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Australian Centre for Ancient DNA
School of Earth & Environmental Sciences
Darling Building
SA 5005

Telephone: +61 8 8313 3952
Facsimile: +61 8 8313 4364

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Research awards
  • Andrew Farrer, awarded the Lawrence Forbes & Decie Denholm PhD scholarship that supports PhD research to the value of $5000 per year (3years).
  • Alan Cooper, awarded the Royal Society of South Australia's highest honour, the Verco Medal, for his significant and outstanding contribution to the field of evolutionary biology and ancient DNA. October 2013
  • Michael Herrera, Best Poster for 2nd Year PhD Candidate, School of Earth & Environmental Sciences. August 2013
  • Alan Cooper, South Australian Scientist of the Year finalist. Dept. of Further Education, Employment, Science & Technology, July, 2013.
  • Julien Soubrier, South Australian PhD Research Excellence finalist. Dept. of Further Education, Employment, Science & Technology, July 2013.
  • Jennifer Shaw, I'm a Scientist, Get me out of here competition for the Wet & Wild segment. April, 2013
  • Jennifer Templeton, 1st prize for Best Poster, Asia-Pacific Sequencing Summit, Bali. September, 2012
  • Jeremy Austin, Unsung Hero of South Australian Science Award, August 2012
  • Alan Cooper, South Australian Scientist of the Year Finalist. Dept. of Further Education, Employment, Science & Technology, July, 2012.
  • Janette Edson, I'm a Scientist, Get me out of here competition for the Lithium Zone segment. May, 2012; and 3 Minute Thesis, 1st Round.

Research activities at the Australian Centre for Ancient DNA(ACAD)

ACAD is one of the leading ancient DNA centres in the world, and with an international reputation for highly-innovative research is developing new platform technolgies and collaborative programs with international research leaders across multiple fields. Expertise at ACAD is catagorised in several major areas/themes. For further information on our research, please select from the lefthand navigation panel.

ACAD has been awarded several million dollars worth of research funding from the Australian Research Council (ARC), State and Federal Government agencies since establishing in 2005, and has several linkages with international collaboroators. We greatly appreciate the support of the ARC and our Business Partners as listed below, for our continued research endeavours:

Australian Federal Police
Australian Genome Research Facility (AGRF)
Biomatters, Ltd, NZ
South Australian Museum
SA Water
Primary Industry Resources South Australia
Forensic Science SA
National Institute of Forensic Science
National Geographic Society, USA
Marsden Funding Agency, NZ

List of successful grants:

ARC and Government


PhD Projects/Honours (Interested students or self funded Postdocs are encouraged to contact one of our staff for collaborative initiatives.
ARC & Government awards

Using ancient microbiomes and genomes to reconstruct human history. Laureate 2014
This project aims to reconstruct human history using ancient microbiomes and genomes. The research will use combined signals of bacterial, genomic and climate data to reconstruct the impacts of migrations, changes in diet, environment, and health in different parts of the world.

Cooper A.

Human identification, ancient DNA and genomics: new approaches using targeted capture and high throughput DNA sequencing (Discovery 2014). DNA based human identification is both critical and central to criminal and coronial investigations, disaster-victim and missing persons identification, repatriation of war dead and counter-terrorism operations. This research project will develop and apply a novel targeted sequence capture and high throughput DNA sequencing approach to simultaneously type thousands of informative identity, ancestry and phenotype markers in a single assay to idenfity suspects/missing persons.

Austin, J.
Using genetics to recover Australia's lost history (Linkage 2014). Using detailed contextual and geneological information from museum archives, this project will generate the frist genetic map of Aboriginal Australia.

Cooper A, Haak W, Mitchell R, Kowal E, Walshe K, Sutton P, Reich D, Easteal S, Stephen J, Vilar M, Tyler-Smith C.

Using phylogenomics to record the impacts of climate change, extinction and population fragmentation. Discovery 2014.
Using ancient DNA, this study will analyse how ancestral genetic diversity is distributed amongst surviving bison populations, and the role of nuclear loci under selection and drift. It will create a novel temporal dataset of genomic adaptation and evolution, and will generate critical data for studies of evolutionary processes such as extinctions, speciation and conservation biology and management.

Cooper A, Taylor J, Higham T, Ludovic O, Reich D

The role of epigenetic modifications in bovid adaptation to environmental change (Linkage 2013).
This projects explores the role of epigenetic change, where gene expression is regulated without changing the DNA sequence, in how animals adapt to rapid climate change. The research will trace epigenetic markers in ancient bison and cows through 30,000 years of climate change, and identify key adaptive genes for the cattle industry.

Cooper A, Suter CM, Wilkinson M, Hiendieder SG, Llamas B, Stephen JR, Taylor JF, Densham DH.

Identifying the diversity and evolution of loci associated with adaptation to aridity/heat and salinity in ancient cereal crops (Linkage 2013).
Using ancient grains of wheat, barley and rye, this research will examine 'lost' genetic diversity at key genes associated with resistance to aridity, salt and disease. This project will make the proteins of key genes, and study their interaction with the environment over time by measuring ions in the grains to reveal the ancient environmental conditions.

Cooper A, Wilkinson MJ, Gilliham M, Stephen JR, Salk DE, Pinhasi R, Higham TF, Densham DH.

Refining the timescale of human evolution and dispersal using ancient DNA (Discovery 2012).
This research aims to improve estimates of our evolutioanry timecale, our relationships to other hominids and our impact on the natural world.

CIs: Wolfgang Haak, Simon Ho, Bastien Llamas, Doron Behar.
Reconstructing the impact of climate change on Australian native species (Discovery 2012).
What is the impact of past climate change on Australian native animals? This research will help identify species and ecosystems at greatest potential risk, and to help predict and minimise the effects of future change.
CIs: Jeremy Austin, Leo Joseph, Marc Suchard, Margaret Byrne
DNA and the missing: ancient DNA and advanced forensic identification (Future Fellowship 2011).
This project will apply expertise in analysis of ancient DNA to build capacity and expertise within Australia to identify highly degraded human remains.
CI: Dr Jeremy Austin
A powerful new genetic view of the recent evolutionary history of humans and their diseases (Discovery 2011).
Bacteria on teeth cause dental disease, but have also recently been associated with broader health issues, including diabetes, stroke and heart issues. In this project ancient DNA will be used to reveal changes in these bacteria as humans moved from a hunter‑gatherer to farmi lifestyle, providing valuable background information for modern dental/medical practice
CIs: Prof Alan Cooper, A/Prof John A Kaidonis, Prof Grant C Townsend, Dr Neville J Gully, Prof Peter M Bartold, Prof Keith D Dobney, Dr Thomas F Higham, Prof Michael Richards, Prof Dr Carles Lalueza-Fox
Reconstructing the human colonisation of the Pacific using modern and ancient chicken DNA (Discovery 2011).
This project will reconstruct one of the last great human migrations, from Island Southeast Asia across the Pacific to Hawaii and Easter Island, using DNA from the domestic chicken, which was carried on the voyage. Ancient and modern DNA, and archaeological data will be used to reveal the source, route, timing, and whether contact was made with South America
CIs: Dr Jeremy J Austin et al.
Comparative Paleogenomics of the Arctic Tundra Ecosystem: the genetic response of plants and animals to climate change (Discovery 2011).
This project will use DNA from deep‑frozen seeds and bones 100,000 years old to record how species respond to climate change ‑ by adapting and surviving or by shifting ranges and moving. Very large numbers of genes will be examined to identify changes across the genomes of four plant and two animal species, and contrast the responses to major climatic shifts.
CIs: Prof Alan Cooper, Asst Prof Eric G DeChaine, Dr Grant D Zazula, Prof Dr Joseph A Cook, Asst Prof Charles C Davis
Enhancement of South Australian high-performance computing facilities (ARC LIEF 2010) Professors Dereck Leinweber, David Adelson, Alan Cooper, Jim Denier, Corey Bradshaw, and J. Roddrick. ,

The impact of severe bushfires on the ecology, demography and genetics of frongs in the Victorian Kinglake region (Linkage 2010, administered by the University of Melbourne)

CIs: Drs Kristen Parris, Jane Melville, Jeremy Austin, and Murry Littlejohn.

From Biodiversity to Health: Performing the first genetic audits of Australia (Future Fellowship 2010).
This project will establish a new technology for the rapid measurement of environmental biodiversity, whether that be in natural resources such as forests, or pathogens in water supplies or hospitals. It will provide some of the first ever comprehensive environmental impact assessments, permitting responsible resource development with major benefits to industry and the economy. It will also provide a common platform for government agencies, from Department of Environment and Heritage to the Federal Police, and will create new tools to improve water management, biosecurity, forensics/policing and human health, as reflected by the wide range of industry partners supporting the project
CI: Professor Alan Cooper.

A shipload of consequences: studying the impact of Old World diseases on native South American populations via ancient DNA (Discovery 2010).
This pioneering project will give the first real-time picture of the genetic changes induced by epidemics in human populations. This will reveal important new information about the likely impact of future epidemics on the genetic diversity of the immune system in modern human populations and will be of substantial use in building epidemiological models. By proposing to combine state‑of‑the‑art science with global problems of humanity, we will address Australia's interests in expanding scientific expertise beyond its borders and place Australia at the leading edge of disease impact studies.

CIs Dr Wolfgang Haak, Dr Bastien Llamas, Dr L Quintana-Murci, and Prof A. Hughes

Multi-model predictions of ecosystem flux under climate change based on novel genetic and image analysis methods (Super Science 2010).
Improorecasts of ecosystem shifts must be a key focus of future ecological research if we are to preserve our unique Australian landscapes. Our proposal is of clear benefit to Australia because of the urgent need for integrated methods to predict the cumulative impact of shifts in climate and land use. We will also contribute innovative tools involving genetic and image analysis, and state‑of‑the‑art modelling. The damage modern human societies are inflicting on global environments has led to a great demand for logistically feasible and cost‑effective ways to prevent biodiversity loss.

CIs: Prof Andrew J Lowe, Prof Corey J Bradshaw, Prof Anton J van den Hengel, Prof Barry W Brook, Prof Alan Cooper

Transformational diagnostics (Super Science 2010).
Australia has established world's leading capabilities in optical fibres and surface science that, when brought together, have the potential to transform applications that require non‑invasive, real‑time and/or portable biological detection tools. We propose a novel and ambitious suite of projects that bring together these capabilities with experts in reproductive health, forensics and explosives to solve pressing problems in each of these areas that have the promise to develop into new industries for Australia as well as to explore rich science opportunities at the boundaries of these disciplines.

CI: Prof Tanya M Monro, Prof Alan Cooper, Prof Lois A Salamonsen, Prof Robert J Norman, Adj/Prof Nigel A Spooner, and Dr Linh Nguyen
Environmental Genomics: Mining, climate change, water, crime and health (Linkage 2009).
The new Environmental Genomics approach will employ high‑powered genome sequencing systems to perform some of the first detailed genetic studies of Australian environments. The resulting high‑resolution data will comprise a genetic audit, providing essential information for the accurate measurement of climate and environmental change. This method will dramatically improve the speed, and power of environmental impact assessments, permitting responsible resource development with major benefits to industry and the economy. It will also create new tools to improve water management and quality, biosecurity, forensics/policing and human health, as reflected by the diverse range of industry partners supporting this project.
CIs: Prof Alan Cooper, Prof Barry Brook, Dr Jose Facelli, Dr Hugh Cross, Dr Mark Stevens, Prof James Paton & Prof Tuckweng Kok.
Evolution, disease and extinction - using ancient and modern DNA to investigate molecular evolution in the Tasmanian devil (Linkage 2009).
This study will provide critical genetic data and tools to monitor and prioritise conservation strategies, including insurance
populations and disease suppression, aimed at preventing extinction. It will strengthen ongoing conservation programs carried out by the Save the Tasmanian Devil Program and will help publicise the plight of the devil both nationally and internationally.
CIs Dr Jeremy Austin, Dr Katherin Belov, Dr M Jones, Dr E Murchison, and Mrs A Pearse
The thylacine - using ancient DNA preserved in fossil bones and museum specimens. (Discovery 2008)
The key issues are the tempo and mode of the extinction event on both mainland Australia and in Tasmania, and the relative roles of human hunting/poisoning, disease and introduced competitors. We are using ancient DNA to precisely track the demographic changes over time and space, and will contrast this information to those within the Tasmanian Devil which managed to avoid extinction in Tasmania.
CIs: Professor Barry Book, Dr Jeremy Austin
Developing new methods to retrieve and analyse preserved genetic information.(Linkage 2008).
This project will position Australia at the leading edge ofreserved DNA, and will use innovative molecular biology approaches to develop a range of new forensic, archaeological and medical applications. It will build Australian knowledge and scientific capacity by developing core expertise and training personnel in areas important for biosecurity, customs and quarantine, forensics/counter‑terrorism, and studies of climate change. It will also create and foster research innovation in molecular biology with spin‑offs for evolution, archaeology, medical and conservation biology research, and will also encourage involvement with the rapidly expanding field of genomics and bioinformatics.
CIs Prof Alan Cooper and Dr Paul Brotherton
Commonwealth Environment Research Facilities. 21st Century Taxonomy: accelerating research and discovery of Australia's biodiversity(CERF 2008). CI Prof Alan Cooper, Ken Aplin, CSIRO Sustainable Ecosystems & Kyle Armstrong
Evolutionary genetics of bovid genomes over 60,000 years. (Discovery 2007) CI Prof Alan Cooper, Prof Jerry Taylor (University of Missouri), & Dr Kefei Chen
Using ancient DNA to investigate the environmental impacts of climate change and humans over the past 50,000 years. (Discovery 2006) CIs Prof Alan Cooper & Prof Tim Flannery (Macquarie University)
Australian Membership of the Integrated Ocean Drilling Program. (LIEF 2006) Collaborating Institutions: University of Western Australia, University of Newcastle, University of Wollongong; University of Melbourne, University of Tasmania, Monash University, University of Sydney, Macquarie University, University of QLD, James Cook University, CSIRO, ANSTO, Australian Inst. of Marine Science, and Marine Geoscience (MARGO)
Expansion and enhancement of the South Australian Regional Facility for Molecular Ecology and Evolution and the Australian Centre for Ancient DNA. (LIEF 2006) CI Prof Alan Cooper, A/Prof Michael Schwarz, (Flinders University), & Prof Steve Donnellan (SA Museum)
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International grants/awards

National Geographic Society, Genographic Project

The Genographic Project is a major international project to genetically map the timing, location and nature of human dispersals around the world. Most of the research effort will concentrate on building a detailed genetic map of populations around the world using mitochondrial and Y-chromosome markers. ACAD is the ancient DNA centre for this project, and will contribute information from ancient specimens from around the world, using new cutting edge molecular approaches to deal with the issues of contamination and DNA template damage.


CIs Prof Alan Cooper & Dr Wolfgang Haak


French-Australian Science & Technology (FAST 2009).

Equid evolution and domestication using new molecular methods
CI Prof Alan Cooper & Ludovic Orlando (CNRS, Lyon, France)
Germanynt Research Cooperation Scheme (DAAD 2009)

Population, Ecological and Evolutionary Genetics
CI Prof Alan Cooper Dr Michael Hofreiter, Max Planck Institute for Evolutionary Anthropology
Marsden Fund (2010): New views from old soils. Reconstructing environmental and climatic change using genetic signals in buried paleosoils. David Lowe, Alan Cooper, and Dr Churchman. University of Otago, NZ

Marsden Fund (2009): New Zealand's megaherbivores: resolving their ecological role and the impact of their extinction on the flora.

PI Jamie Wood, Landcare Research New Zealand Ltd. Others: Janet Wilmshurst, Trevor Worthy, and Alan Cooper.
NSF NESCENT Catalysis meeting (2010): Integrating datasets to investigate megafaunal extinction in the Late Quaternary. Alan Cooper, R. Guralnicfk, Jessica Metcalf.
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