Australasian Science: Australia's authority on science since 1938

DNA Survives the Heat

By Stephen Luntz

Ancient DNA in the Pilbara may give us unprecedented insights into past climate.

DNA generally does not survive well in very hot climates, so for Daithi Murray the discovery of 30,000-year-old sequences from the Pilbara was something of a surprise. As a PhD student at Murdoch University, the Pilbara work is not even Murray’s main focus, but it could fill a frustrating gap in our knowledge about the world’s ancient climates.

Arid zones are hard places in which to establish climatic history. There are no ice cores and seldom any stalactites to incorporate clues about the temperature of the planet as they grow. Fossils can be thin on the ground, and where pollen is found its species can be very hard to identify.

However, Murray has helped reveal a potentially rich source of information about the ancient climate and ecology of some of the most forbidding places on Earth, through the extraction of DNA from 30,000-year-old middens in the Pilbara.

Stick-nest rats once built nests or middens out of material they scavenged from the surrounding territory. They used their own excretions to cement these into impermeable masses. While they once roamed widely across Australia’s drier lands, the lesser stick-nest rat is now probably extinct and its greater cousin is restricted to a few islands and protected areas.

Fossils and bits of pollen have been extracted from these middens in the past, along with those of similar species in North America, Africa and the Middle East. While these have been the best source of information we have about the historical ecology of arid lands, these sources have had plenty of limitations.

Murray tried applying High-Throughput Sequencing to biological material from Pilbara middens, and was rewarded with over 20,000 DNA sequences from four samples. Some samples were identified as coming from plants and animals endemic to the region, but others were more of a surprise.

DNA from “the common brushtail possum (Trichosurus vulpecula) was found in one midden in the Cavenagh Range, Western Australia,” says Murray. It was last recorded in the area in the 1930s.

Only after the DNA had been extracted did Murray discover that carbon dating aged one sample at 30,000 years from an area of the Pilbara where temperatures above 40°C are common.

So far Murray says: “We don’t have enough samples to learn about the ancient climate of the region. This is more of a proof-of-principle.” However, it should now be possible to learn which species occupied locations at different times, from which conclusions can be drawn about the conditions required for this to occur.

Part of the extraordinary survival of the DNA in this instance may be because the middens were located in caves where temperatures are relatively even and weathering reduced. “We also think the high concentration of urea may have a role, making it an anoxic environment as well as one where there is very little water,” Murray explains. Similarly, eggshells and hair have both preserved DNA much better than bone.

Murray’s main project is focused on extracting DNA from caves in the more climatically friendly south-west of Western Australia, particularly at a place known as the Devil’s Lair. “It has evidence of occupation from 50,000 years ago, amongst the oldest continuous occupation sites outside Africa,” says Murray. “If we can get 50,000-year-old DNA we’ll be very happy.”

Another site from the same region shows evidence of periods of human use interrupted by periods where animals reclaimed the site, offering an opportunity for comparison.

Murray says he was “always interested in science, and my biology teacher in the last 2 years of school had a big influence on me”. Nevertheless, he planned to study English Literature until he took a year off before university and decided to see “if I could make a go of science”. After an undergraduate degree focused on molecular biology at the Royal Holloway College, University of London, he found himself seeking ancient DNA during his Honours year.

“I wasn’t keen to do it,” Murray says, “but in England you get much less choice on your Honours topic than you do here. However, the day I got DNA from an ancient bone the experience was amazing, something that old that no one has been able to get anything from.”

Murray decided the quest for ancient DNA was “interesting and fun” and enrolled in a PhD at Murdoch University. “It’s difficult to convince people of the utility of this work,” he acknowledges, “but we can’t know how to protect species if we don’t know what was there in the first place.”