First complete genome data extracted from ancient Egyptian mummies

An international team of researchers have successfully recovered and analysed ancient DNA from Egyptian mummies dating from approximately 1400 BCE to 400 BCE, including the first genome-wide data from three individuals. The study found that modern Egyptians share more ancestry with sub-Saharan Africans than ancient Egyptians did, whereas ancient Egyptians were found to be most closely related to ancient people from the Middle East and Western Asia.

This study counters prior scepticism about the possibility of recovering reliable ancient DNA from Egyptian mummies. Despite the potential issues of degradation and contamination caused by climate and mummification methods, the authors were able to use high-throughput DNA sequencing and robust authentication methods to ensure the ancient origin and reliability of the data. The study, published in the journal Nature Communications, shows that Egyptian mummies can be a reliable source of ancient DNA, and can contribute to a more accurate and refined understanding of Egypt’s history.

Egypt is a promising location for the study of ancient populations. It has a rich and well-documented history, and its geographic location and many interactions with populations from surrounding areas, in Africa, Asia and Europe, make it a dynamic region. Recent advances in the study of ancient DNA present an opportunity to test existing understandings of Egyptian history using ancient genetic data.

However, genetic studies of ancient Egyptian mummies are rare due to methodological and contamination issues. Although some of the first extractions of ancient DNA were from mummified remains, scientists have raised doubts as to whether genetic data, especially the nuclear DNA which encodes for the majority of the genome, from mummies would be reliable, and whether it could be recovered at all.

“The potential preservation of DNA has to be regarded with scepticism,” said Johannes Krause, Director at the Max Planck Institute for the Science of Human History and senior author of the study. “The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, contribute to DNA degradation and are thought to make the long-term survival of DNA in Egyptian mummies unlikely.”

For this study, the team, led by the University of Tübingen and the Max Planck Institute for the Science of Human History in Germany, and including researchers from the University of Cambridge, looked at genetic differentiation and population continuity over a 1,300 year timespan, and compared these results to modern populations.

The team sampled 151 mummified individuals from the archaeological site of Abusir el-Meleq, along the Nile River in Middle Egypt, from two anthropological collections hosted and curated at the University of Tübingen and the Felix von Luschan Skull Collection at the Museum of Prehistory of the Staatliche Museen zu Berlin, Stiftung Preussicher Kulturbesitz.

In total, the authors recovered partial genomes from 90 individuals, and genome-wide datasets from three individuals. They were able to use the data gathered to test previous hypotheses drawn from archaeological and historical data, and from studies of modern DNA.

“In particular, we were interested in looking at changes and continuities in the genetic makeup of the ancient inhabitants of Abusir el-Meleq,” said Alexander Peltzer, one of the lead authors of the study from the University of Tübingen.

The team wanted to determine if the investigated ancient populations were affected at the genetic level by foreign conquest and domination during the time period under study, and compared these populations to modern Egyptian comparative populations.

“There is literary and archaeological evidence for foreign influence at the site, including the presence of individuals with Greek and Latin names and the use of foreign material culture,” said co-author W. Paul van Pelt from Cambridge’s Division of Archaeology. “However, neither of these provides direct evidence for the presence of foreigners or of individuals with a migration background, because many markers of Greek and Roman identity became ‘status symbols’ and were adopted by natives and foreigners alike. The combined use of artefacts, textual evidence and ancient DNA data allows a more holistic study of past identities and cultural exchange or ‘entanglement’.”

The study found that the inhabitants of Absur el-Meleq were most closely related to ancient populations in the Levant, and were also closely related to Neolithic populations from the Anatolian Peninsula and Europe. “The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1,300 year timespan we studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule,” said Wolfgang Haak, group leader at the Max Planck Institute for the Science of Human History, and a co-author of the paper.

The data shows that modern Egyptians share approximately 8% more ancestry on the nuclear level with sub-Saharan African populations than the inhabitants of Abusir el-Meleq, suggesting that an increase in sub-Saharan African gene flow into Egypt occurred within the last 2,000 years. Possible causal factors may have been improved mobility down the Nile River, increased long-distance trade between sub-Saharan Africa and Egypt, and the trans-Saharan slave trade that began approximately 1,300 years ago.

Reference:
​Verena J. Schuenemann et al. ‘Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods.’ Nature Communications (2017). DOI: 10.1038/ncomms15694

​Adapted from a press release from the Max Planck Institute for the Science of Human History.