Repository of DUTH

Unraveling the genetic history of prehistoric human populations in Hellenic Region through Bioinformatic Analysis (Master thesis)

Χούπα, Νεφέλη-Μαρία/ Choupa, Maria-Nefeli

In this study, NGS genomic data from previously published archaeogenetic studies were used, resulting in a final set of 526 samples after quality checks: 146 prehistoric and 370 modern samples. The prehistoric samples originate from the Central and Eastern Mediterranean, mainly Greece, spanning from the Neolithic to the Iron Age, with a focus on the Bronze Age. The modern samples primarily come from the Eastern Mediterranean and the Balkans and only their final, clean format was used in analysis. In silico bioinformatic analysis was performed on these data to clean and convert them into a final form suitable for subsequent population genetic analysis. The GATK pipeline was employed as the main tool. The PCA analysis results revealed a non-normal distribution of ancient data, which deviated from the normal distribution of modern samples. This discrepancy prevented the archaeogenetic interpretation of the results, limiting the analysis to describing the genetic relationships between ancient populations and those with the present-day populations. To investigate whether this issue arose from errors in the pre-processing stage, a PCA analysis was conducted on a second dataset of clean and properly processed genomic data from the AADR database. This dataset included the same samples as this study but was enriched with additional archaeogenetic and modern genomic data from geographically and temporally distant populations. The results showed a normal distribution for the second dataset and confirmed the findings reported in the literature. Based on these findings, it was determined that there were significant omissions in the bioinformatics processing steps, highlighting the need for methodological improvements and additional population analysis to ensure the reliability of the results and their archaeogenetic interpretability.