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Researchers Successfully Sequence Mitochondrial Genomes from Egyptian Mummies

Sarcophagus of Tadja, Abusir el-Meleq

NEW YORK (GenomeWeb) – Sequence data from dozens of ancient samples suggests Egyptian mummies may have been more closely related to individuals in present-day Jordan, Lebanon, Yemen, and other sites in the Near East than to populations residing in Egypt today.

An international team led by investigators in Germany sequenced mitochondrial genomes from 90 Egyptian mummies at an archaeological site called Abusir el-Meleq. The group also generated SNP data for three of the mummies, comparing sequence and SNP data for the mummies with available mitochondrial genome sequence data for hundreds of individuals from ancient and present-day populations in Egypt and Ethiopia.

As they reported in Nature Communications, the researchers found that the remains, which ranged in age from nearly 1,600 to more than 3,400 years, provided a look at populations that moved through the region and transitions between Pre-Ptolemaic, Ptolemaic, and Roman Periods. More generally, their results suggest that such samples can yield useful genetic information, despite conditions considered sub-optimal for DNA preservation.

"[O]ur results revise previous skepticism towards the DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures," co-corresponding authors Johannes Krause, Stephan Schiffels, and Wolfgang Haak, at the University of Tubingen and/or Max Planck Institute for the Science of Human History, and their colleagues wrote. "The methodology presented here opens up promising avenues for future genetic research and can greatly contribute towards a more accurate and refined understanding of Egypt's population history."

The team focused on ancient samples from present-day Egypt, where populations from nearby and far-flung locales have come together over different periods of time during historical human migrations. Given Egypt's location and population interactions documented there, the authors called it "an ideal region to study population dynamics."

"Especially from the first millennium BCE onwards, Egypt saw a growing number of foreigners living and working within its borders and was subjected to an almost continuous sequence of foreign domination by Libyans, Assyrians, Kushites, Persians, Greeks, Romans, Arabs, Turks, and Brits," the authors wrote. "The movement of people, goods, and ideas throughout Egypt's long history has given rise to an intricate cultural and genetic exchange and entanglement, involving themes that resonate strongly with contemporary discourse on integration and globalization."

Starting from bone, soft tissue, or tooth samples from mummies at the Abusir el-Meleq site, the researchers amplified ancient DNA libraries for 151 individuals and enriched for human mitochondrial DNA with bead capture hybridization before sequencing the ancient genetic material with the Illumina HiSeq 2500 instrument. They also used a custom SNP in solution capture tool called pileupCaller to profile 1.24 million variants in the nuclear genome in samples from 40 mummies that had yielded especially high levels of mtDNA, generating profiles at between 132,000 and more than 508,300 SNPs apiece for three of the male mummies.

Despite the influence of potentially DNA-degrading temperature, humidity, and mummification chemicals, the team was able to generate 11-fold to more than 4,200-fold coverage of the mitochondrial genomes. The sequences were subsequently compared with 100 modern Egyptian individuals, 125 Ethiopian individuals, and individuals from other modern and ancient populations in the region to uncover ties between the mummified Egyptian samples and the ancient populations.

But the mummies also shared mitochondrial genome similarities with current populations in the Levant and Near East, the researchers reported — and those findings were further supported when they folded in information from the mummies' nuclear genomes and genomes from thousands of sequenced individuals from ancient and modern populations.

In general, the authors noted that they obtained similar levels of DNA from mummy bone or teeth samples, though soft tissue from the mummies tended to contain far less preserved DNA.