Scientists have long assumed that ancient DNA could not survive in Africa’s warm climates, where heat and humidity degrade genetic material far faster than in cold northern regions.
A new study challenges that assumption, showing that DNA can be preserved in large mammal fossils from South African caves for up to 50,000 years.
Researchers tested 144 fossils from antelope, buffalo, and other species, aged between 1,500 and 110,000 years old.
They found that most fossils with preserved DNA were younger than 11,700 years old, but one sample—a mountain reedbuck from Boomplaas Cave in the Western Cape—yielded DNA that may be the oldest animal DNA ever found in Africa, potentially by 30,000 years.
The team is still confirming that finding with radiocarbon dating.
The study, published by researchers with expertise in African hoofed mammals and ancient DNA, focused on fossils from six archaeological cave sites in the Eastern Cape and Western Cape provinces.
The species tested included Cape grysbok, grey rhebok, reedbuck, eland, African buffalo, and the extinct giant long-horned buffalo.
The fossils were excavated between 1950 and 1995 and have been housed at the Iziko Museums of South Africa in Cape Town.
The researchers subsampled the fossils by drilling with a dentist drill to obtain 50mg of tooth or bone powder for DNA extraction.
One of the key findings is that DNA preservation varied more by site than by species. Nelson Bay Cave in Plettenberg Bay, on the southern Cape coast, preserved DNA better than other sites.
That cave also produced the oldest African animal DNA sequenced before this study—a blue antelope tooth about 9,300 years old—as well as three teeth from the extinct giant long-horned buffalo, aged 12,000 to 21,000 years old, from which the team successfully obtained ancient DNA.
The researchers also found that not all DNA extracted from fossils belongs to the target species. In the 65 fossils that contained ancient DNA, an average of only 2% of the retrieved DNA was from the target species.
Fossils younger than 2,000 years old tended to have more—up to 30%—because there has been less time for degradation and mixing with microbial DNA.
DNA from animals in South African caves
The study also examined collagen, the protein that makes up 22% to 50% of vertebrate teeth and bones. Collagen preservation is already used for radiocarbon dating, and previous research has suggested a link between collagen and DNA preservation.
The new analysis found a 77% correlation between the two, but only at some sites. That is still an encouraging result, the researchers say, because measuring collagen is less costly than retrieving and sequencing ancient DNA.
This means collagen preservation could serve as a proxy for DNA preservation, helping researchers decide which fossils to target for DNA sequencing and radiocarbon dating.
The broader significance of the work is that it opens a new window into how Africa’s extinct mammals can be studied.
Until now, ancient DNA studies of African large mammals have been rare, and most focused on humans and domestic species within the past 2,000 years.
The new findings suggest it is possible to genetically study African mammals that went extinct during or after the last ice age.
The researchers also note that data from ancient DNA can serve as a baseline of genetic diversity before the major declines caused by human activities over the past two centuries.
Such baseline data are crucial for monitoring biodiversity change and conserving African wildlife.
Collagen as a proxy for DNA
The study gives researchers who want to use ancient DNA and collagen in their work on African fossils an idea of what to expect and what to consider when designing future studies.
Source: The Conversation