Ancient-genome studies grapple with Africa’s past – Nature.com

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Genome analysis of ancient people from Africa reveals a complicated migration history for the human species.

Ignored for too long by researchers, ancient humans who lived in Africa thousands of years ago are finally having their genomes studied. Two projects released results this week on the genomes of around 20 individuals, which together reveal that the history of our species on the continent was far more complex than previously thought.

Africas neglect until now by ancient-DNA researchers was largely down to the continents scorching climate. Because heat speeds the deterioration of DNA, scientists have focused on sequencing remains from cooler European sites and Siberian permafrost. The first success in Africa came in 2015 when researchers sequenced the genome of a 4,500-year-old man from Ethiopia who was preserved in a relatively chilly mountainous cave.

But advances in removing contamination and the discovery that a tinyinner ear bone is chock full ofancient DNA has convincedresearchers that the technology is finally ready to grapple withAfricas past.

Stephan Schiffels, a population geneticist at the Max Planck Institute for the Science of Human History, in Jena, Germany, says gaps in the knowledge of sub-Saharan African history are embarrassing especially in light of how much researchers know about ancient peoples in Eurasia. This makes it all the more important to use DNA to uncover Africa's hidden history of human migration, he says.

That is what a team led by Pontus Skoglund and David Reich, population geneticists at Harvard Medical School in Boston, Massachusetts, have now done. In a talk on 3 July at the Society for Molecular Biologys annual meeting in Austin, Texas, Skoglund said his team had examined the genomes of 15 ancient individuals and described detailed analysis of 11 of them who lived as long as 6,000 years ago in eastern and southern Africa.

They showed ancient humans moved around on the continent far more than was appreciated. The genome of a 3,000-year-old individual from Tanzania bore the ancestry of both ancient East African hunter-gatherers and early farmers from the Middle East. That supports past studies that documented a back to Africa migration several thousand years ago: these migrants were closely related to early farmers from the Levant region in the Middle East.

The Tanzanian fossil was found at an archaeological site linked to animal herding, or pastoralism, and some of its genetic signatures have also been found in present-day pastoralists in southern Africa, Skoglund said. This suggests that east Africans brought herding to southern Africa.

The unpublished study from Skoglunds team revealed additional movement. The genome of a 2,000-year-old individual from southern Africa was related to contemporary southern African hunter-gatherers known as the San, as well as to ancient hunter-gatherers the team sequenced from Malawi and Tanzania but not to the current inhabitants of eastern Africa.

The reason for this, Skoglund suggested, is a well-documented migration of Bantu groups from Western Africa, who brought agriculture and distinct language to eastern and southern Africa around 1,000-2,000 years ago. This Bantu expansion seems to have completely replaced local hunter-gatherers. An individual who lived on Tanzanias Zanzibar peninsula 750 year ago, after the migration, shared no ancestry with earlier hunter-gatherers from southern or east Africa.

A separate team, led by Mattias Jakobsson at Uppsala University in Sweden, found evidence for the same migrations in the genome of a boy who lived 2,000 years ago near Balito Bay in South Africa and 6 other ancient southern Africans. Their study1 was posted to the bioRxiv preprint server last month.

Proof of migrations such as the Bantu expansion have been found at archaeological sites, as well as in the DNA of contemporary Africans, says Schiffels. But it is still nice to have direct evidence of these movements, he notes.

Ancient African genomes also have the potential to illuminate much earlier events. Jakobssons team used the Ballito Bay boys genome to infer that Homo sapiens emerged at least 260,000 years ago far earlier than previous genetic studies have suggested. Skoglunds team, meanwhile, used their ancient genomes to help uncover a possible ghost population that diverged from the founding population of H. sapiens before any other African group and later contributed to the genetic make-up of some present-day West Africans.

IainMathieson, a population geneticist at the University of Pennsylvania in Philadelphia,hopes that ancient African DNA can explain our species migration out of Africa, some 50,000-100,000 years ago, by painting a genetic picture of the continents inhabitants around this time.

This might require DNA far older than several thousand years which could mandateanother major technical advance. Analysis of bones thought to be about 300,000 years old from Morocco, attributed to the earliest-known H. sapiens, has so far yielded no usable DNA. "It's early days," for ancient African genomics, says Mathieson, "it really is."

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Ancient-genome studies grapple with Africa's past - Nature.com