Africa proved a bigger challenge. There were fewer skeletons in museums, and most searches for genetic material failed. The environment was partly to blame: DNA is more likely to survive in colder places.
“It’s been mad, watching all the advances in what we understand about European prehistory,” said Jessica C. Thompson, an archaeologist at Emory University who does field work in Malawi.
Dr. Thompson was heartened by the discovery of ancient DNA in Ethiopia in 2015. Those scientists succeeded for two reasons: The skeleton they discovered had been lying for thousands of years in a cool cave in the Ethiopian highlands, and the researchers developed new technological methods increasing the odds of finding even tiny bits of DNA.
More recently, Dr. Thompson teamed up with experts in ancient DNA and began searching for skeletons in Malawi. Much of the country comprises tropical lowlands, but it also includes high-elevation plateaus where nighttime temperatures can plunge below freezing.
Eventually she and her colleagues discovered DNA-bearing skeletons as old as 6,000 years in caves in the highlands. Other bones were discovered by archaeologists working in African countries, as well as in museum collections.
David Reich, a geneticist at Harvard Medical School and a co-author of the new study, and his colleagues analyzed DNA from 16 of these fossils, along with the one previously found in Ethiopia, comparing the genetic material to that of living people throughout Africa as well as on other continents.
This analysis allowed them to determine how living Africans descended from ancient populations, which are older in Africa than anywhere else on Earth.
“Africa is now going to be fully included in the ancient genomics revolution,” Dr. Reich said. “We’re going to be able to do a lot of things in Africa that we’ve been able to do in Europe and elsewhere.”
Africa is where our species evolved at least 300,000 years ago. Previous genetic analysis of living Africans had suggested that their ancestors began splitting into distinct groups over 200,000 years ago. Roughly 70,000 years ago some Africans moved out of Africa, becoming the ancestors of non-Africans.
In earlier studies, researchers had concluded that the hunter-gatherers who live today in the Kalahari Desert and other parts of southern Africa descend from the branch believed to be the first to have divided from other Africans.
But the new study suggests that there may be even older branches in the tree. “Something more complicated is going on,” Dr. Reich said.
Dr. Reich and his colleagues found that some people in West Africa share a unique collection of genetic variants that suggest an even deeper ancestry, raising the possibility that an earlier population of humans in West Africa diverged from rest.
“That’s quite a big new idea,” Dr. Busby said.
The new study also sheds light on exactly which Africans spread to other continents. The 4,500-year-old Ethiopian man discovered in 2015 had DNA linking him to non-Africans.
Today, only a single, small population of living Africans shares the same genetic link: Tanzanian hunter-gatherers called the Hadza.
“They’re the group of living Africans most closely related to non-Africans,” Dr. Reich said.
Once humans expanded out of Africa, there was little or no flow of genes between Africans and non-Africans for tens of thousands of years, the new study indicates.
But Dr. Reich and his colleagues discovered that a 3,100-year-old girl in Tanzania was profoundly different from the older East Africans. A third of her ancestry could be traced to early farmers in the Near East.
Previous studies of living East Africans had hinted at some Near Eastern ancestry. But the new analysis shows that people from the Near East spread into East Africa at least 3,100 years ago.
“This puts a time stamp on this connection,” said Pontus Skoglund, a postdoctoral researcher in Dr. Reich’s lab and co-author of the new study.
Near Eastern genes were also found in a skeleton from South Africa about 1,200 years old; according to the researchers, some living South Africans carry this DNA today.
In all, these genetic patterns suggest that early farmers or herders from the Near East swept down through Egypt into East Africa several thousand years ago. They then kept expanding over the centuries until their descendants reached the southern edge of the continent.
Around the same time, another expansion driven by agriculture was taking place in West Africa.
A people known as the Bantu spread from the region around present-day Cameroon and Nigeria. They left a trail of distinctive iron tools that archaeologists have used to trace their migration into southern and eastern Africa about 2,000 years ago.
Archaeologists have studied this expansion for decades to learn what happened as the Bantu arrived in other parts of the continent. The new genetic findings suggest that in some places, they may have pushed out the hunter-gatherers.
Up until 2,000 years ago, Dr. Thompson and her colleagues found, people in Malawi belonged to the same ancestral group as hunter-gatherers in southern Africa. “This was a hugely widespread population,” she said.
But something happened: Living Malawians have no genetic connection to those who lived there before. These ancient people must have disappeared virtually without descendants in Malawi.
It’s possible, Dr. Thompson said, that Bantu farmers drove hunter-gatherers out of places like Malawi. The surviving hunter-gatherers ended up in deserts and other places that weren’t good for crops and livestock.
In East Africa, the transition may not have been so stark. There, modern people can trace much of their ancestry to the Bantu, suggesting a blending of populations.
But some people also inherited a mix of other ancestries, including genes from the Near East and some from the ancient East African hunter-gatherers.
Dr. Thompson is now digging into archaeological sites for evidence of the Bantu arrival in Malawi, looking for tools, bones and perhaps even more DNA.
“We want to see if we can catch the timing of that transition and see if there was trade between the groups, or if the whole area was taken over,” she said.
Ancient DNA in skeletons from western Africa would be just as valuable; it may hold profound secrets about the early history of our species.
But it won’t be easy to find: The early archaeological record there is sparse, and there are few cold caves to search. “It is the major gap in our ancient DNA coverage,” Dr. Skoglund said.
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