Prof Lee Berger of Wits University with a Homo naledi skull from the Rising Star cave system in the Cradle of Humankind. If DNA can be extracted from bones at the site, it could reveal whether there are links between Homo naledi and our species. Picture: ALON SKUY
Prof Lee Berger of Wits University with a Homo naledi skull from the Rising Star cave system in the Cradle of Humankind. If DNA can be extracted from bones at the site, it could reveal whether there are links between Homo naledi and our species. Picture: ALON SKUY

From deep inside a cave, some of humankind’s deepest family secrets could soon come tumbling out from a distant relative.

If DNA is extracted from the bones in the Dinaledi Chamber in the Rising Star cave system in the Cradle of Humankind, geneticists might be able to place where Homo naledi sits on the family tree and whether we still carry traces of the species.

"There is a real possibility that our species interbred with Homo naledi, and DNA will be able to tell us that," says Prof Lee Berger of Wits University, the leader of the team that discovered the new hominid species.

Research by scientists at the University of Buffalo in the US recently discovered that a gene found in saliva of some modern sub-Saharan populations was so different from other humans that it suggested genetic contribution from another species.

"It seems that interbreeding between different early hominin species is not the exception, it’s the norm," says Dr Omer Gokcumen, an assistant professor of biological sciences at the University of Buffalo.

The researchers believe this interbreeding may have happened 150,000 years ago. "This unknown human relative could be a species that has been discovered, such as a subspecies of Homo erectus, or an undiscovered hominin. We call it a ‘ghost’ species because we don’t have the fossils," says Gokcumen.

Humans have been known to breed with other species. Studies have identified traces of Neanderthal DNA in humans. Europeans have on average 2% to 4% of Neanderthal DNA in their genetic make-up.

But so far, three independent laboratories have failed to sequence any DNA from the Homo naledi remains. The oldest DNA sequenced came from a horse bone between 560,000 and 780,000 years old. The bone was buried in permafrost in Canada, which preserved it.

But conditions in Africa are far harsher, say researchers.

"The upper limit of success in obtained DNA from material seems to be between 40,000 and 50,000 years," says Prof Himla Soodyall, director of the Human Genomic Diversity and Disease Research Unit at Wits University. "The process of fossilisation also denatures the DNA, so you are breaking it down to points that are irrecoverable, even with technology."

But the search for Homo naledi DNA will continue.

"We will definitely continue to look for DNA and we hope we will have success," says Berger.

Palaeoanthropology is not the only discipline drawing on the help of DNA sleuths to peer into the past. It could help in understanding the evolution of diseases, and in SA, archaeologists are using it to trace lost migrations. The double helices are also shedding light on the origins of language.

SA has a unique collection of ancient DNA. Some South Africans carry the oldest lineages known to man, which stretch back 100,000 years.

Soodyall and her colleagues discovered these lineages when they began delving into the genetics of the Karretjie people of the Karoo. They are nomads who get their name from their use of donkey carts.

The researchers decided to study the Karretjie people after watching a documentary made by Prof Mike de Jong.

In years to come, it might not be DNA extracted from bone that could add to human history, but genetic material scraped from teeth

"When we read some of his work and watched the documentary, we noticed that the Karretjie people had features that were around when Bleek was studying San linguistics," says Soodyall.

"We asked whether it is possible that these are San descendants, at a time when people are saying there are no longer San in the country."

Wilhelm Bleek and his sister-in-law, Lucy Lloyd, were linguists who studied San languages in the 19th century.

Soodyall and her team were right: the Karretjie people have a direct link to the San and some of the oldest genetic lineages known to man. The oldest came from a subject who lives in an informal settlement in Colesburg, in the Northern Cape.

"When it comes to questions relating to prehistory, our tool kit is genetics and we try and compare what we find with other disciplines, so we can expand our understanding of the past in a multidisciplinary sort of way," she explains.

Tracing human migrations through artefacts is difficult. However, three years ago, archaeologist Prof Marlize Lombard of the University of Johannesburg and geneticist Dr Carina Schlebusch of Uppala University in Sweden mapped out a migration route followed by one of SA’s forgotten people.

They believe this was a route used by the ancestors of the Khoi and traced it by looking for a part of the gene associated with the ability of adults to drink milk. This part of the gene is known as the allele LP SNP 14010 G and is used by geneticists to track pastoralists who had milk in their diets.

Lombard and Schlebusch found this migration had taken place 1,300 years ago and there was little record of it.

"There was disagreement whether early forms of herding were culturally introduced to local populations or whether a herding population migrated to the region," explains Lombard.

"Based on genetic work focusing on lactase persistence, we now know that East African herders admixed with local hunter-gatherer communities."

In the future, the presence or absence of other alleles might assist in telling other tales from the forgotten past.

As humans move into a new territory, there is often subjugation of one group by another. In SA, this began long before colonisation and is told through Y chromosome DNA analysis. The Y chromosome is passed down from father to son.

Brigitte Pakendorf of the Laboratoire Dynamique du Langage in Lyon, France, explains that there was usually a one-way gene flow when a stronger group moved into an area.

"The incoming groups that pass on the Y chromosome take up mainly maternal lineages from the indigenous population," she says.

Males of the dominant group pass on their DNA to the females of those they have oppressed. This, she explains, was seen with the Bantu passing on their DNA to the San.

Later, European males seeded Khoi women with their Y chromosomes.

Pakendorf paired linguistics and genetics to understand how language evolved among the descendants of the Khoi and San. Her test subjects were in Botswana and Namibia.

As with Y chromosome gene flow, the language of the oppressor also leaves a lasting impression on indigenous populations.

"That’s why Khoisan language speakers ended up speaking Bantu languages and Afrikaans," Pakendorf says. She believes more research needs to be done before firm conclusions can be reached.

In years to come, it might not be DNA extracted from bone that could add to human history, but genetic material scraped from teeth.

Academics believe hardened plaque on teeth might be an excellent preserver of genetic material that might harbour the signatures of pathogens that have been around for hundreds of thousands of years.

"I think that within the next decade, multidisciplinary projects that include genetic research will dramatically enrich our ability to interpret the archaeological past and probably topple some accepted wisdoms," says Lombard.

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