Genetic Analysis and Genealogy of Ancient Bone Samples

Document Type: Narrative Review

Authors

Human Genetics Research Center, Baqiyatallah University of Medical Sciences Tehran, Iran

Abstract

The analysis of ancient DNA (aDNA) can inspire both the public and the scientific community. Knowing about ancient human genomes and comparing them with those of modern humans can give us a new perspective on evolution and the migration of humans over time. aDNA is DNA isolated from ancient specimens. It can also be loosely described as any DNA recovered from biological samples that have not been preserved specifically for later DNA analysis. Examples include DNA recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores, Holocene plankton in marine and lake sediments, and so on. Due to considerable anthropological, archaeological, and public interest, human remains receive ample attention from the DNA community. Genetic genealogy is the use of DNA testing in combination with traditional genealogical methods to infer relationships between individuals and to find ancestors. Genetic genealogy involves the use of genealogical DNA testing to determine the level and type of genetic relationship between individuals. DNA markers such as autosomal single nucleotide polymorphisms (SNPs), Y SNPs, and mitochondrial DNA (mtDNA) SNPs are used. By analyzing the sequence of mtDNA and the Y-chromosome, the path of human migration throughout history and the common ancestor of humans can be identified. mtDNA analysis is a field of research in genetics and molecular archaeology that is efficient in less than ideal conditions, such as with biologically degraded materials. The mtDNA molecule not only has a high copy number, but it can also be extracted from very decayed biological specimens. Its D-loop region is polymorphic, consisting of two hypervariable regions (HVI and HVII) with a large variety in different human populations. The analysis of such mtDNA regions using ancient excavated human bones will determine the genetic composition of human mtDNA known as haplogroups and can be used to identify ancient ethnic groups, trace descendants of ancestors, and follow man’s migration trails.

Keywords


  1. Allentoft ME, Sikora M, Sjogren KG, et al. Population genomics of Bronze Age Eurasia. Nature. 2015;522(7555):167-172. doi:10.1038/nature14507.
  2. Alonso A, Martin P, Albarran C, et al. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci Int. 2004;139(2-3):141- 149. doi:10.1016/j.forsciint.2003.10.008.
  3. Costa MD, Pereira JB, Pala M, et al. A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nat Commun. 2013;4:2543. doi:10.1038/ncomms3543.
  4. Gamba C, Jones ER, Teasdale MD, et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat Commun. 2014;5:5257. doi:10.1038/ncomms6257.
  5. Haber M, Doumet-Serhal C, Scheib C, et al. Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences. Am J Hum Genet. 2017;101(2):274-282. doi:10.1016/j.ajhg.2017.06.013.
  6. Kilinc GM, Omrak A, Ozer F, et al. The Demographic Development of the First Farmers in Anatolia. Curr Biol. 2016;26(19):2659-2666. doi:10.1016/j.cub.2016.07.057.
  7. Lazaridis I, Mittnik A, Patterson N, et al. Genetic origins of the Minoans and Mycenaeans. Nature. 2017;548(7666):214-218. doi:10.1038/nature23310.
  8. Margaryan A, Derenko M, Hovhannisyan H, et al. Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus. Curr Biol. 2017;27(13):2023-2028.e2027. doi:10.1016/j.cub.2017.05.087.
  9. Mathieson I, Lazaridis I, Rohland N, et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 2015;528(7583):499- 503. doi:10.1038/nature16152.
  10. Mohammadi A, Ghorbani Alvanegh A, Khafaei M, et al. A New and Efficient Method for DNA Extraction from Human Skeletal Remains Usable in DNA Typing. J Appl Biotechnol Rep. 2017;4(2):609-614.
  11. Olalde I, Brace S, Allentoft ME, et al. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature. 2018;555(7695):190-196. doi:10.1038/nature25738.
  12. Valdiosera C, Gunther T, Vera-Rodriguez JC, et al. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia. Proc Natl Acad Sci U S A. 2018;115(13):3428-3433. doi:10.1073/pnas.1717762115.
  13. Zargari P, Habibi Azarian S, Ahmadi K, Erfanmanesh P, Tavallaie M. New Perspective on Tappeh Hesar. SM J Biol. 2016;2(2):1012.
  14. Lazaridis I, Nadel D, Rollefson G, et al. The genetic structure of the world’s first farmers. bioRxiv. 2016:059311. doi:10.1101/059311.
  15. Alakoc YD, Aka PS, Egin Y, Akar N. Factor V Leiden in an Urartian, dating back to 1000 BC. Clin Appl Thromb Hemost. 2010;16(6):679-683. doi:10.1177/1076029609338045.
  16. Pakendorf B, Stoneking M. Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet. 2005;6:165-183. doi:10.1146/annurev.genom.6.080604.162249.
  17. Nesheva D. Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution. Balkan J Med Genet. 2014;17(1):5-14. doi:10.2478/bjmg-2014-0019.
  18. Paabo S. Molecular cloning of Ancient Egyptian mummy DNA. Nature. 1985;314(6012):644-645. doi:10.1038/314644a0.
  19. Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature. 1987;325(6099):31-36. doi:10.1038/325031a0.
  20. Wallace DC, Brown MD, Lott MT. Mitochondrial DNA variation in human evolution and disease. Gene. 1999;238(1):211-230. doi:10.1016/S0378-1119(99)00295-4.
  21. Miller NF. Economy and settlement in the Near East: analyses of ancient sites and materials. Pennsylvania: UPenn Museum of Archaeology. 1990:47-61.
  22. Schmidt EF. Excavations at Tepe Hissar, Damghan. Philadelphia: University of Pennsylvania Press; 1937. doi:10.1017/S0003598X00014174.
  23. Dyson RH, Howard SM. Tappeh Hesār: reports of the restudy project, 1976. Firenze: Casa editrice Le Lettere; 1989.
  24. Oudbashi O, Davami P, Emami SMA. Bronze in archaeology: a review of the archaeometallurgy of bronze in ancient Iran. Intech; 2012:153-172. doi:10.5772/32687.
  25. Crawford MH. Anthropological genetics: theory, methods and applications. New York: Cambridge University Press; 2007.
  26. Gilbert MT, Bandelt HJ, Hofreiter M, Barnes I. Assessing ancient DNA studies. Trends Ecol Evol. 2005;20(10):541-544. doi:10.1016/j.tree.2005.07.005.
  27. van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 2009;30(2):E386-394. doi:10.1002/humu.20921.
  28. Rock AW, Dur A, van Oven M, Parson W. Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA). Forensic Sci Int Genet. 2013;7(6):601-609. doi:10.1016/j.fsigen.2013.07.005.
  29. Fan L, Yao YG. An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination. Mitochondrion. 2013;13(4):360-363. doi:10.1016/j.mito.2013.04.011.
  30. Lott MT, Leipzig JN, Derbeneva O, et al. mtDNA Variation and Analysis Using Mitomap and Mitomaster. Curr Protoc Bioinformatics. 2013;44:1.23.21-26. doi:10.1002/0471250953.bi0123s44.
  31. Stoneking M, Krause J. Learning about human population history from ancient and modern genomes. Nat Rev Genet. 2011;12(9):603-614. doi:10.1038/nrg3029.
  32. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nat Rev Genet. 2001;2(5):353-359. doi:10.1038/35072071.
  33. James HA, Petraglia M. Modern human origins and the evolution of behavior in the later Pleistocene record of South Asia. Curr Anthropol. 2005;46(S5):S3-S27. doi:10.1086/444365.
  34. Petraglia MD, Haslam M, Fuller DQ, Boivin N, Clarkson C. Out of Africa: new hypotheses and evidence for the dispersal of Homo sapiens along the Indian Ocean rim. Ann Hum Biol. 2010;37(3):288-311. doi:10.3109/03014461003639249.
  35. Achilli A, Rengo C, Magri C, et al. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet. 2004;75(5):910-918. doi:10.1086/425590.
  36. Pereira L, Richards M, Goios A, et al. High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res. 2005;15(1):19-24. doi:10.1101/gr.3182305.
  37. Non A. Analyses of genetic data within an interdisciplinary framework to investigate recent human evolutionary history and complex. University of Florida; 2010:80.
  38. Loogvali EL, Roostalu U, Malyarchuk BA, et al. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol. 2004;21(11):2012-2021. doi:10.1093/molbev/msh209.
  39. Metspalu M, Kivisild T, Metspalu E, et al. Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet. 2004;5:26. doi:10.1186/1471-2156-5-26.
  40. Aali A, Abar A, Boenke N, et al. The archaeology of the salt miners. Bochum: Deutsches Bergbau-Museum Bochum; 2014.