Genetic relatedness estimation using ancient genomic data

Ghalichi, Ayshin
One distinct feature of the early Neolithic settlements in the Near East was their burial customs. Both in the Levant and in Anatolia, people dug graves inside their houses, and multiple individuals were buried in these intramural graves; a custom that reached its climax in Çatalhöyük. Archaeological evidence suggests that individuals buried in a house were socially related, which has motivated anthropologists to estimate biological relatedness among individuals who share the same grave. Such information, which could be obtained from ancient DNA data, could shed light on the social structure of these ancient communities, and be valuable for archaeological studies. The challenge of working with ancient DNA is that it is highly degraded and usually in minute amounts, which results in limited DNA data availability. Importantly, in ancient DNA datasets usually only one allele can be detected per individual. There exist a number of meth- ods to estimate genetic relatedness designed for modern high coverage genomic data, but their performance on ancient DNA data has not been tested. Here we vapply two of these methods, KING and PLINK, on low coverage whole genome data from real family pedigrees, as well as ancient DNA data from simulated pedigrees. We further propose a new approach to calculate relatedness between ancient individuals, which would require minimal coverage and SNP numbers to accurately estimate relatedness. We show that our approach can more effi- ciently estimate the relatedness coefficients compared to the KING and PLINK software. Our approach is expected to promote the application of ancient DNA to address new archaeological questions.


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Several archaeological and genetic studies indicated that Southeastern Anatolia was the only center of domestication for sheep. The study presented here aims to understand how and when domestic sheep were transported across Anatolia into west from the domestication center by using ancient DNA. In order to achieve that, ancient DNA was extracted from 234 sheep bone samples dating between Epipaleolithic and 2800 BCE from 9 archaeological excavations (Tepecik-Çiftlik, Yeşilova, Ulucak, Aktopraklık, Barcın, Çat...
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Citation Formats
A. Ghalichi, “Genetic relatedness estimation using ancient genomic data,” M.S. - Master of Science, Middle East Technical University, 2017.