. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 2015; 522:207-11. https://doi.org/10.1038/nature14317
  21. Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, et al. Genomic insights into the origin of farming in the ancient Near East. Nature. 2016; 536:419-24. https://doi.org/10.1038/nature19310
  22. Posth C, Nagele K, Colleran H, Valentin F, Bedford S, Kami KW, et al. Language continuity despite population replacement in Remote Oceania. Nat Ecol Evol. 2018; 2:731-40. https://doi.org/10.1038/s41559-018-0498-2
  23. Patterson NJ, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, et al. Ancient admixture in human history. Genetics. 2012; 192:1065-93. https://doi.org/10.1534/genetics.112.145037
  24. Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2014; 505:87-91. https://doi.org/10.1038/nature12736
  25. Reich D, Thangaraj K, Patterson N, Price AL, Singh L. Reconstructing Indian population history. Nature. 2009; 461:489-94. https://doi.org/10.1038/nature08365
  26. Moorjani P, Thangaraj K, Patterson N, Lipson M, Loh PR, Govindaraj P, et al. Genetic evidence for recent population mixture in India. Am J Hum Genet. 2013; 93:422-38. https://doi.org/10.1016/j.ajhg.2013.07.006
  27. Narasimhan VM, Patterson NJ, Moorjani P, Lazaridis I, Mark L, Mallick S, et al. The Genomic Formation of South and Central Asia. bioRxiv. 2018. DOI:10.1101/292581.
  28. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, et al. Reconstructing native American population history. Nature. 2012; 488:370-4. https://doi.org/10.1038/nature11258
  29. Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford Jr TW, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014; 506:225-9. https://doi.org/10.1038/nature13025
  30. Neves WA, Hubbe M. Cranial morphology of early Americans from Lagoa Santa, Brazil: Implications for the settlement of the New World. Proc Natl Acad Sci U S A. 2005; 102:18309-14. https://doi.org/10.1073/pnas.0507185102
  31. Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hunemeier T, Petzl-Erler ML, et al. Genetic evidence for two founding populations of the Americas. Nature. 2015; 525:104-8. https://doi.org/10.1038/nature14895
  32. Raghavan M, Steinrucken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science. 2015. DOI:10.1126/science.aab3884.
  33. Moreno-Mayar JV, Potter BA, Vinner L, Steinrucken M, Rasmussen S, Terhorst J, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature. 2018; 553:203-7. https://doi.org/10.1038/nature25173
  34. Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, et al. Early human dispersals within the Americas. Science. 2018. DOI:10.1126/science.aav2621.
  35. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011; 334:94-8. https://doi.org/10.1126/science.1211177
  36. Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, et al. A genomic history of Aboriginal Australia. Nature. 2016; 538:207-14. https://doi.org/10.1038/nature18299
  37. Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nurnberg P, et al. Demographic history of Oceania inferred from genome-wide data. Curr Biol. 2010; 20:1983-92. https://doi.org/10.1016/j.cub.2010.10.040
  38. Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, et al. Genomic insights into the peopling of the Southwest Pacific. Nature. 2016; 538:510-3. https://doi.org/10.1038/nature19844
  39. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, et al. The genetic structure and history of Africans and African Americans. Science. 2009; 324:1035-44. https://doi.org/10.1126/science.1172257
  40. Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, et al. Reconstructing prehistoric African population structure. Cell. 2017; 171:59-71. https://doi.org/10.1016/j.cell.2017.08.049
  41. van de Loosdrecht M, Bouzouggar A, Humphrey L, Posth C, Barton N, Aximu-Petri A, et al. Pleistocene North African genomes link Near Eastern and sub-saharan African human populations. Science. 2018; 360:548-52. https://doi.org/10.1126/science.aar8380
  42. HUGO Pan-Asian SNP Consortium. Mapping human genetic diversity in Asia. Science. 2009; 326:1541-5. https://doi.org/10.1126/science.1177074
  43. McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, et al. The prehistoric peopling of Southeast Asia. Science. 2018; 361:88-92. https://doi.org/10.1126/science.aat3628
  44. Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M, et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science. 2018; 361:92-5. https://doi.org/10.1126/science.aat3188
  45. Xu S, Yin X, Li S, Jin W, Lou H, Yang L, et al. Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am J Hum Genet. 2009; 85:762-74. https://doi.org/10.1016/j.ajhg.2009.10.015
  46. Chiang CW, Mangul S, Robles C, Sankararaman S. A comprehensive map of genetic variation in the world's largest ethnic group-Han Chinese. Mol Biol Evol. 2018; 35:2736-50. https://doi.org/10.1093/molbev/msy170
  47. Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, et al. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J Hum Genet. 2012; 57:787-95. https://doi.org/10.1038/jhg.2012.114
  48. Jinam TA, Kanzawa-Kiriyama H, Inoue I, Tokunaga K, Omoto K, Saitou N. Unique characteristics of the Ainu population in Northern Japan. J Hum Genet. 2015; 60:565-71. https://doi.org/10.1038/jhg.2015.79
  49. Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, et al. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet. 2017; 62:213-21. https://doi.org/10.1038/jhg.2016.110
  50. Siska V, Jones ER, Jeon S, Bhak Y, Kim HM, Cho YS, et al. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Sci Adv. 2017; 3:e1601877. DOI:10.1126/sciadv.1601877.
  51. Kim W, Shin DJ, Harihara S, Kim YJ. Y chromosomal DNA variation in east Asian populations and its potential for inferring the peopling of Korea. J Hum Genet. 2000; 45:76-83. https://doi.org/10.1007/s100380050015
  52. Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, et al. Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum Genet. 2003; 114:27-35. https://doi.org/10.1007/s00439-003-1019-0
  53. Jin HJ, Tyler-Smith C, Kim W. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PloS One. 2009; 4:e4210. DOI:10.1371/journal.pone.0004210.
  54. Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, et al. High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea. Invest Genet. 2011; 2:10. DOI:10.1186/2041-2223-2-10.
  55. Hong SB, Kim KC, Kim W. Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population. Forensic Sci Int Genet. 2015; 17:99-103. https://doi.org/10.1016/j.fsigen.2015.03.017
  56. Lee KS, Chung YJ, Han SH, Lee MH, Han MS, Choi DH. The genetic analysis on ancient human bone in jar coffin excavated from Naju Bokam-ni 3rd tumulus. Conserv Stud. 1999; 20:5-19. Korean.
  57. Seo MS, Lee KS, Chung YJ, Lee MH. Personal identification of the excavated ancient human bone through molecular-biological methods. Conserv Stud. 2001; 22:27-40. Korean.
  58. Seo MS, Lee KS, Chung YJ, Kim KK, Pak YJ. A genetic analysis of human remains from the Myeongam-ri site, Asan City. Conserv Stud. 2002; 23:59-75. Korean.
  59. Seo MS, Chung YJ, Lee KS, Park KW. Genetic characteristics of mtDNA and STR marker in human bone excavated from Mokgam-dong, Siheung in Korea. Conserv Stud. 2003; 24:153-67. Korean.
  60. Lee J, Kim J, Choi C, Han Y, Lee S, Cho Y, et al. An investigation of Baekje mortuary practices using DNA analysis. J Korean Archaeol Soc. 2006; 61:70-91. Korean.
  61. Jee S, Park J, Seo M, Hong J, Chung Y. Molecular genetic and histological analysis for the excavated human bone. Conserv Stud. 2007; 28:75-90. Korean.
  62. Lee J, Ha D, Pak S, Woo EJ, Lee C, Kim D, et al. The relations of the dead: identifying the relationship of individuals buried at Imdang, Gyeongsan, through the analysis of mitochondrial DNA from human skeletal remains interred in large mounded tombs. J Korean Archaeol Soc. 2008; 68: 128-55. Korean.
  63. Ha D. A study on the status of the victims of the Silla sacrificial burials at Imdang. J Korean Archaeol Soc. 2011; 79:175-204. Korean.
  64. Jee SH, Kim YJ, Chung YJ, Seo MS, Pak Y. A paleogenetic analysis of human skeletal remains from the Myeongam-ri site, Asan in Korea. J Conserv Sci. 2008; 23:81-93. Korean.
  65. Kang S, Kwon E, Moon E, Cho E, Seo M, Kim Y, et al. Usefulness of biochemical analysis for human skeletal remains assigned to the Joseon Dynasty in Oknam-ri site in Seocheon, Korea. J Conserv Sci. 2010; 26:95-107. Korean.
  66. Seo MS, Cho EM, Kim YJ, Kim SH, Kang SY. The genetic analysis study of ancient human bones excavated at Janggi-dong site, Gimpo. J Conserv Sci. 2014; 30:409-16. Korean. https://doi.org/10.12654/JCS.2014.30.4.09
  67. Lee WJ, Woo EJ, Oh CS, Yoo JA, Kim YS, Hong JH, et al. Bio-anthropological studies on human skeletons from the 6th century tomb of ancient Silla Kingdom in South Korea. PloS One. 2016; 11:e0156632. DOI:10.1371/journal.pone.0156632.
  68. Seo MS, Lee KS. Genetic analysis of ancient human bones excavated in Sacheon Nuk-do and Gyeongsan Yimdang-dong, Korea. Conserv Stud. 2004; 25:47-74. Korean.
  69. Lee HY, Yoo JE, Park MJ, Kim CY, Shin KJ. Genetic characterization and assessment of authenticity of ancient Korean skeletal remains. Hum Biol. 2008; 80:239-50. https://doi.org/10.3378/1534-6617-80.3.239
  70. Jin HJ, Kim KC, Kim W. Phylogenetic analysis of two haploid markers of 500-years-old human remains found in a central region of Korea. Gene Genom. 2015; 37:33-43. https://doi.org/10.1007/s13258-014-0226-5