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Research Funding Since 2005

Australian Research Council

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.

Lead investigator: Alan Cooper
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.
Lead investigator: Jeremy Austin
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.
CIs: 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.
CIs: 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.
CIs: 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.
Lead investigator: 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 Austin, Dr Jaime Gongora, Prof Terry Hunt, Dr David Burney, Dr Greger Larson, Prof Keith Dobney, Prof Jeremy Taylor.
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

21st Century Taxonomy: accelerating research and discovery of Australia's biodiversity(CERF 2008).

This grant was funded under the Commonwealth Environment Research Facilities scheme.

CIs: Prof Alan Cooper, Ken Aplin, CSIRO Sustainable Ecosystems & Kyle Armstrong
Evolutionary genetics of bovid genomes over 60,000 years. (Discovery 2007) CIs: 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)

UoA Investigator Prof Alan Cooper
Expansion and enhancement of the South Australian Regional Facility for Molecular Ecology and Evolution and the Australian Centre for Ancient DNA. (LIEF 2006) CIs: Prof Alan Cooper, A/Prof Michael Schwarz, (Flinders University), & Prof Steve Donnellan (SA Museum)
Australian Centre for Ancient DNA
School of Biological Sciences
Darling Building
North Terrace Campus

The University of Adelaide
South Australia 5005


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