Ancient DNA from West Africa reveals deep human history

Excavation of the burial site at the Shum Laka rock shelter in Cameroon that contained the remains of two children who lived around 8,000 years ago (Photo by Isabelle Ribot, January 1994)

An international research team including Scott MacEachern, Duke Kunshan’s vice chancellor for academic affairs, has produced the first whole-genome ancient human DNA sequences from West and Central Africa.

Scientists recovered the data from two pairs of children buried at an iconic archaeological site in Cameroon from between 3,000 and 8,000 years ago, at the transition from the Stone Age to the Iron Age.

The work, led by Harvard Medical School, sheds light on the deep ancestral relationships among early Homo sapiens in sub-Saharan Africa and illuminates previously unknown ‘ghost’ populations that contributed small portions of DNA to present-day African groups. The findings were published in Nature on Jan. 22.

Scott MacEachern, professor of archaeology and Duke Kunshan’s vice chancellor for academic affairs (Photo by Pierre de Maret, January 1994)

Archaeologists unearthed the children’s remains at Shum Laka, a rock shelter in the so-called Grassfields region of Cameroon, which linguists have long pinpointed as the probable cradle of Bantu languages.

‘Shum Laka is one of the most important archaeological sites in West/Central Africa not only for the skeletons that were discovered there but more broadly because it has yielded evidence of cultural changes over the past 30,000 years. It is also in the area where the Bantu languages originated, the most widespread group of languages in Africa today,’ said MacEachern, a professor of archeology. ‘My contribution was in helping to provide a wider context for understanding the prehistory of the region, where I’ve worked since the 1980s.’

Archaeologists from Belgium and Cameroon first excavated Shum Laka in the 1980s and 1990s. Excavations have yielded 18 human skeletons, mostly children, while the stone tools, plant and animal remains, and pottery that have been unearthed indicate long-term forest-based hunting and gathering and an eventual transition to intensive tree fruit exploitation.

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 more similar to Central African hunter-gatherers.

One of the sampled individuals ‘ an adolescent male ‘ carried a rare Y chromosome haplogroup that is found almost nowhere outside western Cameroon today. This unique discovery shows that this most-ancient-known haplogroup among human males has been present in West and Central Africa for more than 8,000 years, probably much longer.

A general view of the Shum Laka excavation site

While the findings do not speak directly to the origins of Bantu language, they do shed light on multiple phases of the deep history of Homo sapiens. Researchers examined the DNA of the Shum Laka children alongside published DNA from ancient hunter-gatherers from eastern and southern Africa, as well as DNA from many present-day African groups. Combining these datasets, they were able to construct a model of diverging lineages over the course of the human past.

‘Data from ancient DNA, used in combination with evidence from archaeology and other disciplines, is dramatically changing our understanding of the human past,’ said MacEachern. ‘We see this research as an initial contribution in an area that is of immense importance in understanding African prehistory and the history of humanity more broadly.’

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