Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Progress
  • Published:

The genetical archaeology of the human genome

Abstract

Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Slatkin, M. & Hudson, D. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555–562 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Majoram, P. & Donnelly, P. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics 136, 673–683 (1994).

    Google Scholar 

  3. Rogers, A. Genetic evidence for a Pleistocene population explosion. Evolution 49, 608–615 (1995).

    Article  PubMed  Google Scholar 

  4. Cann, R.L., Stoneking, M. & Wilson, A.C. Mitochondrial DNA and human populations. Nature 325, 31–36 (1987).

    Article  CAS  PubMed  Google Scholar 

  5. Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. & Wilson, A.C. African populations and the evolution of human mitochondrial DNA. Science 253, 1503–1507 (1991).

    Article  CAS  PubMed  Google Scholar 

  6. Ruvolo, M. et al. Mitochondrial COII sequences and modern human origins. Mol. Biol. Evol. 10, 1115–1135 (1993).

    CAS  PubMed  Google Scholar 

  7. Horai, S., Hayasaka, K., Kondo, R., Tsugane, K. & Takahata, N. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA 92, 532–536 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stoneking, M., Sherry, S.T., Redd, A.J. & Vigilant, L. New approaches to dating suggest a recent age for the human mtDNA ancestor. Phil. Trans. R. Soc. Lond. B 337, 167–175 (1992).

    Article  CAS  Google Scholar 

  9. Pesole, G., Sbisa, E., Preparata, G. & Saccone, C. The evolution of the mitochondrial D-loop region and the origin of modern man. Mol. Biol. Evol. 9, 587–598 (1992).

    CAS  PubMed  Google Scholar 

  10. Wills, C. When did Eve live? An evolutionary detective story. Evolution 49, 593–607 (1995).

    Article  PubMed  Google Scholar 

  11. Dorit, R.L., Akashi, H. & Gilbert, W. Absence of polymorphism at the ZFY locus on the human Y chromosome. Science 268, 1183–1185 (1995).

    Article  CAS  PubMed  Google Scholar 

  12. Weiss, G. & von Haeseler, A. How many Ys? Science 272, 1358–1360 (1996).

    Google Scholar 

  13. Hammer, M.F. A recent common ancestry for human Y chromosomes. Nature 378, 376–378 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Fu, Y.-X. & Li, W.-H. The age of the common ancestor of human Y chromosomes. Nature (in the press).

  15. Takahata, N. Allelic genealogy and human evolution. Mol Biol. Evol. 10, 2–22 (1993).

    CAS  PubMed  Google Scholar 

  16. Morin, P.A. et al. Kin selection, social structure, gene flow and the evolution of chimpanzees. Science 265, 1193–1201 (1994).

    Article  CAS  PubMed  Google Scholar 

  17. Ferris, S.D., Brown, W.M., Davidson, W.S. & Wilson, A.C. Extensive polymorphism in the mitochondrial DNA of apes. Proc. Natl. Acad. Sci. USA 78, 6319–6323 (1991).

    Article  Google Scholar 

  18. Ruvolo, M. et al. Gene trees and hominoid phylogeny. Proc. Natl. Acad. Sci. USA 91, 8900–8904 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Blanchard, J.L. & Schmidt, G.W. Mitochondrial DNA migration events in yeast and humans: Integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Mol. Biol. Evol. 13, 537–548 (1996).

    Article  CAS  PubMed  Google Scholar 

  20. Crouau-Roy, B., Service, S., Slatkin, M. & Freimer, N. A fine-scale comparison of the human and chimpanzee genomes: linkage, linkage disequilibrium and sequence analysis. Hum. Mol. Genet. 8, 1131–1137 (1996).

    Article  Google Scholar 

  21. Nei, M. & Graur, D. Extent of protein polymorphism and the neutral mutation theory. Evol. Biol. 17, 73–118 (1984).

    Article  Google Scholar 

  22. Li, W.H. & Sadler, L.A. Low nucleotide diversity in man. Genetics 129, 513–523 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Hedrick, P. Evolutionary genetics of the major histocompatibility complex. Am. Naturalist 143, 945–964 (1994).

    Article  Google Scholar 

  24. Gyllensten, U.B., Sundvall, M. & Erlich, H.A. Alielic diversity is generated by intraexon exchange at the DRB1 locus of primates. Proc. Natl. Acad. Sci. USA 88, 3686–3690 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Takahata, N., Satta, Y. & Klein, J. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130, 925–938 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Ayala, F.J. The myth of Eve: molecular biology and human origins. Science 270, 1930–1936 (1995).

    Article  CAS  PubMed  Google Scholar 

  27. Ayala, F.J. & Escalante, A.A. The evolution of human populations: A molecular perspective. Mol. Phyl. Evol. 5, 188–201 (1996).

    Article  CAS  Google Scholar 

  28. Titus-Trachtenberg, E.A., Rickards, O., De Stefano, G.F. & Erlich, H.A. Analysis of HLA class II haplotypes in the Cayapa Indians of Ecuador: A novel DRBI allele reveals evidence of convergent evolution and balancing selection at position 86. Am. J. Hum. Genet. 55, 160–167 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Gustafsson, K. et al. Structure of miniature swine class II DRB genes: conservation of hypervariable amino acid residues between distantly related species. Proc. Natl. Acad. Sci. USA 87, 9798–9802 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gustafsson, K. & Andersson, L. Structure and polymorphism of horse MHC class II DRB genes: convergent evolution in the antigen binding site. Immunogenet. 39, 355–358 (1994).

    Article  CAS  Google Scholar 

  31. Maddison, D.R. African origin of human mitochondrial DNA reexamined. Syst. Zool. 40, 355–363 (1991).

    Article  Google Scholar 

  32. Templeton, A.L. Human origins and analysis of mitochondrial DNA sequences. Science 255, 737 (1992).

    Article  CAS  PubMed  Google Scholar 

  33. Hedges, S.B., Kumar, S., Tamura, K. & Stoneking, M. Human origins and analysis of mitochondrial DNA sequences. Science 255, 737–739 (1992).

    Article  CAS  PubMed  Google Scholar 

  34. Maddison, D.R., Ruvolo, M. & Swofford, D.L. Geographic origins of human mitochondrial DNA phylogenetic inference from control region sequences. Syst. Biol. 41, 111–124 (1992).

    Article  Google Scholar 

  35. Penny, D., Steel, M., Waddell, P.J. & Hendy, M.D. Improved analyses of human mtDNA sequences support a recent African origin of Homo sapiens. Mol. Biol. Evol. 12, 863–882 (1995).

    CAS  PubMed  Google Scholar 

  36. Strimmer, K. & von Haeseler, A. (1996) Quartet puzzling: A maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964–969 (1996).

    Article  CAS  Google Scholar 

  37. D'Andrade, R. & Morin, P.A. A principal components and individual-by-site analysis of chimpanzee and human mitochondrial DNA. Am. Anthropol. 98(2), 2–20 (1996).

    Google Scholar 

  38. Zischler, H., Geisert, H., von Haeseler, A. & Pääbo, S. A nuclear “fossil” of the mitochondrial D-loop and the origin of modern humans. Nature 378, 489–492 (1995).

    Article  CAS  PubMed  Google Scholar 

  39. Wainscoat, S. et al. Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms. Nature 319, 491–493 (1986).

    Article  CAS  PubMed  Google Scholar 

  40. Tishkoff, S.A. et al. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271, 1380–1387 (1996).

    Article  CAS  PubMed  Google Scholar 

  41. Manderscheid, E.J. & Rogers, A.R. Genetic admixture in the late Pleistocene. Am. J. Phys. Anthropol. (in the press).

  42. Nei, M. & Takezaki, N. The root of the phylogenetic tree of human populations. Mol. Biol. Evol. 13, 170–177 (1996).

    Article  CAS  PubMed  Google Scholar 

  43. Goldstein, D.B., Linares, A.R., Cavalli-Sforza, L.L. & Feldman, M.W. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 92, 6723–6727 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Tishkoff, S.A. et al. A global haplotype analysis of mytonic dystrophy CTG-repeats in humans and other primates. Am. J. Hum. Genet. 57, A42 (1995).

    Google Scholar 

  45. Armour, J.A.L. et al. Minisatellite diversity supports a recent African origin for modern humans. Nature Genet. 13, 154–160 (1996).

    Article  CAS  PubMed  Google Scholar 

  46. Sajantila, A. et al. Genes and languages in Europe: an analysis of mitochondrial lineages. Genome Res. 5, 42–52 (1995).

    Article  CAS  PubMed  Google Scholar 

  47. Sajantila, A. & Pääbo, S. Language replacement in Scandinavia. Nature Genet. 11, 359–360 (1995).

    Article  CAS  PubMed  Google Scholar 

  48. Mountain, J.L., Hebert, J.M., Bhattacharyya, S., Underhill, P.A., Ottolenghi, C., Gadgil, M. & Cavalli-Sforza, L.L. Demographic history of India and mtDNA-sequence diversity. Am. J. Hum. Genet. 56, 979–992 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Watson, L., Bauer, K., Aman, R., Weiss, G., von Haeseler, A. & Pääbo, S. MtDNA sequence diversity in Africa. Am. J. Hum. Gen. 59, 437–444 (1996).

    CAS  Google Scholar 

  50. Cavalli-Sforza, L.L. & Ammermann, A. The neolithic transition and the genetics of populations in Europe. (Princeton University Press, 1984).

    Google Scholar 

  51. Rogers, A. & Harpendinger, H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569 (1992).

    CAS  PubMed  Google Scholar 

  52. Sherry, S.T. et al. Mismatch distributions of mtDNA reveal recent human population expansions. Hum. Biol. 66, 761–775 (1994).

    CAS  PubMed  Google Scholar 

  53. Ivanov, P.L. et al. Mitochondrial sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nature Genet. 12, 417–420 (1996).

    Article  CAS  PubMed  Google Scholar 

  54. Howell, N., Kubacka, I. & Mackey, D.A. How rapidly does the human mitochondrial genome evolve? Am. J. Hum. Genet. 59, 501–509 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Pääbo, S. Mutations in the mitochondrial microcosm. Am. J. Hum. Genet. 59, 493–496 (1996).

    PubMed  PubMed Central  Google Scholar 

  56. Sajantila, A. et al. Mitochondrial and Y chromosome lineage analyses reveal founder effect in the Finnish population. Proc. Natl. Acad. Sci. USA, (in the press).

  57. Richards, M. et al. Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am. J. Hum. Genet. 59, 185–203 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Felsenstein, J., Phylogenitic Inference Programs (PHYLIP), University of Washington, Seattle and University Herbarium, University of California, Berkeley. (1993).

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Svante Pääbo.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Haeseler, A., Sajantila, A. & Pääbo, S. The genetical archaeology of the human genome. Nat Genet 14, 135–140 (1996). https://doi.org/10.1038/ng1096-135

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1096-135

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing