Original Article | Published:

Mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations

Journal of Human Genetics volume 59, pages 2836 (2014) | Download Citation

Abstract

Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island, who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and analysis of molecular variance revealed that Vedda people’s mitochondrial sequences are more related to the Sinhalese and Sri Lankan Tamils’ than the Indian Tamils’ sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.

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References

  1. 1.

    The peopling of Sri Lanka: the national question and some problems of history and ethnicity. Ethn. Soc. Change Sri Lanka 1–19 (1985).

  2. 2.

    Statistical Abstract of the Democratic Socialist Republic of Sri Lanka, 2001 Department of Census and Statistics, Ministry of Finance, Colombo, Sri Lanka (2002).

  3. 3.

    3, (Gunter Narr Verlag, Tubingen (1979).

  4. 4.

    in The Vanishing Aborigines ed. Samarasinghe D. A., 34–47 (ICES: Colombo, 1990).

  5. 5.

    & The Veddas, (Cambridge University Press: Cambridge, 1911).

  6. 6.

    Current Trends in Linguistics v, (Mouton: The Hague, 1969).

  7. 7.

    Human responses to late quaternary climatic changes in Central Sri Lanka. J. Natn. Sci. Found. Sri Lanka 33, 157–159 (2005).

  8. 8.

    Prehistory of Sri Lanka: An Ecological Perspective, (Department of Archaeology survey, Government of Sri Lanka Colombo, 1992).

  9. 9.

    In Spolia Zeylanica, Vol. 39 ed. Wikramasinghe N., 13–27 (Department of National Museum: Colombo, 2002).

  10. 10.

    Recent Discoveries and Studies of the Human Skeletal Remains of Ancient Sri Lankans: A palaeoanthropological update, (MD Publications Pvt. Ltd.: New Delhi, 1993).

  11. 11.

    , , , , & Haplotype data for 12 Y-chromosome STR loci of Sri Lankans. Forensic Sci. Int. Genet. 4, e119–e120 (2010).

  12. 12.

    , , & Genetic variation at 11 autosomal STR loci in the aboriginal people, the Veddahs of Sri Lanka. Forensic Sci. Int. Genet. 4, 142 (2010).

  13. 13.

    , , , & Genetic profile of 11 autosomal STR loci among the four major ethnic groups in Sri Lanka. Forensic Sci. Int. Genet. 3, e105–e106 (2009).

  14. 14.

    (ed.). Preparation and analysis of DNA, (John Wiley and Son: USA, 1995).

  15. 15.

    , , , , , et al. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum. Mutat. 32, 25–32 (2011).

  16. 16.

    & Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386–E394 (2009).

  17. 17.

    & An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination. Mitochondrion 13, 360–363 (2013).

  18. 18.

    & DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009).

  19. 19.

    & Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).

  20. 20.

    , , , , & Genetic relationship of Chinese ethnic populations revealed by mtDNA sequence diversity. Am. J. Phys. Anthropol. 118, 63–76 (2002).

  21. 21.

    , , & MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007).

  22. 22.

    (ed.) Molecular Evolutionary Genetics, (Columbia University Press: New York, 1987).

  23. 23.

    & GENALEX6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes. 6, 288–295 (2006).

  24. 24.

    , , , , , et al. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am. J. Hum. Genet. 75, 966–978 (2004).

  25. 25.

    , , , , , et al. Genetic affinities of the central Indian tribal populations. PLoS One 7, e32546 (2012).

  26. 26.

    , & Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48 (1999).

  27. 27.

    & Estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 1, 269–285 (1984).

  28. 28.

    , , , , & Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur. J. Hum. Genet. 11, 253–264 (2003).

  29. 29.

    , , , & Inter- and extra-Indian admixture and genetic diversity in reunion island revealed by analysis of mitochondrial DNA. Ann. Hum. Genet. 73, 314–334 (2009).

  30. 30.

    , , , , , 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. 5, 26 (2004).

  31. 31.

    The physical anthropology of Ceylon. Ceylon MNational Museum's Ethnographic Series Publication No.2 (1961).

  32. 32.

    The Mahavamsa, or the Great Chronicle of Ceylon, (Pali Text Society: Sri Lanka, 1964).

  33. 33.

    The Dipavamsa, or the chronicle of the island of Ceylon. Ceylon Hist. J. 7, 1–266 (1957).

  34. 34.

    , , , & African populations and the evolution of human mitochondrial DNA. Science 253, 1503–1507 (1991).

  35. 35.

    , , , , & mtDNA sequence diversity in Africa. Am. J. Hum. Genet. 59, 437–444 (1996).

  36. 36.

    & Why hunter-gatherer populations do not show signs of pleistocene demographic expansions. Proc. Natl Acad Sci. USA 96, 10597–10602 (1999).

  37. 37.

    , , , , & mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations. Am. J. Hum. Genet. 66, 1362–1383 (2000).

  38. 38.

    , , , , , et al. The genetic origins of the Andaman Islanders. Am. J. Hum. Genet. 72, 178–184 (2003).

  39. 39.

    , , , , , et al. Genetic affinities of the Andaman Islanders, a vanishing human population. Curr. Biol. 13, 86–93 (2003).

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Acknowledgements

We are grateful to all the people who have donated their hair samples for making this study possible. We would like to thank Dr Upeksha Samaraweerachchi, Deepal Edirisinghe, Nirmala Ranaweera, Dayarathna Ranaweera, Sanjeewa Jayakody, G.G. Sirisena, U.S. Yapa, K. Sanath, Achala Chandradasa, T. Kumarasiri, M. Pushpawathi, Nimesha Palliyaguruge and H. Ranaweera for their excellent help in the field trips. Our special thanks extended to Professor Dr Senake Bandaranayake, Associate Professor Dr Suraphan Na Bangchang and Dr Bhoom Suktitipat and the three anonymous reviewers for their critical comments of the manuscript and their constructive discussions, to Dr Russell Thomson for the proof-reading of this manuscript and to Professor Drs Hans Jurgen Bandelt and Walther Parson for their valuable comments on the dataset validation. We also thank scholars who kindly provided their published mtDNA HVS-1 sequences. This work was partly supported by Siriraj Graduate Thesis Scholarship, Faculty of Medicine Siriraj Hospital Mahidol University, Thailand to LR. PL is supported by ‘Chalermphrakiat’ Grant, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand.

Author information

Author notes

    • Lanka Ranaweera
    •  & Supannee Kaewsutthi

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand

    • Lanka Ranaweera
    • , Supannee Kaewsutthi
    • , Aung Win Tun
    • , Hathaichanoke Boonyarit
    •  & Patcharee Lertrit
  2. Faculty of Sociology and Anthropology, Thammasat University, PraChan, Bangkok, Thailand

    • Samerchai Poolsuwan

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Corresponding author

Correspondence to Patcharee Lertrit.

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DOI

https://doi.org/10.1038/jhg.2013.112

Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)