Ancient DNA From West Africa Reveals ‘Ghost’ Lineage

Saint Louis University

Africa is the homeland of our species and harbors greater human genetic diversity than any other part of the planet. Studies of ancient DNA from African archaeological sites can shed important light on the deep origins of humankind. The research team sequenced DNA from four children buried 8,000 and 3,000 years ago at Shum Laka in Cameroon, a site excavated by a Belgian and Cameroonian team 30 years ago.

The findings, "Ancient West African foragers in the context of African population history," published Jan. 22 in Nature, represent the first ancient DNA from West or Central Africa, and some of the oldest DNA recovered from an African tropical context. They enable a new understanding of the deep ancestral relationships among early Homo sapiens in sub-Saharan Africa.

This study was the product of collaboration among geneticists, archaeologists, biological anthropologists and museum curators based in North America (including Harvard Medical School and the Université de Montréal); Europe (Royal Belgian Museum of Natural Sciences, Royal Museum for Central Africa, Université Libre de Bruxelles and Saint Louis University's Madrid campus); Cameroon (University of Yaoundé, University of Buea); and China (Duke Kunshan University).

A unique archaeological site with exceptional preservation

Shum Laka is a rock shelter located in the 'Grassfields' region of Cameroon, a place long pinpointed by linguists as the probable cradle of Bantu languages, a widespread and diverse group of languages spoken by more than a third of Africans today.

"Linguists, archaeologists and geneticists have been studying the origin and spread of Bantu languages for decades, and the Grassfields region is key to this question," said Mary Prendergast, Ph.D., a professor of anthropology and chair of humanities at Saint Louis University's campus in Madrid, and a co-supervising author of the study. "The consensus is that the Bantu language group originated in west-central Africa, before spreading across the southern half of the continent after about 4,000 years ago."

This expansion is thought to be the reason why most people from central, eastern and southern Africa are genetically closely related to each other and to West Africans.

The Shum Laka rockshelter was excavated in the 1980s and 1990s by archaeologists from Belgium and Cameroon. It boasts an impressive and well-dated archaeological record, with radiocarbon dates spanning the past 30,000 years. Stone tools, plant and animal remains, and eventually pottery collectively indicate long-term forest-based hunting and gathering and an eventual transition to intensive tree fruit exploitation.

Excavation of a double burial at the Shum Laka rock shelter (Grassfields region of Cameroon) containing the remains of two boys who lived ~8,000 years ago and who were genetically from the same family. Ancient DNA reveals that these two individuals and another pair of children buried five millennia later at Shum Laka were from a stable population that was then almost completely displaced by the very different populations living in Cameroon today (Image: Isabelle Ribot, January 1994).

Scientists at Harvard Medical School sampled petrous (inner-ear) bones from six individuals buried at Shum Laka. Four of these samples produced ancient DNA, and were directly dated at the Pennsylvania State University Radiocarbon Laboratory. The molecular preservation was impressive given the burial conditions, and enabled whole-genome ancient DNA analysis.

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A newly documented population of hunter-gatherers

Surprisingly, the ancient DNA sequenced from the four children - one pair buried 8,000 years ago, the other 3,000 years ago - reveals ancestry very different from that of most Bantu-speakers today. Instead, they are closer to central African hunter-gatherers.

"This result suggests that Bantu-speakers living in Cameroon and across Africa today do not descend from the population to which the Shum Laka children belonged," said Mark Lipson, Ph.D., Harvard Medical School, lead author of the study. "This underscores the ancient genetic diversity in this region and points to a previously unknown population that contributed only small proportions of DNA to present-day African groups."

Bamileke dancers in Batié, West Province, Cameroon. (CC BY-SA 3.0)

Four Human Lineages Found

While the findings do not speak directly to Bantu language origins, they do shed new light on multiple phases of the deep history of Homo sapiens.

"Our analysis indicates the existence of at least four major deep human lineages that contributed to people living today, and which diverged from each other between about 250,000 and 200,000 years ago," said David Reich, Ph.D., of Harvard Medical School, senior author of the study.

These lineages are ancestral to present-day central African hunter-gatherers, southern African hunter-gatherers, and all other modern humans, with a fourth lineage being a previously unknown 'ghost population' that contributed a small amount of ancestry to both western and eastern Africans.

Previous models for human origins suggested that present-day southern African hunter-gatherers, who split from other populations about 250,000-200,000 years ago, represent the deepest known branch of modern human variation. However, Lipson said, "the new analysis suggests that the lineage contributing to central African hunter-gatherers is similarly ancient and diverged from other African populations around the same time."

This finding adds to a growing consensus among archaeologists and geneticists that human origins in Africa may have involved deeply divergent, geographically separated populations.

"These results highlight how the human landscape in Africa just a few thousand years ago was profoundly different from what it is today, and emphasize the power of ancient DNA to lift the veil over the human past that has been cast by recent population movements," Reich said.

The international research team plans to return to Shum Laka this year, in part to help communicate findings to the Cameroonian academic and broader communities. "Interdisciplinary collaborations like this one are an essential part of ancient DNA research," says Reich.

Top image: The Shum Laka rock shelter in Cameroon, home to an ancient population that bears little genetic resemblance to most people who live in the region today.    Source: Pierre de Maret

This article is drawn from a release by Saint Louis University titled, ‘Nature study: First ancient DNA from West Africa illuminates the deep human past’ sourced from Eurekalert.

Source: Lipson, M., Ribot, I., Mallick, S. et al. Ancient West African foragers in the context of African population history. Nature (2020). https://doi.org/10.1038/s41586-020-1929-1