An Attempt to Extract Ancient DNA from the Petrous Part of the Temporal Bones and Roots of Teeth of Skeletal Remains Found in the Intermediate Climatic Zone in Sri Lanka

Abstract

Ancient DNA (aDNA) is used to explore the genetic landscape of the past and investigate the movement, mixture, and adaptation events that shaped present-day patterns of human genetic diversity. The present study was designed to explore the genetic composition of the ancient people of Sri Lanka. Despite the low amino acid racemization often found in skeletal remains of Sri Lanka, we attempted to extract DNA from skeletal remains of 5 individuals found from several sites in intermediate climatic zone in Sri Lanka by using methodologies particularly designed for highly damaged and degraded DNA. We attempted to extract and sequence DNA from the petrous part of the temporal bones and tooth roots of remains excavated from Sigiriya <em>Potana, Pellemalala</em> (4,500 YBP) and <em>Mini-atheliya</em> (1,000 – 5,000 YBP) in Sri Lanka. The bone processing, DNA extraction and amplification were performed in three separate rooms with dedicated equipment as accordance to the recommendation for analysis of aDNA. All measures were strictly taken to minimize contamination with modern samples. Using the DNA extracts, we prepared dual-indexed single-stranded libraries treated with uracil-DNA glycosylase (UDG) to reduce the rate of ancient DNA damage. Prior to sequencing, in-solution target hybridization was used to enrich the sequences that overlap the mitochondrial genome and about 1.24 million genome-wide SNPs. Sufficient data passing quality control standards for any of the five individuals studied was not obtained. Coverage of the mitochondrial genome ranged between 0.04-0.45x, with damage rates at the terminal nucleotide that were not indicative of authentic ancient DNA. A range of 453-2,838 SNPs out of ~1.24 million targets were covered across the nuclear genome, translating to a maximum coverage of 0.004x. The damage rates at the terminal nucleotide were not indicative of authentic ancient DNA. The low numbers of SNPs hit on the X and Y chromosomes precluded the confident assessment of genetic sex in all individuals but it is possible that the ancient skeletal sample represented by Sigiriya <em>Potana</em> is a female individual. Although the recent published work on using the petrous part of the temporal bone has generated many times more data than other skeletal elements, even this technique did not work to generate aDNA on this set of prehistoric skeletal remains found in the intermediate climatic zone in Sri Lanka. It is possible that other sites might provide better taphonomic preservation conditions than the sites we analysed, and in addition a priority should be to attempt ancient DNA analysis from skeletal remains found in Sri Lanka’s dry zone.