Genome-wide DNA technology promises greater insights into how ancient cultures survived and thrived. In an interdisciplinary study published on February 23, 2022, in the journal Nature (“Ancient DNA reveals deep population structure in sub-Saharan African foragers“), a collaborative team of archaeologists, geneticists, conservationists and curators outline their findings from the analysis of human remains from African archaeological sites in Malawi in Tanzania and Zambia. The remains of six individuals dating back to between 18,000 and 5,000 years ago, that are analyzed in the study are the earliest DNA dataset from the continent to date.

“This more than doubles the antiquity of reported ancient DNA data from sub-Saharan Africa,” said David Reich, PhD, professor at Harvard University, investigator at the Howard Hughes Medical Institute and senior author of the paper.

In addition to the new genetic data, the study reanalyzed published data from 28 other African remains, improving the DNA dataset for 15 ancient African foragers. Although earlier studies have provided genetic and archaeological evidence suggesting significant changes in Sub-Saharan African populations in the Late Pleistocene and early Holocene periods around 125 to 12 thousand years ago, it is difficult to arrive at inferences about this period due to largescale migrations and admixtures in the past 5000 years.

The improved data reported in the current study enabled the team to outline major demographic shifts that occurred about 80,000 and 20,000 years ago. The results show, about 50,000 years ago, people from different regions of the continent moved and settled in other areas and developed social networks over longer distances to trade, communicate and mate. In addition to a ubiquitous central African ancestry, the study shows that the individuals in the current study came from at least three different populations.

“We’ve never been able to directly explore these proposed demographic shifts, until now,” said Elizabeth Sawchuk, PhD, a Banting postdoctoral Fellow at the University of Alberta and research assistant professor at Stony Brook University who is an author of the study. “It has been difficult to reconstruct events in our deeper past using the DNA of people living today, and artifacts like stone tools and beads can’t tell us the whole story. Ancient DNA provides direct insight into the people themselves, which was the missing part of the puzzle.”

The limited long-rage gene flow in the data also shows, about 20,000 years ago the population structure was stable indicating people had stopped moving around to the extend they did earlier. Sawchuk said, “Maybe it was because by that point, previously established social networks allowed for the flow of information and technologies without people having to move.”

Jessica Thompson, PhD, assistant professor of anthropology at Yale University who was one of the authors of the paper who uncovered the remains said, “Our genetic study confirms an archaeological pattern of more local behavior in eastern Africa over time. At first people found reproductive partners from wide geographic and cultural pools. Later, they prioritized partners who lived closer, and who were potentially more culturally similar.”

Mary Prendergast, PhD, an associate professor of anthropology at Rice University is a senior author of the paper.

Mary Prendergast, PhD, an associate professor of anthropology at Rice University and an author of the paper said there are arguments that the development and expansion of long-distance trade networks around this time helped humans weather the last Ice Age. “Humans began relying on each other in new ways. This creativity and innovation might be what allowed people to thrive.”

Predergast said, “By applying the latest methods to extract and sequence ancient DNA from archaeological human skeletons, this study breaks the tropical ceiling, doubling the antiquity of ancient DNA from sub-Saharan Africa, where accessing the deep past is challenging due to warm and humid conditions that degrade DNA.”

Potiphar Kaliba, PhD, director of research at the Malawi Department of Museums and Monuments and an author of the study said, “This work shows why it’s so important to invest in the stewardship of human remains and archaeological artifacts in African museums.” The current study used skeletal samples for DNA analysis that were excavated nearly 50 years ago and have been preserved despite the heat and humidity of the tropics, Kaliba noted.

“The work also helps address global imbalances in research”, Prendergast said. “Despite having the greatest genetic diversity on the planet, and being the cradle of human origins, Africa remains understudied in archaeogenetics, with fewer than 1% of ancient human genomes coming from the continent. There are around 30 times more published ancient DNA sequences from Europe than from Africa. Given that Africa harbors the greatest human genetic diversity on the planet, we have much more to learn.”

John Yellen, PhD, Program Director of Archaeology and Archaeometry at the U.S. National Science Foundation (NSF) said, “By associating archaeological artifacts with ancient DNA, the researchers have created a remarkable framework for exploring the prehistory of humans in Africa.” Radiocarbon dating analysis in the study was funded by the NSF Archaeometry program.

Prendergast said, this work was made possible by strong collaborations with African scholars across disciplines including archaeology, genetics, and museum curation. The large interdisciplinary team included scholars from Canada, Kenya, Malawi, Tanzania, the United States, Zambia and other countries.