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Ancient African Genomes Reveal Early Human Lineages, Population Histories

NEW YORK – By sequencing the genomes of ancient individuals from sub-Saharan Africa, an international team led by investigators in the US and Spain has gotten a glimpse of the populations present at a culturally important time and place in Central Africa.

Using targeted enrichment and shotgun sequencing, the researchers assessed ancient remains from two children who died during the Metal Age around 3,000 years ago and from two late Stone Age children who died around 8,000 years ago. They then compared those individuals — all found at the Shum Laka site in northwestern Cameroon — to genotyped individuals from modern-day populations in the Central African country and beyond.

The mitochondrial and Y chromosome haplogroup sequences identified in the ancient Cameroonians shared closer genetic ties to hunter-gatherer populations in Central Africa than to Bantu-speaking populations believed to have originated in the Cameroon-Nigeria region, the team noted. Based on the diverse lineages present in the ancient samples, meanwhile, the investigators estimated that four or more lineages were present in humans as far back as 200,000 or 300,000 years ago.

"On the basis of our current understanding, the presence of at least four modern human lineages that diversified about 250,000 to 200,000 [years before present] and are represented in people living today provides further support for archeological evidence that suggests this era was a pivotal period for human evolution in Africa," first and corresponding author Mark Lipson, a genetics researcher at Harvard Medical School, and his co-authors explained in their study, published online today in Nature.

"Further genetic studies may reveal additional complexities in deep human population history, although some early human groups will probably remain known only through fossils," they noted.

Human remains going back some 30,000 years have been identified at the Shum Laka archeological site, the team explained, including a rich set of fossils representing a time of cultural change from the late Stone Age to early Iron Age.

"These cultural changes and their early appearance at Shum Laka are particularly intriguing because during the late Holocene epoch, the area around the present-day border between Cameroon and Nigeria was probably the cradle of the Bantu language group, and of populations whose descendants would spread across much of the southern half of Africa between about 3,000 and 1,500 [years before present], resulting in the vast range and diversity of Bantu languages today."

Starting from 18 Shum Laka skeletons, the researchers successfully generated DNA sequence data for four individuals spanning from Stone Age to Metal Age, using targeted enrichment and sequencing to focus on roughly 1.2 million SNPs. To that, they added whole-genome shotgun sequence data for two of the individuals, whose genomes were covered to 18.5-fold and 3.9-fold, on average.

When the team analyzed the sequences alongside array-based genotyping data for 63 individuals from five modern-day populations in Cameroon, it saw signs that the ancient Cameroonians were more closely related to today's hunter-gatherer populations in central Africa than to present-day Bantu-speaking populations.

The ancient samples were marked by ancestry from four lineages going back hundreds of thousands of years, including a group marked by an early-diverging version of the Y chromosome, the researchers reported.

"In addition to the well-characterized deep lineages, we also detect at least one deep ghost source that contributed to West Africans and East African hunter-gatherers," they explained, calling the deep ancestry detected in West Africa "notable."

Their broader analysis pointed to more recent population splits in Africa, estimated at 60,000 to 80,000 years ago, which led to lineages that include present-day populations in West Africa, East Africa, and lineages outside of Africa. The available data also highlighted a relatively early split between hunter-gatherers in central Africa and other populations in the region.

"Our results suggest that Central African hunter-gatherers split at close to the same time [as southern African hunter-gatherers] (or perhaps slightly earlier)," the authors noted.