Abstract
Due to high-throughput sequencing and targeted enrichment methods, ancient DNA (aDNA) analysis is emerging as a valuable tool for the investigation of ancient Egypt’s demographic history. However, the recovery of aDNA from Egyptian human remains is challenging due to poor DNA preservation and a high contamination risk. Thus, so far, less than five ancient Egyptian genome-wide datasets have been published. In addition, mitochondrial genomes are almost exclusively limited to a timespan ranging from the New Kingdom to the Roman Period (1550 BCE - 395 CE) as well as to a single archaeological site (Abusir el-Meleq). To extend the pool of ancient Egyptian genome datasets, both mitochondrial and genome-wide, we report the results of a genetic study of 100 ancient Egyptian human remains. Overall, these individuals exhibit an endogenous human DNA content between 0.01% and 40.84%. Using an enrichment capture targeting the mitochondrial DNA (mtDNA), we were able to reconstruct complete mitogenomes for 25 individuals dating from the Predynastic Period to the Coptic Period (ca. 3500 cal. BCE - 650 cal. CE) and encompassing the archaeological sites of Asyut, Akhmim, Deir el-Bahari, Deir el-Medina, Thebes, the Valley of the Queens, and Gebelein. These genomes exhibit a mtDNA haplogroup diversity similar to ancient Egyptian haplogroup profiles published by Schuenemann et al. (2017). This provides further evidence for shared maternal ancestries between western Eurasian or northern African populations and ancient Egyptians during and after the New Kingdom. In addition, we also found western Eurasian mtDNA haplogroups in individuals dated to periods prior to the New Kingdom. Furthermore, we performed a whole-genome enrichment capture on seven individuals to test these findings also on a genome-wide scale. Overall, this study provides further insights into the demographic history of ancient Egyptians considering a broader geographical context and the older periods of Egypt’s past.