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Suda’s first ancient human DNA to scale the genome

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Sudan’s first genome-wide ancient human DNA data reveals new information about the ancestry and social organization of people who lived over 1,000 years ago in the Nile Valley, a major crossroads genetic and cultural.

Nature Communication has published DNA analyzes of 66 individuals from a site in ancient Nubia known as Kulubnarti, located on the Nile in Sudan, just south of the Egyptian border.

“Before this work, there were only three old genome-wide samples available from Egypt for the entire Nile Valley,” says first author Kendra Sirak, who started the project. as a doctoral student at Emory University. “And yet the region was, and still is, an incredibly important part of the world in terms of movement, meeting and mixing of people. “

Sirak was the last graduate student of the late George Armelagos, a former professor of anthropology at Emory and a pioneer in bringing the disciplines of archeology and biology together. While still a graduate student in the 1960s, Armelagos was part of a team that excavated ancient skeletons from Sudanese Nubia, so that the bones were not lost forever when the Nile was dammed.

“Nubia has been a place of human habitation for tens of thousands of years,” says Sirak, who is now a researcher at Harvard University. “These ancient genetic data help fill in some major gaps in our understanding of who these people were. “

The 66 individuals date from 1,080 to 1,320 years ago, during the Christian period of Sudanese Nubia, before the genetic and cultural changes that occurred with the introduction of Islam. The analyzes showed how the Kulubnarti gene pool was formed over at least a millennium through multiple waves of mixing, some local and others distant. They had ancestors seen today in some populations of Sudan, as well as ancestors that were ultimately of Western Eurasian origin and probably brought to Nubia from Egypt.

“A key finding is that social status did not have a close relationship with biological kinship or ancestry in this ancient population, which lived through a period of cultural and social change,” says Jessica Thompson, co-lead author of the article. Thompson, a former Sirak thesis supervisor in Emory’s Department of Anthropology, is now at Yale University.

The remains of the individuals came from two cemeteries with Christian-style burials which, according to previous evidence, were socially stratified. In a cemetery, located on an island in the Nile, the skeletal remains carried more markers of stress, disease and malnutrition, and the average age of those buried was just over 10 years old. In contrast, the average age at death in the other cemetery, located on the mainland, was 18.

One hypothesis that developed from this skeletal evidence was that the island’s cemetery was for an “underclass” of Kulubnarti, possibly laborers for family members of landowners buried in the cemetery of the continent. It was a mystery whether social stratification may have developed because a population came from a different origin.

Genome-wide analysis suggests this was not the case – the people buried in the separate cemeteries came from a single genetic population.

“It appears that the people of this region did not use biological ancestry as a basis for social differentiation,” says Thompson. “This reinforces the fact that the social division of people on the basis of their genetic ancestry is a recent phenomenon, without any foundation in universal human tendencies.”

Another key finding from DNA analyzes shows that some people as close as second-degree relatives were buried on the other side of the cemetery. Examples of second degree relationships include grandparents with grandchildren, aunts and uncles with nieces and nephews, and half-siblings.

“This indicates that there was a certain fluidity between the two groups of people,” Sirak says. “There was no intergenerational caste system which meant that someone had to belong to the same social group as everyone close to them. “

Another interesting twist is that much of the Eurasian ancestry within the population came from women. “A lot of times when you think of ancestry and the way genes move, you think of men who trade, conquer or propagate religion,” says Sirak. “But the genetic data here reveals that female mobility was really crucial in shaping Kulubnarti’s gene pool.”

One possible explanation is that the Kulubnarti was a patrilocal system, meaning that men tended to stay where they were born and women moved away from their home countries.

“The Nubians of the Kulubnarti Christian period are fascinating,” says Sirak. “They survived in an arid, isolated and desolate region where life has never been easy. I like to think that old DNA research is giving new life to these people of 1,000 years ago by giving them a more nuanced view. Whenever you study someone’s remains, their physical being, you owe it to them to tell the most accurate, respectful, and meaningful story possible.

Sirak came to Emory as a graduate student in 2012 to study human bones and paleopathology under Armelagos. By this time, he and other faculty members had made Emory’s anthropology department a powerhouse of the biocultural approach to the field. In particular, Armelagos, his colleagues and graduate students studied the remains of Sudanese Nubians to learn about patterns of health, disease and death in the past.

A long-missing piece in studies of this population, however, was genetic analysis. So in 2013, Armelagos sent Sirak to one of the best ancient DNA labs in the world, University College Dublin, with Nubian bone samples.

“I had no interest in genetics,” Sirak recalls, “but George was a visionary who believed that DNA would become an essential part of anthropological research. “

Sirak quickly became addicted when she saw how she could combine her interest in ancient bones with knowledge of DNA. She has formed collaborations not only in Dublin, but in the genetics department at Harvard Medical School and elsewhere, investigating the mysteries surrounding the deaths stretching back decades to antiquity.

Armelagos was 77 years old and still mentored Sirak, his last graduate student, when he died of pancreatic cancer in 2014. Dennis Van Gerven, professor emeritus of anthropology at the University of Colorado at Boulder, a resumed mentoring from Sirak, with Thompson. Van Gerven was one of Armelagos’ first group of students, and he also spent decades studying Sudanese Nubians.

Sirak stuck to his doctoral thesis plan of trying to collect enough ancient DNA from Nubian remains for analysis.

“Ancient DNA is difficult to recover in extremely hot areas because DNA tends to degrade under heat,” she explains.

However, genetic sequencing techniques kept improving and Sirak was working at the peak of the effort. In 2015, while still a graduate student of Emory, she was among the researchers who realized that a particular part of petrous bone consistently produced the most DNA. This pyramid-shaped bone houses several parts of the inner ear related to hearing and balance. Additionally, Sirak has developed a technique to pierce a skull and reach that particular part of petrous bone in the most non-invasive way possible, while still obtaining enough bone powder for DNA analysis. The use of this part of petrous bone is now the gold standard in ancient DNA analysis.

In 2018, Sirak received his PhD from Emory and then worked in the lab of David Reich, a geneticist at Harvard Medical School who specializes in population genetics of ancient humans.

She and her colleagues have continued to push the boundaries of what is possible with ancient DNA sequencing. They succeeded in obtaining whole-genome samples from the petrous bones of 66 Sudanese Nubians, ushering in a whole new era of bioarchaeology for the Nile Valley. “I don’t think we would have been successful in this job if we hadn’t been able to focus on the specific part of the petrous bone,” Sirak says.

“It’s amazing to me that George asked me to focus on ancient DNA in 2012, long before these techniques were developed,” she adds. “He had a way to make everyone who worked with him feel really important and powerful and that gave me the confidence to embark on a path of pioneer.”

“George Armelagos’ influence is everywhere,” adds Thompson, explaining that he has also counseled many of the seniors who mentored him early in her career.

Funded by grants from National Geographic Explorer, Sirak is now working with Sudanese colleagues to collect and analyze ancient DNA samples from other geographic locations in the Nile Valley, digging deeper into his past, to add more details to the story of how people moved, mixed and prospered in the region for millennia.

As the last student to graduate from Armelagos – then a mentee of Van Gerven, one of the first Armelagos students – Sirak feels like she has come full circle. The publication of this document is the realization of Armelagos’ last wishes for the project.

“It’s really special for me to be able to use ancient DNA to build on decades of anthropological and archaeological research for the area,” Sirak said. “I know George would be proud and happy. I am now part of this incredible lineage of researchers. And the desire to continue what they started is a huge motivation for me.

In addition to Reich, Thompson and Van Gerven, the main authors of the Nature Communications article include Nick Patterson (Broad Institute of Harvard and MIT) and Ron Pinhasi (University College, Dublin). Co-authors include researchers from these institutions as well as the University of Vienna, the University of Coimbra in Portugal, the Howard Hughes Medical Institute, the University of Pompeu Fabra in Barcelona, ​​the University of Georgia, the University of California, Santa Cruz, and University of Michigan.



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