Ancient skeletons reveal clues to Africa's past

It was only two years ago that researchers found the first ancient human genome in Africa: a skeleton in a cave in Ethiopia yielded DNA that turned out to be 4,500 years old. Recently, a team of scientists reported that they had recovered far older genes from bone fragments in Malawi dating back 8,100 years. The researchers also retrieved DNA from 15 other ancient people in eastern and southern Africa, and compared the genes with those of living Africans. Their analysis, published in the journal Cell, reveals important clues to Africa’s mysterious prehistory, including details of massive migrations that shaped the populations we know today.

Europe was the first place where scientists were able to use ancient DNA to illuminate the deep past. Huge archaeological collections in museums held DNA that, once reconstructed, shed light on the genetic prehistory of the continent as far back as 40,000 years. Africa proved to be 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, USA.

Jessica 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, Jessica 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.

David Reich, a geneticist at Harvard Medical School, USA and co-author of the new study, and his colleagues analysed DNA from 16 of these fossils, along with the one previously found in Ethiopia, comparing the genetic material with that of living people throughout Africa and 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,” David 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 3,00,000 years ago. Previous genetic analysis of living Africans had suggested that their ancestors began splitting into distinct groups more than 2,00,000 years ago. Roughly 70,000 years ago some Africans moved out of Africa, becoming the ancestors of non-Africans. The new study also sheds light on exactly which Africans spread to other continents.

Little flow of genes

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 David 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. Near Eastern genes were also found in a skeleton from South Africa about 1,200 years old. 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. It’s possible, Jessica 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.