Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India (original) (raw)

European Journal of Human Genetics volume 9, pages 695–700 (2001)Cite this article

Abstract

From observations of lack of haplotype sharing based on Y-chromosome specific short tandem repeat (STR) loci, previous reports suggested negligible gene flow among different geographic populations of India. Using Single Nucleotide Polymorphism (SNP) sites in combination with STRs, we observed evidence of haplotype sharing across caste-tribe boundaries in South India. We examined 27 SNPs in the non-recombining region of the Y chromosome to investigate gene flow in 204 individuals belonging to three caste groups (Vizag Brahmins, Peruru Brahmins, Kammas), three tribes (Bagata, Poroja, Valmiki) and an additional group (the Siddis) of African ancestry. Principal component and AMOVA analyses show that the between group component of variation is non-significant (_P_>0.05), while that among populations within the caste and tribal groups is significant (P<0.001). In particular, the Valmikis and Siddis are close to the caste groups. Of a total of 11 distinct SNP-haplotypes observed, the two tribal groups (Bagata and Poroja) lack the haplotypes H4, H4A, H5A and H16, which are seen in the caste groups. In contrast, all three tribal groups exhibit the Southeast Asian haplotype H11 that is absent in the caste populations. The presence of haplotypes H4, H5, H14, and H16 in the Siddis indicate that they have assimilated considerable non-African admixture. The evidence of haplotype sharing between castes and tribes is also found when the H14 lineage was further subdivided by five STR loci. We conclude that even though these SNP-based Y-haplotypes are able to distinguish the populations, gene flow in these South Indian populations is not as negligible as that inferred from other studies based on Y-specific short tandem repeat markers.

Similar content being viewed by others

Article PDF

References

  1. Jobling MA, Tyler-Smith C . Father and sons: The Y chromosome and human evolution Trends in Genetics 1995 11: 449–456
    Article CAS PubMed Google Scholar
  2. Jobling MA, Tyler-Smith C . New uses for new haplotypes the human Y chromosome, disease and selection Trends in Genetics 2000 16: 356–363
    Article CAS PubMed Google Scholar
  3. Underhill PA, Jin L, Lin A et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography Genome Research 1997 7: 996–1005
    Article CAS PubMed PubMed Central Google Scholar
  4. Underhill PA, Shen P, Lin AA et al. Y chromosome sequence variation and the history of human populations Nature Genetics 2000 26: 358–361
    Article CAS PubMed Google Scholar
  5. Malhotra KC . Population structure among the Dhangar caste-cluster of Maharashtra, India. In: Lukacs JR (ed) The people of south Asia: the biological anthropology of India, Pakistan, and Nepal Plenum, New York 1984 pp 295–324
  6. Majumder PP . People of India: Biological diversity and affinities Evolutionary Anthropology 1998 6: 100–110
    Article Google Scholar
  7. Bamshad MJ, Watkins WS, Dixon ME et al. Female gene flow stratifies Hindu castes Nature 1997 395: 851–852
    Google Scholar
  8. Bhattacharyya NP, Basu P, Das M et al. Negligible male gene flow across ethnic boundaries in India, revealed by analysis of Y-chromosomal DNA polymorphisms Genome Research 1999 9: 711–719
    CAS PubMed Google Scholar
  9. Kayser M, Cagila A, Corach D . Evaluation of Y-chromosomal STRs: A multicenter study Int. J Legal Med 1997 110: 125–133
    Article CAS PubMed Google Scholar
  10. Excoffier L, Smouse P, Quattro J . Analysis of molecular variance inferred from metric distances among DNA haplotypes. Application to human mitochondrial DNA restriction data Genetics 1992 131: 479–491
    CAS PubMed PubMed Central Google Scholar
  11. Schneider S, Kueffer JM, Roessli D et al. Arlequin ver 1.1 A software for population genetic data analysis Genetics and Biometry Laboratory, University of Geneva, Switzerland 1997
  12. Su B, Xiao J, Underhill P et al. Y-chromosome evidence for a northward migration of modern human into Eastern Asia during the last ice age Am J Hum Genet 1999 65: 1718–1724
    Article CAS PubMed PubMed Central Google Scholar
  13. Su B, Jin L, Underhill P et al. Polynesian origins: Insights from the Y chromosome Proc Natl Acad Sci USA 2000 97: 8225–8228
    Article CAS PubMed PubMed Central Google Scholar
  14. Basham AL . The Wonder that was India New Delhi, India, Rupa and Co 1981
  15. Enthoven RE . Tribes and castes of Bombay Vol III: Bombay 1922
  16. Palakshappa TC . The Siddis of North Karnataka New Delhi, India, Sterling Publishers 1976
  17. Sorley HT . The Siddis of Kanara – Census of India Vol 1: Part III 1931
  18. Ramana GV, Wang N, Singh L et al. Short tandem-repeat Y-chromosome haplotype data reveals a high level of admixture in the migrant populations, the Siddis, with local Indian populations Human Biology 2001 manuscript submitted

Download references

Acknowledgements

All DNA samples analysed here are anonymised, and were collected with informed consent of the subjects. Research supported by the US Public Health Services Research Grant GM 41399 from the National Institutes of Health.

Author information

Authors and Affiliations

  1. Human Genetics Center, University of Texas, School of Public Health, Houston, TX 77030, Texas, USA
    Gutala Venkata Ramana, Bing Su, Li Jin, Ning Wang & Ranajit Chakraborty
  2. Center for Cellular and Molecular Biology, Hyderabad, India
    Lalji Singh
  3. Department of Genetics, Stanford University, Stanford, CA 94305, USA
    Peter Underhill

Authors

  1. Gutala Venkata Ramana
    You can also search for this author inPubMed Google Scholar
  2. Bing Su
    You can also search for this author inPubMed Google Scholar
  3. Li Jin
    You can also search for this author inPubMed Google Scholar
  4. Lalji Singh
    You can also search for this author inPubMed Google Scholar
  5. Ning Wang
    You can also search for this author inPubMed Google Scholar
  6. Peter Underhill
    You can also search for this author inPubMed Google Scholar
  7. Ranajit Chakraborty
    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toRanajit Chakraborty.

Rights and permissions

About this article

Cite this article

Ramana, G., Su, B., Jin, L. et al. Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India.Eur J Hum Genet 9, 695–700 (2001). https://doi.org/10.1038/sj.ejhg.5200708

Download citation

Keywords

This article is cited by