Today, our study “Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods” got published in Nature Communications. After initial doubts that enbalmed mummies even contain any authentic DNA, we were able to extract valid and authentic DNA from bone and teeth material using well-established NGS methods such as mitochondrial capture (Maricic et al 2010) and nuclear 1240K capture (see Haak et al 2015 for details).
One of the biggest concerns researchers in the area of aDNA have, is the authentication of the obtained material on a molecular level. Recent advances in in-silico authentication methods such as schmutzi (Renaud et al 2015) and X-chromosomal authentication tests available in toolkits such as ANGSD (Korneliussen et al 2014), enabled us to perform in depth authentication of the obtained samples. Contamination is definitely still a problem for lots of samples and we found some samples to be unusable, similar to previous findings by other researchers in different contexts. The big difference however: There are methods to distinguish between contaminated samples and non-contaminated samples now. This especially helps when screening lots of different samples for DNA content, ultimately narrowing down the search drastically.
In order to establish mummified material from Egyptian specimen for genetic analysis, we tested several types of tissue from the same individuals independently for DNA damage, obtained genome coverage and specifically contamination. An expected outcome was, that the soft-tissue (skin, “flesh”) material showed much higher DNA damage than the bone or teeth material. In addition to this, the authentication methods on the mitochondrial level revealed typically very high contamination estimates for soft-tissue samples, which is also to some extent expected and could for example arise from the higher exposition of the soft tissue material to external contamination sources. In case you are interested, the publication is open access.
Ultimately, this means that studies focussing on resolving more of ancient Egyptian history will most likely try to obtain bone or teeth material, as soft tissue material is less likely to yield any authentic DNA (as Alex M. Kim already pointed out recently). I am quite confident that we will see much more updates on ancient Egyptian mummies in the upcoming future.
Verena Schuenemann, Alexander Peltzer, Beatrix Welte, Willem Paul van Pelt, Martyna Molak, Chuan-Chao Wang, Anja Furtwängler, Christian Urban, Ella Reiter, Kay Nieselt, Barbara Teßmann, Michael Francken, Katerina Harvati, Wolfgang Haak, Stephan Schiffels, and Johannes Krause Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods Nature Communications 8:15694 (2017): (doi: 10.1038/ncomms15694)
Renaud, Gabriel, et al. “Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.” Genome biology 16.1 (2015): 224.
Korneliussen, Thorfinn Sand, Anders Albrechtsen, and Rasmus Nielsen. “ANGSD: analysis of next generation sequencing data.” BMC bioinformatics 15.1 (2014): 356.
Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature 522.7555 (2015): 207-211.
Maricic, Tomislav, Mark Whitten, and Svante Pääbo. “Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.” PloS one 5.11 (2010): e14004.