First ancient genomes from West Africa reveal complexity of human ancestry

The ancient DNA of four children who lived thousands of years ago in western Cameroon has unearthed many more questions than answers.Friday, 24 January 2020

Tens of thousands of years ago, humans sought refuge from the elements in a rocky hollow near the crook of Africa’s western coast. They crafted stone tools, ate fresh kills or gathered plants, and eventually buried their dead. Some may have also formed the earliest words of the Bantu languages, which are spoken by hundreds of millions across the continent today.

Yet the precise identity of the Shum Laka residents has long remained a mystery. Buried in acidic soils in the hot and humid climes, many of their remains are broken and crumbling, their DNA thought to be long degraded—until now.

Researchers have announced the sequencing of the first genomes from this site, marking the analysis of the first full ancient genomes from West Africa, according to a study published Wednesday in Nature. The results offer new clues to the complex hominin journey—but unearth more questions than answers.

“When I got the email from the lab saying we have these incredibly high-quality results, my jaw just dropped. I couldn’t believe the preservation,” says study author Mary Prendergast, an anthropologist at Saint Louis University in Madrid.

The analysis focused on DNA from four individuals unearthed at Shum Laka in western Cameroon. They sequenced the full genomes of an eight-year-old boy buried some 3,000 years ago and a 15-year-old boy buried 8,000 years ago. They also studied the genetic variation in the DNA—known as an SNP analysis—of the remains from two four-year-olds, one from each of the same periods.

Comparison of the ancient DNA to modern groups across Africa revealed a few surprises, including that these Shum Laka individuals were not related to modern western Cameroon groups or current Bantu-speakers, who make up roughly one in three Africans today and are thought to trace their ancestry back to the region where Shum Laka nestles.

But with just four samples from this site, the story is likely not complete. As Prendergast points out, numerous populations from various ancestries may have used the Shum Laka site over time, perhaps including the ancestors of all Bantu-speakers.

Carina Schlebusch, an evolutionary geneticist at Uppsala University in Sweden, is intrigued by the result and calls the newly analysed ancient DNA a “welcome addition” to the growing African database. But she also cautions about drawing too many conclusions about the study’s new model that uses these four samples to explore the complex array of African populations and how they mixed over hundreds of thousands of years.

“I think we have a lot more to do, and I don’t think this should be a final verdict,” she says.

Overall, the work speaks to a common and frustrating thread in ancient DNA analysis, Prendergast says: It’s always more complicated than once thought. “You can go in with one set of questions and come out with a very different set of answers that raises a whole new set of questions.”

Precious genetic cargo

Adding ancient DNA to the picture of evolution can reveal human populations that have since vanished and continue on only as traces of DNA in distant relatives.

“It gives you access to additional branches of the human tree,” explains study author Mark Lipson, a geneticist at Harvard Medical School in Boston. 

For the new study, Prendergast and her colleagues were interested in population shifts that took place in Africa as hunting and gathering gave way to farming and herding, starting some 4,000 years ago. Shum Laka seemed an ideal place to study this transition. While the site lacks direct evidence of farming, its pair of burial grounds bookend this period in time; one is around 8,000 years old, the other is roughly 3,000 years old. Soon after the youngest burial, Bantu languages likely started to spread from the region, rippling out to populations south of the Sahara.

To optimise their chance of success, the researchers targeted the DNA stored in the petrous, a super dense bone that encases the inner ear. The toughness of this bone offers extra protection to the delicate twirls of DNA from damaging heat and the region’s acidic soils.

To their delight, they obtained high-quality genetic material from four Shum Laka individuals. They also analysed the DNA of 63 individuals from modern groups near western Cameroon for comparison.

Unexpected relations

Overall, the results weren’t quite what they expected. Even though the four individuals lived some 5,000 years apart, they had remarkably similar genetics, Prendergast says, suggesting the population visited Shum Laka for quite some time.

Each pair also seemed to share family relations during the slices of time they were alive. The pair of 3,000-year-old individuals were second-degree relatives like uncle and niece or half-siblings. The pair of 8,000-year-old individuals were fourth-degree relatives, akin to first cousins once removed.

“Maybe this was like a family cemetery,” Prendergast says. “It might be special for reasons that we can’t fully understand.”

What’s more, the four Shum Laka individuals were not genetically related to the modern residents who live nearby in western Cameroon—nor are they related to the early adventurers that spread Bantu languages throughout Africa. Instead, they seem to be genetically closer to the hunter-gatherers of Central Africa.

“It certainly sheds light on recent population history from Africa,” says Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. But she adds that the result is not entirely surprising since these hunter-gatherers still live in Cameroon today, and it’s likely that their range extended further in the past.

With just four individuals analysed, the results do not rule out the possibility that Bantu-languages originated in this area. Perhaps multiple diverse groups lived in the area at the same time, the study authors note.

Deep roots

In the second half of the analysis, the team explored deep African history, sussing out how Shum Laka fits into the hominin family tree. Its roots are firmly planted in Africa, extending back at least 2.8 million years to the oldest fossil of our genus, Homo, yet found. Our species, Homo sapiens, don’t appear till much further up the trunk, branching off some 260,000 years ago. Yet how the many branches sprout and intertwine is still under debate—and there’s a growing notion that our species’ origin is much more complex than we once imagined. (Read more about a controversial study that attempted to pinpoint where all modern humans arose.)

The team crafted a model that included genetic information from several dozen previously sampled modern individuals from across sub-Saharan Africa, a 4,500-year-old skeleton from Ethiopia, three ancient southern Africans roughly 2,000 years old, the four Shum Laka individuals, as well as two French individuals, a chimpanzee, and a Neanderthal.

Past studies suggest that the deepest-rooted genetic line for Homo sapiens can be found in modern southern African hunter-gatherers, stretching back more than 200,000 years ago. But the new model hints that three other genetic branches split off around the same time.

One is the genetic line of modern hunter-gatherers in Central Africa, which includes the twig of newly analysed Shum Laka samples. Another branch represents a “ghost” population of modern humans whose identities remain unknown. The last branch is one that eventually leads into the East and West African populations, including the band of humans that eventually spread around the world.

The many deep branches of this new model seem to lend weight to the complexity of African population history, says Serena Tucci, an evolutionary geneticist at Princeton soon to join Yale University who was not involved in the work.

But Tucci and other researchers caution that more analysis is needed to confirm the result. “The problem with these models is that there are potentially many models that can fit the data,” Schlebusch says. Each one is set up based on a batch of hypotheses before it is tested, which can limit the possible outcomes. “There might actually be models that we haven’t envisioned yet that might fit the data better—even including groups that we don’t have representatives today.”

More data—including whole-genome analysis—from both modern and ancient Africans is necessary to bring the hazy details of human origins into focus, refining the relationships between populations and timing of genetic splits.

There’s also likely more to glean from the two individuals found at Shum Laka, Schlebusch notes. The study delves into few details about the pair of whole genomes, she says. How did the population size change over time? When did these various splits actually happen?

“It’s great to see that it can be done,” Tishkoff says of the analysis of ancient DNA from Shum Laka. But the story is still far from complete. “There’s a lot more we need to do,” she says. “We just don’t have enough data from Africa.”

Related: These facial reconstructions reveal 4,000 years of English ancestry

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