DNA sequencing extends origin of modern humans
Tests on Ballito Bay skeleton reveal link to Mandinka people in West Africa, writes Shaun Smillie
DNA taken from the skeleton of a hunter gatherer boy found in Ballito Bay has pushed back the date when modern humans first emerged and reveals possible prehistoric trysts with a relative species.
An international team of scientists that includes academics from the universities of Johannesburg and Witwatersrand were able to sequence genomes from the 2,000-year-old skeleton and estimate a split among modern humans occurred 350,000 to 260,000 years ago, somewhere in West Africa.
Fossil evidence from East Africa had previously estimated modern humans had emerged at about 180,000 years.
"This means that modern humans emerged earlier than previously thought," says Mattias Jakobsson, a population geneticist at Uppsala University in Sweden, a project leader.
The team, whose research appears in the latest issue of Science, sequenced the genomes of seven skeletons that were found in southern Africa of individuals that lived between 2,300 and 300 years ago.
What the bones provided was a DNA snapshot of southern African history, stretching from humankind’s deepest roots to more recent migrations that contributed to the genetic makeup of South Africans today.
The three oldest skeletons that dated between 2,300 and 1,800 years were found to be genetically related to the descendants of Khoi-San living today. The four younger skeletons that lived 500 to 300 years ago had DNA they share with modern-day South African Bantu speakers. But, it was the hunter-gatherer boy from Ballito Bay in KwaZulu-Natal who provided a DNA link to the West African Mandinka people.
Only recently have academics discovered that between 350,000 and 260,000 years ago, humans were sharing the landscape with several sister species of Homo. One of the researchers in the study, population geneticist Carina Schlebusch, says there might just be evidence of interbreeding.
"We are seeing some indirect evidence that there might be archaic admixture in West Africa, but not for SA.
"It must have been a homo [species] or an earlier [Homo sapien] species that split from the human lineage before the early split-up we have now at 350,000-260,000 years.
"It now seems that at least two or three Homo species occupied the southern African landscape during this time period, which also represents the early phases of the Middle Stone Age," says Prof Marlize Lombard of the University of Johannesburg.
"It will be interesting to see in the future if we find any evidence of interaction between these groups."
These species, she says, could include the robust Homo heidelbergensis, or an earlier Homo sapien, and the recently discovered Homo naledi.
Humans do have a history of sexual liaison with close relatives. In July, scientists at the University of Buffalo in the US say that they discovered a gene found in saliva in some modern sub-Saharan populations that suggested genetic contribution from another species. They believe that this interbreeding might have happened about 150,000 years ago.
There is no one place in Africa where we can say that modern humans originated and moved to the rest of Africa, rather it was pockets of people evolving from archaic forms to modern forms
Other studies have identified traces of Neanderthal DNA in humans. Europeans are known to have 2%-4% Neanderthal DNA in their genetic make-up. Another hominin group, the Denisovans, have also contributed DNA to humans.
But finding the genetic proof of these sexual affairs will be difficult, according to Schlebusch.
"It wasn’t until we had the Neanderthal and Denisovan sequences that we could detect that there was admixture in non-Africans. It is very difficult to see admixture in Africans as we don’t have the genetic sequences of these other species, like Homo naledi."
This latest genetic data is also pointing to the possibility that modern humans didn’t originate from a single location in Africa.
"There is no one place in Africa where we can say that modern humans originated and moved to the rest of Africa, rather it was pockets of people evolving from archaic forms to modern forms," she says.
These early hunter-gatherer groups, Schlebusch believes, would have gone through periods of isolation caused by climate change. Cooler periods, would have caused drier conditions that would have expanded deserts and limited movement.
The research has also, for the first time, revealed genetic traces of migrating East African pastoralists in modern Khoi-San populations. These farmers began moving into southern Africa a little more than a thousand years ago. "We could not detect this widespread East African admixture previously since we did not have an unadmixed San group to use as reference. Now that we have access to ancient DNA of people who lived on the landscape before the East African migration, we are able to detect the admixture percentages in all San groups," says Schlebusch.
These migrating farmers also left another interesting genetic trace the scientists found on the older skeletons.
Three of the Iron Age individuals were found to be carrying the Duffy-null allele, which protects against malaria, while two skeletons had the sleeping sickness resistance variant in the APOL gene. The Stone Age remains did not have these disease-protecting alleles.
‘This tells us that Iron Age farmers carried these disease-resistance variants when they migrated to southern Africa," says co-first author Helena Malmström, archeo-geneticist at Uppsala University.
Prof Lyn Wadley of Wits University, who was not part of the study, says these findings are being backed up by the archeological record.
"For me, the important thing is that it confirms what the archeology is showing us, that the middle Stone Age goes back 300,000 years from a technological point of view and now we have the genes telling us yes this is when modern humans began. So, we have a very nice link," she says.
Wadley says that archeological discoveries in Morocco and Ethiopia were over 200,000 years. "Then, of course, there was the archaic Homo sapiens at Florisbad, which are dated at 250,000 years ago. So, we have these clues all the way through and now we have this genetic study confirming all of that."
Wadley says there could even be evidence of Stone Age tools in SA dating back 500,000 years. Says Lombard: "We are processing material from several South African individuals dating from a few hundred to several thousand years, and plan to extend our research to include southern African and sub-Saharan individuals too."