50,000-Year-Old DNA Found in South African Teeth Where Heat Should Have Destroyed It

Ancient DNA is typically sought in cold environments where permafrost has protected remains from degradation for millennia. Low temperatures slow chemical reactions and microbial activity, allowing bones and teeth from permafrost regions to retain genetic material even after tens of thousands of years. Hot climates were long considered nearly hopeless for such research because high temperatures accelerate molecular breakdown, leaving only short, damaged fragments of the double helix.

However, a tooth discovered in South Africa has preserved DNA estimated to be around 50,000 years old. This represents the oldest genetic material from animals found south of the Sahara to date. The African continent contains numerous rich fossil sites, particularly in the coastal caves of South Africa, yet paleogeneticists have rarely examined local collections due to the time-consuming nature of analysis and the previous assumption of low success probability.

Scientists decided to test this pessimism by collecting 320 fossil bones and teeth from six caves and rock shelters along the southern coast. The remains belonged to six species of wild bovids, including antelopes and buffaloes, spanning ages from the recent past back to 110,000 years ago. Genetic analysis was performed on 144 samples using a primary method focused on short single-stranded DNA segments that survive long-term degradation, compared against traditional techniques designed for more intact double-stranded fragments.

In a normal state, a DNA molecule consists of two connected strands. After an organism dies, chemical bonds gradually break down, fragmenting the long molecule into numerous pieces. Older bones or teeth contain fewer intact sections, causing conventional methods to miss damaged fragments. The single-stranded approach processes the material differently by separating the remaining double-helix remnants in the lab, enabling construction of genetic libraries even from very short single chains and capturing fragments unsuitable for standard technology.

The difference proved significant: in some samples, the single-stranded method extracted 6.7 times more animal DNA than double-stranded analysis. While damage remained, the sensitive technique made previously unusable material viable. Ancient DNA was recovered from 65 of the 144 samples, achieving a 45% success rate — notably high for a warm region, especially given the age of some remains.

Most successful samples dated to the Holocene epoch, which began about 11,700 years ago and continues today. Younger bones and teeth retained more DNA and produced positive results more frequently. The authors recommend that future projects in South Africa begin with Holocene finds due to their higher success probability. Prior to this study, the oldest genome came from an extinct blue antelope in South Africa dated to roughly 9,300 years; the new work extends this boundary by tens of thousands of years.

Four particularly ancient teeth, aged between approximately 12,000 and 50,000 years, stood out. Three belonged to the extinct long-horned buffalo, while one came from a mountain reedbuck, an African antelope in the bovid family. The oldest specimen confirmed that viable DNA can persist in subtropical climates for tens of thousands of years, challenging the prior exclusion of low-latitude regions from paleogenetic studies.

Although success is not guaranteed in every ancient bone — fewer than half of the samples yielded results, mostly from the Holocene — the four older finds show that the preservation boundary extends much further than previously thought. This new methodology will allow more thorough examination of extensive African cave collections containing remains spanning tens of thousands of years, many of which have never been tested for DNA. Genetic data can reveal evolutionary relationships, population changes, and species extinctions, expanding such inquiries beyond cold regions to southern African remains as well.