Using ancient DNA to understand the past and inform the future

In the Ancient DNA Research Laboratory, located at Murdoch University, Doctor Mike Bunce and his team are leading global studies and discoveries through the isolation and characterisation of ancient and degraded DNA. The DNA helix is a small yet tough molecule that can survive for thousands of years after an organism has died. It is the blueprint of life.

Researchers at the Ancient DNA lab apply their tools and expertise across a wide range of scientific disciplines, including archaeology, paleontology, climate studies, conservation, forensics, and health and disease.

Unlike modern analyses, ancient DNA studies deal with DNA that is highly degraded. Whereas most modern DNA exists as long intact stretches, ancient DNA is damaged and broken into small pieces making its recovery technically challenging.

Archaeology

Dr. Bunce’s research in the applications of ancient DNA techniques is applied across the globe. In the field of archaeology, the study of past cultures, samples of bone, eggshell and sediment are examined.

His team worked on the isolation and sequencing of DNA of the Saqqaq, a pre-historic Greenlander, from a 4000 year old clump of hair that was found during an archaeological excavation. Dr Bunce also runs an extensive research program closer to home, studying the limestone cave system near Margaret River, Western Australia. This is where the Noonygar people have lived for ~50,000 years. In 2011 the team was part of a large international study which sequenced the entire genetic code (a genome) of an Aboriginal Australian from a 90 year old hair sample. During this study the team was able to determine when and how people first arrived in Australia.

Palaeontology

Researchers at the Ancient DNA Lab at Murdoch University are also experts in the recovery of DNA from fossils. These studies continue to add new dimensions to the field of palaeontology, where understandings about the evolutionary process and species extinctions – not just when, but how – can be determined.

They have isolated DNA from many extinct species, including the giant eagle, mammoth, moa, kangaroo and thylacine. In 2010 Charlotte Oskam, a PhD student supervised by Dr. Bunce, developed a method for extracting DNA from a fossil eggshell thus enabling the first ever DNA sequence from the extinct elephant bird of Madagascar. It was the largest bird to have ever lived, weighing in at ~500 kg.

Climate

Lab scientists Dr. James Haile and Adjunct Professor Tom Gilbert have worked extensively on research into Arctic sediments. ‘Old’ DNA, deposited up to 1 million years ago, is extracted from sediments and ice cores from cold, preserved environments, such as Greenland and the Arctic, and analysed at Murdoch’s lab. Dr. Haile and Professor Gilbert have regularly found the DNA of species such as mammoth, bison and woolly rhino preserved in just a few grams of dirt. These ancient DNA tools and studies can identify not just the species, but exactly where and when they lived.

The proximity of the Ancient DNA Lab and Dr. Bunce’s research programs to Southwest Australia, 1 of only 34 international biodiversity ‘hotspots’ around the world, enables them to apply ancient DNA to studies of how that biodiversity has changed over time. They determine how species have responded to changing environments and can also ‘retrodict’ what might lie ahead.

Conservation

The research programs and DNA tools which Dr. Bunce has pioneered are also used for modern applications.

Researchers actively collect animal faeces, both young and old. By examining DNA from these samples Dr. Bunce’s team undertakes ongoing environmental monitoring in a cost effective and non-invasive way. The team is currently investigating the diet of Penguins and Ghost Bats to better understand their food webs and ecosystem interactions.

In terms of conservation it’s not just natural environments where species identification and diet analysis play a role. The Ancient DNA Lab has been working closely with Perth Airport to investigate aviation bird-strikes. Research is being undertaken to identify what species of birds are being hit by planes, and what it is that they are eating at the airport site. In this case DNA studies are being used to form management practices which can minimise contact between birdlife and planes.

Climate

Lab scientists Dr. James Haile and Adjunct Professor Tom Gilbert have worked extensively on research into Arctic sediments. ‘Old’ DNA, deposited up to 1 million years ago, is extracted from sediments and ice cores from cold, preserved environments, such as Greenland and the Arctic, and analysed at Murdoch’s lab. Dr. Haile and Professor Gilbert have regularly found the DNA of species such as mammoth, bison and woolly rhino preserved in just a few grams of dirt. These ancient DNA tools and studies can identify not just the species, but exactly where and when they lived.

The proximity of the Ancient DNA Lab and Dr. Bunce’s research programs to Southwest Australia, 1 of only 34 international biodiversity ‘hotspots’ around the world, enables them to apply ancient DNA to studies of how that biodiversity has changed over time. They determine how species have responded to changing environments and can also ‘retrodict’ what might lie ahead.

Conservation

The research programs and DNA tools which Dr. Bunce has pioneered are also used for modern applications.

Researchers actively collect animal faeces, both young and old. By examining DNA from these samples Dr. Bunce’s team undertakes ongoing environmental monitoring in a cost effective and non-invasive way. The team is currently investigating the diet of Penguins and Ghost Bats to better understand their food webs and ecosystem interactions.

In terms of conservation it’s not just natural environments where species identification and diet analysis play a role. The Ancient DNA Lab has been working closely with Perth Airport to investigate aviation bird-strikes. Research is being undertaken to identify what species of birds are being hit by planes, and what it is that they are eating at the airport site. In this case DNA studies are being used to form management practices which can minimise contact between birdlife and planes.

Forensics

The Murdoch University Ancient DNA Lab has also been working with the Australian Customs and Border Protection Service. The lab specialises in wildlife forensics and has been working on species identification and parentage testing for a wide variety of Customs’ wildlife investigations, including the prosecution of egg smugglers and poachers.

Smugglers and poachers attempt to gain from illegal international trade in parrots and cockatoos but trace amounts of DNA, analysed by the lab from eggshell, can confirm what species is present. Illegal trade in endangered species holds far greater fines but it can be difficult to identify those species based solely on eggshell morphology. The lab has also developed DNA tests which determine paternity in snakes and cockatoos. The tests Murdoch run, either identifying parents or whether the offspring was poached from the wild, enable investigators to prosecute those who illegally harvest animals.

Health and Disease

Dr. Bunce recently worked with Customs in the first ever DNA audit of plants and animals contained within Traditional Chinese Medicines (TCM). The researchers isolated trace amounts of degraded DNA from TCM products and used new DNA sequencing technologies to determine if the TCMs were accurately labeled. It is hoped that this molecular approach will improve consumer safety and enable authorities to detect if endangered species are being illegally used in medicinal products.

Modern human health issues can also benefit from ancient DNA research through the study of old and degraded DNA preserved in bone, tissue and medicines. In 2007 a team of researchers, including Dr. Mike Bunce, obtained DNA from old human tissue blocks from Africa. The team found an HIV-1 ‘fossil’ virus dating back to 50 years ago. Findings such as these provide key insights into how HIV first ‘jumped’ into humans and ho it has changed over time.