You may have heard of DNA being extracted from fossils such as woolly mammoths, cave lions or ancient humans. These remains are all uncovered during expeditions in cold northern landscapes, but a new study has found something totally different: ancient DNA from a 1,000-year-old giant tortoise that fell into a sunken sinkhole on a warm, sunny Caribbean island.

The Bahamas might not sound like the kind of place you'd go for fossils – but prehistoric leftovers are there if you know where to look.

Sawmill Sink is the name of a blue hole – a large, water-filled sinkhole – on Great Abaco Island. There, fossil-hunting scuba divers swim down through the cloudy, toxic water, as deep as 33 metres (100 feet), to reach the bones of ancient island denizens, including a long-gone species of tortoise named Chelonoidis alburyorum.

Divers explore deep inside a blue hole in the Bahamas. Image: Brian Kakuk

These tortoises went extinct – along with all the other Caribbean giant tortoises – around 780 years ago, not long after humans arrived in the region. But in Sawmill Sink, one beautifully preserved skeleton offers clues to the reptiles' past. On the outside, its shell is marred by the bite marks of crocs, but on the inside of its bones linger the remains of collagen protein (which allowed scientists to carbon-date the skeleton) and DNA.

Finding ancient DNA in a tropical tortoise was quite a happy surprise. "The two things that are really good for the long-term preservation of DNA are coldness and dryness," says David Steadman of the Florida Museum of Natural History in a news release. "And the tropics typically provide neither one."

The secret lies in the waters deep within the sinkhole, which are fairly still and mostly devoid of oxygen once you reach below 21 metres (70 feet) or so. Not a place you'd want to live, but a great place to die: these conditions allow for some fantastic fossil preservation, including DNA.

Ancient DNA has taught us a ton about cold-climate species of the late Ice Age, but tropical creatures from that time period are a big genetic blind spot. Steadman and other researchers are especially interested in the history of reptiles from the area: these animals are a major part of local island ecosystems, and used to be much more diverse than they are today.

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The fossil skull of the Chelonoidis alburyorum tortoise that yielded the ancient DNA. Image: Nancy Albury

As with all fossil DNA, the mitochondrial genetic material retrieved from the tortoise's arm bone was degraded and contaminated. Despite this, experts were able to tease out useful material and gain some insights into the reptile's ancestry: C. alburyorum was a close relative of the Chaco tortoise of South America and the giant tortoises of the Galápagos.

"This is the first time anyone has been able to put a tropical species into an evolutionary context with [genetic] data," Steadman says. "And being able to fit together the tortoise's evolutionary history will help us better understand today's tropical species, many of which are endangered."

We know from fossil evidence that tortoises of the Galápagos and Caribbean islands were once thriving in the tropics – but when humans begin to show up in the fossil record, the reptiles start to disappear. "It's probably a blend of direct hunting and habitat loss as the humans started burning the forests in the dry season," Steadman says. The Caribbean giant tortoises are completely gone today, and those of the Galápagos continue to struggle.  

Sawmill Sink's fossils were first discovered in 2004, when Bahamas Caves Research Foundation director Brian Kakuk found a submerged crocodile skull and tortoise shell. Since then, excavations have taught us that these big reptiles lived within a diverse ecosystem of prehistoric lizards, snakes, birds, bats and more. The sinkhole has even produced human remains from the Lucayan people, the original inhabitants of the Bahamas before Europeans arrived.


Top header image: Nancy Albury