Genome-wide ancient human DNA data from Sudan reveals new insights into the Nile Valley past

The first genome-wide ancient human DNA data from Sudan reveals new insights into the ancestry and social organization of people who lived more than 1,000 years ago in the Nile Valley, an important genetic and cultural crossroads.

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

"Before this work, there were only three ancient genome-wide samples available, from Egypt, for the entire Nile Valley," says first author Kendra Sirak, who began the project as a PhD student at Emory University. "And yet the region was, and still 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 the late George Armelagos, former professor of anthropology at Emory and a pioneer in bridging the disciplines of archeology and biology. While still a graduate student in the 1960s, Armelagos was part of a team that excavated ancient skeletons from Sudanese Nubia, so the bones would not 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. "This ancient genetic data helps fill in some major gaps in our understanding of who these people were."

The 66 individuals date back from 1,080 to 1,320 years ago, during the Christian Period of Sudanese Nubia, prior to the genetic and cultural changes that occurred along with the introduction of Islam. The analyses showed how the Kulubnarti gene pool formed over the course of a least a millennium through multiple waves of admixture, some local and some from distant places. They had ancestry seen today in some populations of Sudan, as well as ancestry that was ultimately West Eurasian in origin and likely introduced into Nubia through Egypt.

A key finding is that social status did not have a strong relationship to biological relatedness or to ancestry in this ancient population, who lived during a period of cultural and social change."

Jessica Thompson, co-senior author of the paper

Thompson, a former PhD supervisor of Sirak in Emory's Department of Anthropology, is now at Yale University.

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

One hypothesis that grew out of this skeletal evidence was that the island cemetery was for a Kulubnarti "underclass," possibly laborers for members of landowning families buried in the mainland cemetery. It was a mystery whether the social stratification may have developed because one population came from a different origin.

A genome-wide analysis suggests that was not the case -; the people buried in the separate cemeteries came from a single genetic population.

"It seems that people in this area did not use biological ancestry as a basis for social differentiation," Thompson says. "This reinforces the point that dividing people up socially on the basis of their genetic ancestry is a recent phenomenon, with no basis in universal human tendences."

Another key finding of the genetic analyses shows that some people as close as second-degree relatives were buried across the cemetery divide. Examples of second-degree relationships include grandparents to grandchildren, aunts and uncles to nieces and nephews, and half siblings.

"That indicates that there was some fluidity among the two groups of people," Sirak says. "There wasn't an intergenerational caste system that meant someone was prescribed to being in the same social group as all of their relatives."

A further interesting twist is that much of the Eurasian-derived ancestry within the population came from women. "Often when you think of ancestry and how genes move, you think of males who are trading or conquering or spreading religion," Sirak says. "But the genetic data here reveals that female mobility was really crucial to shaping the gene pool in Kulubnarti."

One possible explanation is that Kulubnarti was a patrilocal system, meaning that males tended to stay where they were born and females moved away from their homelands.

"The Christian Period Nubians from Kulubnarti are fascinating," Sirak says. "They survived in a barren, isolated, desolate region where life was never easy. I like to think that the ancient DNA research is giving a new life to these people from 1,000 years ago by providing a more nuanced view of them. Anytime you're studying someone's remains, their physical being, you owe it to them to tell the most accurate, respectful and meaningful story that you can."

Sirak came to Emory as a graduate student in 2012 to study human bones and paleopathology under Armelagos. By that time, he and fellow faculty members had built Emory's Department of Anthropology into a powerhouse of the biocultural approach to the field. In particular, Armelagos, his colleagues and graduate students studied the remains of the Sudanese Nubians to learn about patterns of health, illness and death in the past.

A long missing piece in the 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 samples of the Nubian bones.

"I had no interest in genetics," Sirak recalls, "but George was a visionary who believed that DNA was going to become a critical part of anthropological research."

Sirak soon became hooked when she saw how she could combine her interest in ancient bones with insights from DNA. She formed collaborations not just in Dublin but at Harvard Medical School's Department of Genetics and elsewhere, investigating mysteries surrounding deaths going back anywhere from decades to ancient times.

Armelagos was 77 and still mentoring Sirak, his last graduate student, when he died of pancreatic cancer in 2014. Dennis Van Gerven, an emeritus professor of anthropology at the University of Colorado at Boulder, took over Sirak's mentorship, along with Thompson. Van Gerven was among Armelagos' first group of students, and he also spent decades studying the Sudanese Nubians.

Sirak stuck with her PhD dissertation project of trying to collect enough ancient DNA from the Nubian remains for analysis.

"Ancient DNA is difficult to recover from areas that are extremely hot, because DNA tends to degrade in heat," she explains.

Genetic sequencing techniques kept improving, however, and Sirak was working at the forefront of the effort. In 2015, while still an Emory graduate student, she was among the researchers who realized that a particular part of the petrous bone consistently yielded the most DNA. This pyramid-shaped bone houses several parts of the inner ear related to hearing and balance. In addition, Sirak developed a technique to drill into a skull and reach this particular 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 now the gold standard in ancient DNA analysis.

In 2018, Sirak received her PhD from Emory and went on to work 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's possible with ancient DNA sequencing. They managed to get whole-genome samples from the petrous bones of 66 of the Sudanese Nubians, ushering in a whole new era of bioarchaeology for the Nile Valley. "I don't think we would have succeeded in this work had we not known to focus on the specific part of the petrous bone," Sirak says.

"It's incredible to me that George asked me to focus on ancient DNA back in 2012, long before these techniques were developed," she adds. "He had a way of making anyone who was working with him really feel important and powerful and that gave me the confidence to strike out on a pioneering path."

"George Armelagos' influence is everywhere," adds Thompson, explaining that he also advised many senior people who mentored 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.

As the last graduate student of Armelagos -; and then a mentee of Van Gerven, one of Armelagos' first students -; Sirak feels like she is completing a circle. The publication of the current paper 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 archeological research for the region," Sirak says. "I know that George would be proud and thrilled. I'm part of this amazing lineage of researchers now. And the desire to continue what they started is a huge motivation for me."