Skip to main content
PMC home page
Philosophical Transactions of the Royal Society B: Biological Sciences logoLink to Philosophical Transactions of the Royal Society B: Biological Sciences
. 1999 Jan 29;354(1379):141–152. doi: 10.1098/rstb.1999.0367

Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers.

E Hagelberg 1, M Kayser 1, M Nagy 1, L Roewer 1, H Zimdahl 1, M Krawczak 1, P Lió 1, W Schiefenhövel 1
PMCID: PMC1692446  PMID: 10091254

Abstract

Present-day Pacific islanders are thought to be the descendants of Neolithic agriculturalists who expanded from island South-east Asia several thousand years ago. They speak languages belonging to the Austronesian language family, spoken today in an area spanning half of the circumference of the world, from Madagascar to Easter Island, and from Taiwan to New Zealand. To investigate the genetic affinities of the Austronesian-speaking peoples, we analysed mitochondrial DNA, HLA and Y-chromosome polymorphisms in individuals from eight geographical locations in Asia and the Pacific (China, Taiwan, Java, New Guinea highlands, New Guinea coast, Trobriand Islands, New Britain and Western Samoa). Our results show that the demographic expansion of the Austronesians has left a genetic footprint. However, there is no simple correlation between languages and genes in the Pacific.

Full Text

The Full Text of this article is available as a PDF (248.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Cann R. L., Stoneking M., Wilson A. C. Mitochondrial DNA and human evolution. Nature. 1987 Jan 1;325(6099):31–36. doi: 10.1038/325031a0. [DOI] [PubMed] [Google Scholar]
  3. Deka R., Jin L., Shriver M. D., Yu L. M., Saha N., Barrantes R., Chakraborty R., Ferrell R. E. Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations. Genome Res. 1996 Dec;6(12):1177–1184. doi: 10.1101/gr.6.12.1177. [DOI] [PubMed] [Google Scholar]
  4. Excoffier L., Smouse P. E., Quattro J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992 Jun;131(2):479–491. doi: 10.1093/genetics/131.2.479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Forster P., Kayser M., Meyer E., Roewer L., Pfeiffer H., Benkmann H., Brinkmann B. Phylogenetic resolution of complex mutational features at Y-STR DYS390 in aboriginal Australians and Papuans. Mol Biol Evol. 1998 Sep;15(9):1108–1114. doi: 10.1093/oxfordjournals.molbev.a026018. [DOI] [PubMed] [Google Scholar]
  6. Gao X., Bhatia K., Trent R. J., Serjeantson S. W. HLA-DR,DQ nucleotide sequence polymorphisms in five Melanesian populations. Tissue Antigens. 1992 Jul;40(1):31–37. doi: 10.1111/j.1399-0039.1992.tb01954.x. [DOI] [PubMed] [Google Scholar]
  7. Gao X., Veale A., Serjeantson S. W. HLA class II diversity in Australian aborigines: unusual HLA-DRB1 alleles. Immunogenetics. 1992;36(5):333–337. doi: 10.1007/BF00215663. [DOI] [PubMed] [Google Scholar]
  8. Hagelberg E. Ancient and modern mitochondrial DNA sequences and the colonization of the Pacific. Electrophoresis. 1997 Aug;18(9):1529–1533. doi: 10.1002/elps.1150180907. [DOI] [PubMed] [Google Scholar]
  9. Hagelberg E., Clegg J. B. Genetic polymorphisms in prehistoric Pacific islanders determined by analysis of ancient bone DNA. Proc Biol Sci. 1993 May 22;252(1334):163–170. doi: 10.1098/rspb.1993.0061. [DOI] [PubMed] [Google Scholar]
  10. Hagelberg E., Quevedo S., Turbon D., Clegg J. B. DNA from ancient Easter Islanders. Nature. 1994 May 5;369(6475):25–26. doi: 10.1038/369025a0. [DOI] [PubMed] [Google Scholar]
  11. Hammer M. F. A recent common ancestry for human Y chromosomes. Nature. 1995 Nov 23;378(6555):376–378. doi: 10.1038/378376a0. [DOI] [PubMed] [Google Scholar]
  12. Hammer M. F. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol. 1994 Sep;11(5):749–761. doi: 10.1093/oxfordjournals.molbev.a040155. [DOI] [PubMed] [Google Scholar]
  13. Hammer M. F., Karafet T., Rasanayagam A., Wood E. T., Altheide T. K., Jenkins T., Griffiths R. C., Templeton A. R., Zegura S. L. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol Biol Evol. 1998 Apr;15(4):427–441. doi: 10.1093/oxfordjournals.molbev.a025939. [DOI] [PubMed] [Google Scholar]
  14. Hammer M. F., Spurdle A. B., Karafet T., Bonner M. R., Wood E. T., Novelletto A., Malaspina P., Mitchell R. J., Horai S., Jenkins T. The geographic distribution of human Y chromosome variation. Genetics. 1997 Mar;145(3):787–805. doi: 10.1093/genetics/145.3.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hashimoto M., Kinoshita T., Yamasaki M., Tanaka H., Imanishi T., Ihara H., Ichikawa Y., Fukunishi T. Gene frequencies and haplotypic associations within the HLA region in 916 unrelated Japanese individuals. Tissue Antigens. 1994 Sep;44(3):166–173. doi: 10.1111/j.1399-0039.1994.tb02375.x. [DOI] [PubMed] [Google Scholar]
  16. Hertzberg M., Mickleson K. N., Serjeantson S. W., Prior J. F., Trent R. J. An Asian-specific 9-bp deletion of mitochondrial DNA is frequently found in Polynesians. Am J Hum Genet. 1989 Apr;44(4):504–510. [PMC free article] [PubMed] [Google Scholar]
  17. Heyer E., Puymirat J., Dieltjes P., Bakker E., de Knijff P. Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum Mol Genet. 1997 May;6(5):799–803. doi: 10.1093/hmg/6.5.799. [DOI] [PubMed] [Google Scholar]
  18. Jobling M. A., Tyler-Smith C. Fathers and sons: the Y chromosome and human evolution. Trends Genet. 1995 Nov;11(11):449–456. doi: 10.1016/s0168-9525(00)89144-1. [DOI] [PubMed] [Google Scholar]
  19. Kayser M., Caglià A., Corach D., Fretwell N., Gehrig C., Graziosi G., Heidorn F., Herrmann S., Herzog B., Hidding M. Evaluation of Y-chromosomal STRs: a multicenter study. Int J Legal Med. 1997;110(3):125-33, 141-9. doi: 10.1007/s004140050051. [DOI] [PubMed] [Google Scholar]
  20. Lum J. K., Rickards O., Ching C., Cann R. L. Polynesian mitochondrial DNAs reveal three deep maternal lineage clusters. Hum Biol. 1994 Aug;66(4):567–590. [PubMed] [Google Scholar]
  21. Melton T., Peterson R., Redd A. J., Saha N., Sofro A. S., Martinson J., Stoneking M. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am J Hum Genet. 1995 Aug;57(2):403–414. [PMC free article] [PubMed] [Google Scholar]
  22. O'Shaughnessy D. F., Hill A. V., Bowden D. K., Weatherall D. J., Clegg J. B. Globin genes in Micronesia: origins and affinities of Pacific Island peoples. Am J Hum Genet. 1990 Jan;46(1):144–155. [PMC free article] [PubMed] [Google Scholar]
  23. Redd A. J., Takezaki N., Sherry S. T., McGarvey S. T., Sofro A. S., Stoneking M. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol Biol Evol. 1995 Jul;12(4):604–615. doi: 10.1093/oxfordjournals.molbev.a040240. [DOI] [PubMed] [Google Scholar]
  24. Roberts-Thomson J. M., Martinson J. J., Norwich J. T., Harding R. M., Clegg J. B., Boettcher B. An ancient common origin of aboriginal Australians and New Guinea highlanders is supported by alpha-globin haplotype analysis. Am J Hum Genet. 1996 May;58(5):1017–1024. [PMC free article] [PubMed] [Google Scholar]
  25. Roewer L., Kayser M., Dieltjes P., Nagy M., Bakker E., Krawczak M., de Knijff P. Analysis of molecular variance (AMOVA) of Y-chromosome-specific microsatellites in two closely related human populations. Hum Mol Genet. 1996 Jul;5(7):1029–1033. doi: 10.1093/hmg/5.7.1029. [DOI] [PubMed] [Google Scholar]
  26. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  27. Seielstad M. T., Hebert J. M., Lin A. A., Underhill P. A., Ibrahim M., Vollrath D., Cavalli-Sforza L. L. Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum Mol Genet. 1994 Dec;3(12):2159–2161. doi: 10.1093/hmg/3.12.2159. [DOI] [PubMed] [Google Scholar]
  28. Soodyall H., Jenkins T., Stoneking M. 'Polynesian' mtDNA in the Malagasy. Nat Genet. 1995 Aug;10(4):377–378. doi: 10.1038/ng0895-377. [DOI] [PubMed] [Google Scholar]
  29. Spurdle A. B., Woodfield D. G., Hammer M. F., Jenkins T. The genetic affinity of Polynesians: evidence from Y chromosome polymorphisms. Ann Hum Genet. 1994 Jul;58(Pt 3):251–263. doi: 10.1111/j.1469-1809.1994.tb01889.x. [DOI] [PubMed] [Google Scholar]
  30. Stoneking M., Jorde L. B., Bhatia K., Wilson A. C. Geographic variation in human mitochondrial DNA from Papua New Guinea. Genetics. 1990 Mar;124(3):717–733. doi: 10.1093/genetics/124.3.717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sykes B., Leiboff A., Low-Beer J., Tetzner S., Richards M. The origins of the Polynesians: an interpretation from mitochondrial lineage analysis. Am J Hum Genet. 1995 Dec;57(6):1463–1475. [PMC free article] [PubMed] [Google Scholar]
  32. Thomas M. G., Cook C. E., Miller K. W., Waring M. J., Hagelberg E. Molecular instability in the COII-tRNA(Lys) intergenic region of the human mitochondrial genome: multiple origins of the 9-bp deletion and heteroplasmy for expanded repeats. Philos Trans R Soc Lond B Biol Sci. 1998 Jun 29;353(1371):955–965. doi: 10.1098/rstb.1998.0260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Underhill P. A., Jin L., Lin A. A., Mehdi S. Q., Jenkins T., Vollrath D., Davis R. W., Cavalli-Sforza L. L., Oefner P. J. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 1997 Oct;7(10):996–1005. doi: 10.1101/gr.7.10.996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Underhill P. A., Jin L., Zemans R., Oefner P. J., Cavalli-Sforza L. L. A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):196–200. doi: 10.1073/pnas.93.1.196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Veitia R., Ion A., Barbaux S., Jobling M. A., Souleyreau N., Ennis K., Ostrer H., Tosi M., Meo T., Chibani J. Mutations and sequence variants in the testis-determining region of the Y chromosome in individuals with a 46,XY female phenotype. Hum Genet. 1997 May;99(5):648–652. doi: 10.1007/s004390050422. [DOI] [PubMed] [Google Scholar]
  36. Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
  37. Wallace D. C. 1994 William Allan Award Address. Mitochondrial DNA variation in human evolution, degenerative disease, and aging. Am J Hum Genet. 1995 Aug;57(2):201–223. [PMC free article] [PubMed] [Google Scholar]
  38. Whitfield L. S., Sulston J. E., Goodfellow P. N. Sequence variation of the human Y chromosome. Nature. 1995 Nov 23;378(6555):379–380. doi: 10.1038/378379a0. [DOI] [PubMed] [Google Scholar]
  39. Wrischnik L. A., Higuchi R. G., Stoneking M., Erlich H. A., Arnheim N., Wilson A. C. Length mutations in human mitochondrial DNA: direct sequencing of enzymatically amplified DNA. Nucleic Acids Res. 1987 Jan 26;15(2):529–542. doi: 10.1093/nar/15.2.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Zerjal T., Dashnyam B., Pandya A., Kayser M., Roewer L., Santos F. R., Schiefenhövel W., Fretwell N., Jobling M. A., Harihara S. Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet. 1997 May;60(5):1174–1183. [PMC free article] [PubMed] [Google Scholar]

Articles from Philosophical Transactions of the Royal Society B: Biological Sciences are provided here courtesy of The Royal Society

RESOURCES