First ancient DNA from West/Central Africa illuminates deep human past

An international team led by Harvard Medical School scientists has produced the first genome-wide ancient human DNA sequences from west and central Africa.

General view of the excavation of Shum Laka’s rockshelter (Grassfields region of Cameroon). This site was home to a
human population that lived in the region for at least five millennia and bore little genetic relatedness to the people
who live in the region today. Analysis of whole genome ancient DNA data from the people who lived at this site
provided insights into the existence of several never-before-appreciated, early-branching
African human lineages [Credit: Pierre de Maret, January 1994]

The data, recovered from four individuals buried at an iconic archaeological site in Cameroon between 3,000 and 8,000 years ago, enhance our understanding of the deep ancestral relationships among populations in sub-Saharan Africa, which remains the region of greatest human diversity today.

The findings, published in Nature, provide new clues in the search to identify the populations that first spoke and spread Bantu languages. The work also illuminates previously unknown "ghost" populations that contributed small portions of DNA to present-day African groups.

Map of Africa with Cameroon in dark blue and approximate location of Shum Laka marked with star. Image adapted from Alvaro1984 18/Wikimedia Commons

Research highlights:

- DNA came from the remains of two pairs of children who lived around 3,000 years ago and 8,000 years ago, respectively, during the transition from the Stone Age to the Iron Age.

- The children were buried at Shum Laka, a rock shelter in the Grassfields region of northwestern Cameroon where ancient people lived for tens of thousands of years. The site has yielded prolific artifacts along with 18 human skeletons and lies in the region where researchers suspect Bantu languages and cultures originated. The spread of Bantu languages--and the groups that spoke them--over the past 4,000 years is thought to explain why the majority of people from central, eastern and southern Africa are closely related to one another and to west/central Africans.

- Surprisingly, all four individuals are most closely related to present-day central African hunter-gatherers, who have very different ancestry from most Bantu speakers. This suggests that present-day Bantu speakers in western Cameroon and across Africa did not descend from the sequenced children's population.

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 [Credit: Isabelle Ribot, January 1994]

- One individual's genome includes the earliest-diverging Y chromosome type, found almost nowhere outside western Cameroon today. The findings show that this oldest lineage of modern human males has been present in that region for more than 8,000 years, and perhaps much longer.

- Genetic analyses indicate that there were at least four major lineages deep in human history, between 200,000 and 300,000 years ago. This radiation hadn't been identified previously from genetic data.

- Contrary to common models, the data suggest that central African hunter-gatherers diverged from other African populations around the same time as southern African hunter-gatherers did.

- Analyses reveal another set of four branching human lineages between 60,000 and 80,000 years ago, including the lineage known to have given rise to all present-day non-Africans.

- The Shum Laka individuals themselves harbor ancestry from multiple deep lineages, including a previously unknown, early-diverging ancestry source in West Africa.

Source: Harvard Medical School [January 22, 2020]

Human-caused biodiversity decline started millions of years ago

The human-caused biodiversity decline started much earlier than researchers used to believe. According to a new study published in the scientific journal Ecology Letters the process was not started by our own species but by some of our ancestors.

Dinofelis, painting by Mauricio Antón. The picture shows a saber-toothed cat Dinofelis eating
while one of our ancestors are watching. Dinofelis has been considered a predator that our
ancestors were greatly fearing. But new research suggests that it was human ancestors that
may have caused the eventual extinction of the species along with other major predators
[Credit: University of Gothenburg]

The work was done by an international team of scientists from Sweden, Switzerland and the United Kingdom.

The researchers point out in the study that the ongoing biological diversity crisis is not a new phenomenon, but represents an acceleration of a process that human ancestors began millions of years ago.

"The extinctions that we see in the fossils are often explained as the results of climatic changes but the changes in Africa within the last few million years were relative minor and our analyses show that climatic changes were not the main cause of the observed extinctions," explains Søren Faurby, researcher at Gothenburg University and the main author of the study.

"Our analyzes show that the best explanation for the extinction of carnivores in East Africa is instead that they are caused by direct competition for food with our extinct ancestors," adds Daniele Silvestro, computational biologist and co-author of the study.

Carnivores disappeared

Our ancestors have been common throughout eastern Africa for several million years and during this time there were multiple extinctions according to Lars Werdelin, co-author and expert on African fossils.

"By investigating the African fossils, we can see a drastic reduction in the number of large carnivores, a decrease that started about 4 million years ago. About the same time, our ancestors may have started using a new technology to get food called kleptoparasitism," he explains.

Kleptoparasitism means stealing recently killed animals from other predators. For example, when a lion steals a dead antelope from a cheetah.

The researchers are now proposing, based on fossil evidence, that human ancestors stole recently killed animals from other predators. This would lead to starvation of the individual animals and over time to extinction of their entire species.

"This may be the reason why most large carnivores in Africa have developed strategies to defend their prey. For example, by picking up the prey in a tree that we see leopards doing. Other carnivores have instead evolved social behavior as we see in lions, who among other things work together to defend their prey," explains Søren Faurby

Humans today affect the world and the species that live in it more than ever before.

"But this does not mean that we previously lived in harmony with nature. Monopolization of resources is a skill we and our ancestors have had for millions of years, but only now are we able to understand and change our behavior and strive for a sustainable future. 'If you are very strong, you must also be very kind'," concludes Søren Faurby and quotes Astrid Lindgrens book about Pippi Longstocking.

Source: University of Gothenburg [January 17, 2020]