Ancient African genome offers migration clues for the first humans.

Nature shares DNA research on the remains of four children in what is now Cameroon, revealing clues about how they lived and where they came from thousands of years ago:

he findings underscore the yawning gap in scientists’ understanding of African population history, relative to that of Eurasia, the Americas and even Oceania. Researchers have sequenced more than 1,000 ancient human genomes from these regions, versus fewer than 80 from Africa, few of which are older than 10,000 years.

“We don’t have a clear picture right now,” says David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, who co-led the study. “Africa is the most diverse place on Earth. It’s where our particular sub-lineage of humans originated.” It’s no surprise, he adds, that even the relatively recent history of its populations is hard to decipher today.

Researchers led by Reich and Mary Prendergast, an archaeologist at Saint Louis University — Madrid Campus and Harvard Medical School, analysed remains from a rock shelter in Cameroon called Shum Laka. The cave-like site holds human remains that are up to 30,000 years old, but Reich and Prendergast only managed to obtain sufficient quantities of DNA to generate full genomes for two young boys, who lived 8,000 and 3,000 years ago. They also collected more limited genome data from a boy and a girl from the same periods, respectively. A genetic analysis, published on 22 January in Nature, suggests that the boy and girl from 3,000 years ago were second-degree relatives, such as half-siblings or an uncle and niece. The 8,000-year-old pair were fourth-degree relatives, perhaps distant cousins.

Despite a gap of 5,000 years in some cases, all four of the children’s genomes were remarkably similar to one another. But compared with the DNA of modern Africans, their genomes were more closely related to those of the hunter-gatherer groups in west central Africa that are sometimes known as Pygmies than they were to those of contemporary Cameroonians or other Bantu-speaking populations.

The disconnect between remains from Shum Laka and contemporary Bantu speakers was surprising, says Reich, and it suggests that the population the ancient children belonged to was not among those that migrated out of the area during the Bantu expansion. It’s possible that other groups from the area carried Bantu languages around Africa, but Reich says his team’s data should encourage researchers to explore whether the migration began elsewhere — perhaps further west, in present-day Nigeria.

The four children seem to descend from a group of Homo sapiens that branched off from the common ancestors of our species more than 200,000 years ago — perhaps even earlier than the ancestors of distinct Indigenous southern African groups known collectively as Khoesan peoples. Previous studies of modern human genomes had suggested that these groups descended from the oldest distinct lineage of Homo sapiens.

The Shum Laka genomes helped Reich and his colleagues to identify other early events, including the establishment of distinct lineages belonging to West Africans, East Africans and the ancestors of all non-Africans, as well as later splits among the ancestors of contemporary West Africans.