3D-model of the human body. Credit: Michael Strck
The Nile Valley is an important genetic and cultural crossroads, and the first genome-wide ancient human DNA data from Sudan reveals new insights into the ancestry and social organization of people who lived there more than 1,000 years ago.
Nature Communications published the results of the analysis of the 66 individuals' genes from a site in ancient Nubia, located on the Nile River in Sudan, just south of the Egyptian border.
There were only three ancient genome-wide samples available from Egypt before this work, says the first author, who began the project as a PhD student. The region is an incredibly important part of the world in terms of the movement, meeting and mixing of people.
Sirak was the last graduate student of George Armelagos, a pioneer in the field of archeology and biology. Armelagos was part of a team that excavated ancient skeletons from Sudanese Nubia so they wouldn't be lost forever when the Nile was dammed.
"Nubia was a place of human habitation for tens of thousands of years," says Sirak, who is now a staff scientist at Harvard University. The ancient genetic data fills in some major gaps in our understanding of who these people were.
The 66 individuals are from the Christian Period of Sudanese Nubia before the introduction of Islam. The analyses showed how the Kulubnarti gene pool formed over the course of a millennium. Today, they have their ancestry seen in some populations of Sudan, as well as the ancestry that was originally from West Eurasian and introduced into Nubia through Egypt.
Jessica Thompson, a co-senior author of the paper, says that social status did not have a strong relationship to biological relatedness or ancestry in the ancient population. Thompson was a supervisor of Sirak in the Department of Anthropology.
The remains of the individuals came from two cemeteries with Christian-style burials. The average age of those buried in a cemetery on an island in the Nile was just over 10 years old. The average age at death in the other cemetery was 18 years.
One hypothesis was that the island cemetery was for the Kulubnarti "underclass" who were buried in the mainland cemetery. It was not clear if the social stratification was developed because of one population or if it was due to another population.
The people buried in the separate cemeteries came from a single genetic population, according to a genome-wide analysis.
Thompson says that people in this area did not use biological ancestry as a basis for social differentiation. This reinforces the point that the recent phenomenon of dividing people up on the basis of their genetic ancestry is not universal.
The genetic analyses show that some people were buried across the cemetery divide. Second degree relationships include grandparents to granddaughters, aunts and uncles to niece and nephews, and half siblings.
Sirak says that it indicates that there was some movement among the two groups of people. Someone was not prescribed to be in the same social group as all of their relatives because of an intergenerational caste system.
A further interesting twist is that most of the ancestry within the population came from women. Sirak says that when you think of ancestry and how genes move, you think of males who are trading or conquering or spreading religion. The genetic data shows that female mobility was important in shaping the genes.
One possible explanation is that males tended to stay where they were born and females moved away from their homelands.
Sirak says the Christian Period Nubians are fascinating. They lived in a barren, isolated, desolate region where life was never easy. I think that the ancient DNA research is giving a new life to the people from 1000 years ago, by giving them a more nuanced view of them. You owe it to them to tell the most accurate, respectful and meaningful story that you can when you're studying someone's remains.
Sirak was a graduate student at the time studying human bones and paleopathology. He and other faculty members built the Department of Anthropology into a powerhouse of the biocultural approach to the field. Armelagos, his colleagues and graduate students studied the remains of the Sudanese Nubians to learn more about their past.
Genetic analysis was missing from the studies of this population. Sirak was sent to the University College Dublin with samples of the Nubian bones.
Sirak had no interest in genetics, but George was a visionary who believed that DNA was going to become a critical part of anthropological research.
Sirak was attracted to the idea of combining her interest in ancient bones with her knowledge of DNA. She collaborated with other people at Harvard Medical School's Department of Genetics and other places to investigate mysteries surrounding deaths going back to ancient times.
Sirak was Armelagos' last graduate student and he died of Pancreatic Cancer in 2014). Sirak's mentorship was taken over by Dennis Van Gerven, an anthropology professor at the University of Colorado at Boulder. Van Gerven studied the Sudanese Nubians for decades while he was a student at Armelagos.
Sirak's project was to collect enough ancient DNA from the Nubian remains for analysis.
She says that ancient DNA is difficult to recover from areas that are very hot.
Sirak was working at the forefront of the effort to improve genetic sequencing techniques. She was among the researchers who realized that a particular part of the petrous bone consistently yielded the most DNA. There are parts of the inner ear that are related to hearing and balance. Sirak developed a technique to drill into a skull and reach a specific part of the petrous bone in the most non-invasive way possible, while also getting enough bone powder for DNA analysis. The use of this part of the petrous bone is the gold standard in ancient DNA analysis.
Sirak received her PhD from Emory University in the fall of 2018, and then worked in the lab of David Reich, a geneticist at Harvard Medical School who specializes in the population genetics of ancient humans.
She and her colleagues continued to push the boundaries of what is possible with ancient DNA sequencing. They were able to get whole-genome samples from the petrous bones of 66 Sudanese Nubians. Sirak says that they would not have succeeded in the work if they had not focused on the part of the petrous bone.
She says that George asked her to focus on ancient DNA in 2012 before the techniques were developed. "He made anyone who was working with him feel important and powerful and that gave me the confidence to strike out on a new path."
Thompson said that George Armelagos' influence is everywhere, and that he advised many senior people who helped her early in her career.
Funded by National Geographic Explorer grants, Sirak is now working with Sudanese colleagues to gather and analyze ancient DNA samples from other geographic locations in the Nile Valley, going even deeper into its past, to add more details to the story of how people moved, mixed and thrived in the region across millennia
Sirak was the last graduate student of Armelagos and a mentor of Van Gerven, one of Armelagos' first students. The current paper is the realization of Armelagos' last wishes.
Sirak says it's special to be able to use ancient DNA to build on decades of anthropological and archeological research for the region. I know that George would be happy. I'm a part of this amazing group of researchers. The desire to continue what they started is a huge motivation for me.
The senior authors of the Nature Communications paper include Reich, Thompson and Van Gerven. The University of Vienna, the University of Coimbra in Portugal, the Howard Hughes Medical Institute, the University of Georgia, the University of California, Santa Cruz, and the University of Michigan are also co-authors.
The site of Kulubnarti in Christian Period Nubia was the subject of a paper by Sirak and colleagues. There is a DOI of 10.1038/s41467-021-2735.
Nature Communications is a journal.
The first genome-wide ancient human DNA from Sudan was retrieved on December 17th, 2021.
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