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Ancient African Genomes Offer Peek at Continent's Population Histories Over 8,000 Years

NEW YORK (GenomeWeb) – An international team has sequenced the genomes of 15 ancient Africans, retracing human population histories and interactions on the continent as far back as 8,000 years ago.

As they reported online today in Cell, the researchers sequenced three 1,200- to 2,300-year old individuals from an area in present day South Africa, as well as 12 individuals estimated to be 400 to 8,100 years old from Kenya, Tanzania, or Malawi. They analyzed the genomes alongside available sequences from a 4,500-year-old Ethiopian and the genomes of hundreds of individuals from populations in Africa and beyond.

Using these data, the team found evidence for extensive San hunter-gatherer-related ancestry across hunter-gatherer populations from broad swaths of Africa. The genetic patterns reported also reflected more recent migration and replacement of some of the hunter-gatherer populations by farming populations originating in western Africa, along with herding population movement from Tanzania to parts of northeastern and southern Africa.

"Our documentation of a radically different landscape of human populations before and after the spread of food producers highlights the difficulty of reconstructing the African past based solely on analysis of present-day populations, and the importance of using ancient DNA to study deep African population history in an era in which technological improvements have now made it feasible," first author Pontus Skoglund, a genetics researcher at Harvard Medical School, and his co-authors wrote.

For their study, the researchers used Illumina HiSeq 2500 instruments to shotgun sequence the three ancient individuals from South Africa's western Cape region. They also used in-solution enrichment to target more than a million SNPs to generate between 0.7 and two-fold average genome coverage for the 12 ancient individuals from eastern and south-central Africa.

Patterns in these and the already sequenced genomes suggested hunter-gatherer populations were previously more widespread in Africa, the team reported, with population structures coinciding with the continent's north-to-south geography. The group noted that population structuring was particularly pronounced in western Africa, perhaps stretching back to a point prior to hunter-gatherer divergence in southern Africa.

"The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups, or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others," the authors wrote.

In particular, the researchers reported that the ancestors of southern Africa's San population had a much larger geographic reach until a few thousand years ago. An estimated 2,500 to 8,100 years ago, they estimated that members of an ancestral San population contributed some two-thirds of the ancestry in hunter-gatherer populations in Malawi. And as recently as 1,400 years ago, San-related ancestry made up roughly one-third of the ancestry in Tanzanian hunter-gatherers.

More recently, however, the findings suggested that pastoralist populations displaced or replaced many of the hunter-gatherer groups by migrating into eastern and southern Africa, and remained isolated for some time after their arrival in new regions.

When the researchers searched for signs of natural selection using the newly sequenced genomes, meanwhile, they saw potential selective sweeps or polygenic variation affecting sequences with apparent ties to taste and growth.