Thursday, 1 June 2017

How Science Works - Ancient Egyptian DNA

Geographic context, of the samples used in this study.
Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods : Nature Communications

The thing about writing science books is that the moment you publish them they start to go out of date. The reason for this is obvious to anyone familiar with how science works and how knowledge is continually improving and being refined. Creationists, with their preference for certainty, no matter how false, over truth, this continual self-checking and self-revising nature of science is both baffling and disturbing.

As though to illustrate this point, no sooner had I put the finishing touches to my most recent book, "What Makes You So Special?", and submitted it for publication, than a paper was published that answered one of the mysteries that I alluded to in it. I had briefly covered, amongst other things, the origin of the Ancient Egyptians and their part of the human story. The mystery was who exactly the Ancient Egyptians were and where they came from.

The answer has been made possible by a new technique which has enabled DNA of sufficient quality to be extracted and compared to the DNA of other human groups. There is probably a lot more yet to come from these studies, including identifying what foreign incursions there were into Egypt in ancient times.

Abstract
Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Introduction
Egypt provides a privileged setting for the study of population genetics as a result of its long and involved population history. Owing to its rich natural resources and strategic location on the crossroads of continents, the country had intense, historically documented interactions with important cultural areas in Africa, Asia and Europe ranging from international trade to foreign invasion and rule. 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 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 globalization1.

Until now the study of Egypt’s population history has been largely based on literary and archaeological sources and inferences drawn from genetic diversity in present-day Egyptians. Both approaches have made crucial contributions to the debate but are not without limitations. On the one hand, the interpretation of literary and archaeological sources is often complicated by selective representation and preservation and the fact that markers of foreign identity, such as, for example, Greek or Latin names and ethnics, quickly became ‘status symbols’ and were adopted by natives and foreigners alike2,3,4. On the other hand, results obtained by modern genetic studies are based on extrapolations from their modern data sets and make critical assumptions on population structure and time5. The analysis of ancient DNA provides a crucial piece in the puzzle of Egypt’s population history and can serve as an important corrective or supplement to inferences drawn from literary, archaeological and modern DNA data.

Despite their potential to address research questions relating to population migrations, genetic studies of ancient Egyptian mummies and skeletal material remain rare, although research on Egyptian mummies helped to pioneer the field of ancient DNA research with the first reported retrieval of ancient human DNA6. Since then progress has been challenged by issues surrounding the authentication of the retrieved DNA and potential contaminations inherent to the direct PCR method7. Furthermore, the potential DNA preservation in Egyptian mummies was met with general scepticism: The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, in particular sodium carbonate, all contribute to DNA degradation and are thought to render the long-term survival of DNA in Egyptian mummies improbable8. Experimental DNA decay rates in papyri have also been used to question the validity and general reliability of reported ancient Egyptian DNA results9. The recent genetic analysis of King Tutankhamun’s family10 is one of the latest controversial studies that gave rise to this extensive scholarly debate11. New data obtained with high-throughput sequencing methods have the potential to overcome the methodological and contamination issues surrounding the PCR method and could help settle the debate surrounding ancient Egyptian DNA preservation8. However, the first high-throughput sequences obtained from ancient Egyptian mummies12 were not supported by rigorous authenticity and contamination tests.

Here, we provide the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing the authenticity of the retrieved ancient DNA via characteristic nucleotide misincorporation patterns13,14 and statistical contamination tests15 to ensure the ancient origin of our obtained data.

[...]


What was uncertain was whether the Ancient Egyptians were a Saharan people who had been pushed into the Nile Valley as the Sahara dried up, an African people who migrated down the Nile from Sudan or Ethiopia, or a people from the Middle East or Asia Minor, the descendants of earlier migrants out of Africa and now returning. One suggestion was that the Upper and Lower Kingdoms, based on Thebes (modern Luxor) and Memphis in the Nile Delta respectively, may not even have been the same people originally. The Upper Kingdom could have been populated by African people while the people of Lower Kingdom could have been Middle Eastern or North African.

This DNA study shows a couple of interesting things: firstly, the Ancient Egyptians were from outside of Africa, probably from the Middle East, Arabia and Asia Minor and secondly, there has been a large influx of Africans into Egypt in the post-Roman era. I know from experience that, as you travel south from Luxor to Aswan, the people become more African-looking. This is consistent with a migration of genes, if not actual people, from further south. The fact that ancient Egyptian DNA was from a mixture of people shows that, at least in that part of the world at that time, there was already considerable intermingling of peoples.

The study is a neat illustration of how improved scientific techniques lead to improved knowledge and so, in this case, to a better understanding of history.

Unfortunately, it means my book will need a small update in the next edition.

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