Africa is the birthplace of our species, but ancient DNA from the continent has so far provided relatively few clues to our history there, partly because researchers have struggled to recover genetic samples that survived the hot, humid climate. Now, an analysis of ancient DNA from six individuals from southeastern Africa offers a glimpse of the lives, movements, and relations of people who occupied the continent between 18,000 and 5000 years ago; it also hints at the complex commingling of African populations even further back. For instance, the work suggests that during the last ice age, some African societies may have become more sedentary and isolated as their environments fragmented.
The study, published today in Nature, is “terrific,” says Susan Pfeiffer, an anthropologist emeritus at the University of Toronto. “It’s like a little hint of what I hope will be a wonderfully rich story.”
To get a clearer picture of ancient Africa, a team led by North American researchers and including 13 scientists from five African nations analyzed samples from the remains of four infants and two adults buried in Malawi, Tanzania, and Zambia. The team managed to extract enough DNA to partially sequence the genomes. Five samples came from inner ear bones, which are dense and preserve DNA well.
Two infant boys from the Hora rock shelter in Malawi were buried on their sides in a flexed position about 14,000 years ago. “I spent a lot of time thinking about the circumstances that led to them dying so young and … about how carefully their communities had interred them,” says Yale University anthropologist Jessica Thompson, who led the Hora excavation in 2019. The most recent remains, of an adult woman from Zambia’s Kalemba rock shelter, were radiocarbon dated to about 5000 years ago. The oldest remains belonged to a woman found in Tanzania’s Mlambalasi rock shelter amid ostrich eggshell beads radiocarbon dated to about 18,000 years ago. Previously, the oldest human genome from sub-Saharan Africa was 9000 years old.
Thompson and colleagues analyzed the six new partial genomes plus 28 previously reported from across the continent. The team ran the data through a computer program that compares similar snippets of DNA to estimate relatedness; they reconstructed a rough family tree dating back 18,000 years.
Their model suggests the 34 individuals descend from three major source populations. Two of them, from northeastern Africa and southern Africa, were already known. But the third population, from Central Africa and most closely related to people today who live a foraging lifestyle there, came as a surprise.
The distinct genetic signatures of those ancestral populations indicate they were mostly isolated from one another for vast amounts of time before eventually coming together, suggests David Reich, a population geneticist at Harvard Medical School who co-led the study. “If you look at Europeans and East Asians, maybe they’re separated by 40,000 or 50,000 years,” he says. “These three groups were basically separated 200,000 years ago, then come together … maybe 80,000 to 50,000 years ago.” That range is only a rough estimate, Reich notes, given none of the new genomes dates beyond 20,000 years ago.
But that time frame for commingling matches developments in material culture, says co-author Mary Prendergast, an archaeologist at Rice University. In African artifacts of that period, “we see a ton of hints that people are connecting in different ways,” she says, mixing and matching artifacts from distant places.
Considered in that context, the new DNA data suggest sometime after 20,000 years ago, ancient Africans stayed closer to home. Stone tools found in their rock shelters take on a local flair. And their DNA suggests that starting around this time, people traveled shorter distances to find mates.
That date range marks the Last Glacial Maximum, which affected climate worldwide, points out Rick Potts, a paleoanthropologist at the Smithsonian Institution’s National Museum of Natural History. Across tropical Africa, forests contracted and grasslands grew in between, forming fragmented savannalike “islands” for many species—perhaps humans among them. “It’s interesting to think about whether sub-Saharan African foragers were mapping onto a kind of refugium model.”
The six new genomes are a welcome addition to Africa’s sparse record of ancient DNA, says Sarah Tishkoff, a geneticist at the University of Pennsylvania. But she’s not swayed by the team’s ideas about what happened before 20,000 years ago. “There’s a lot of assumptions in that analysis,” she says, and it’s not clear to her that the authors considered alternative explanations.
The analysis included some remains from museums, highlighting the key role of collections, says study co-author Maggie Katongo, a curator at Zambia’s Livingstone Museum and a doctoral student at Rice University. “When you do this research, you want to give back to the community,” she adds. “We want to make sure that whatever comes from this research is made public for all people in Zambia.”