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The mitochondrial genomes of two Pre-historic Hunter Gatherers in Sri Lanka


Sri Lanka is an island in the Indian Ocean connected by the sea routes of the Western and Eastern worlds. Although settlements of anatomically modern humans date back to 48,000 years, to date there is no genetic information on pre-historic individuals in Sri Lanka. We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese. Both haplogroups are Indian derived and observed in the South Asian region and rarely outside the region.

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Fig. 1

Data availability

Mitochondrial genome files are deposited into the GenBank (FASTA: accession numbers MZ895064–MZ895065) and SRA (FASTQ: accession PRJNA889366) databases.


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We thank Prof. M. Raghavan and team (University of Chicago, USA) for training ASF. Anjana Welikala and Lakshika Jayasekara for sharing unpublished data to calculate the Sri Lankan mt haplogroup frequency. National Research Council, Sri Lanka (Grant No: 17-042) for funding.

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Authors and Affiliations



RR, KHT, EHK, RS, and NR: conceptualization. RS, AW, and DD: assembled archeological materials and dating. ASF and NR: performed the experiments. ASF: did the data processing, analysis and quality control. RR, KHT, RS, and NR: supervision. ASF, RR, and KHT: wrote the original manuscript. EHK, RS, and NR: critically reviewed the manuscript. All the authors read and approved the final version of the manuscript.

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Correspondence to R. Ranasinghe.

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Fernando, A.S., Wanninayaka, A., Dewage, D. et al. The mitochondrial genomes of two Pre-historic Hunter Gatherers in Sri Lanka. J Hum Genet 68, 103–105 (2023).

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