| The University of Adelaide | Home | Faculties & Divisions | Search |
 |
|
 |
 |
You are here: |
|
Australian Centre for Ancient DNA Telephone: +61 8 8303 3952 |
Research Activities at ACAD
|
ARC & GovernmentA shipload of consequences: studying the impact of Old World diseases on native South American populations via ancient DNA (Discovery) |
CIs Dr Wolfgang Haak, Dr Bastien Llamas, Dr L Quintana-Murci, and Prof A. Hughes |
| Evolution, disease and extinction - using ancient and modern DNA to investigate molecular evolution in the Tasmanian devil (Linkage) | CIs Dr Jeremy Austin, Dr Katherin Belov, Dr M Jones, Dr E Murchison, and Mrs A Pearse |
| Phylogeography, evlution and taxonomy of humanity's greatest pest, Rattus rattus: epidemiological, archaeological and conservation implications (Discovery) | CIs Prof Alan Cooper, Dr Ken Aplin, Prof Steve Donnellan |
| Using ancient DNA to investigate the environmental impacts of climate change and humans over the past 50,000 years. (Discovery) | CIs Prof Alan Cooper & Prof Tim Flannery (Macquarie University) |
| Expansion and enhancement of the South Australian Regional Facility for Molecular Ecology and Evolution and the Australian Centre for Ancient DNA. (LIEF) | CI Prof Alan Cooper, A/Prof Michael Schwarz, (Flinders University), & Prof Steve Donnellan (SA Museum) |
| Evolutionary genetics of bovid genomes over 60,000 years. (Discovery) | CI Prof Alan Cooper, Prof Jerry Taylor (University of Missouri), & Dr Kefei Chen |
| Developing new methods to retrieve and analyse preserved genetic information.(Linkage) | CI Prof Alan Cooper., Dr Paul Brotherton |
| Australian Membership of the Integrated Ocean Drilling Program. (LIEF) | 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) |
| Commonwealth Environment Research Facilities (CERF): 21st Century Taxonomy: accelerating research and discovery of Australia's biodiversity | CI Prof Alan Cooper, Ken Aplin, CSIRO Sustainable Ecosystems & Kyle Armstrong |
| Environmental Genomics: Mining, climate change, water, crime and health (Linkage) | CIs Alan Cooper, Barry Brook, Jose Facelli, Hugh Cross, Mark Stevens, James Paton & Tuckweng Kok, including Business Paters, SA Water, PIRSA, Aust. Genome Research Facility, SA Museum. |
 |
National Geographic Society, Genographic ProjectThe 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. |
CI Prof Alan Cooper & Dr Wolfgang Haak |
|
|
| French-Australian Science & Technology (FAST) Linkage Equid evolution and domestication using new molecular methods |
CI Prof Alan Cooper & Ludovic Orlando (CNRS, Lyon, France) |
|
|
| Germany Joint Research Cooperation Scheme (DAAD) Population, Ecological and Evolutionary Genetics |
CI Prof Alan Cooper Dr Michael Hofreiter, Max Planck Institute for Evolutionary Anthropology |
|
Marsden Fund 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. |
|
| Retrieving long-term genetic records of environmental change from sediments, stalactites and corals. | Sediments, stalactites and corals all contain organic material
which has been deposited during their formation. These molecules contain
genetic records of the surrounding environment at the time, including the
local plant, animal and microbial communities. The DNA can be used to examine
changes in the composition and diversity of species over time, creating
a large number of research possibilities as sediments and stalactites are
found around the world, while corals occur in a variety of sites. This project will develop methods to extract DNA from sediment, stalactite and coral samples obtained from around Australia, subantarctic islands, and overseas. A postdoc is currently analysing mammal and plant DNA from sediment samples, and will help supervise the project along with Prof. Cooper and Dr Jeremy Austin. An interest in molecular biology and chemistry would be a distinct advantage, as the surrounding matrix must be removed to exposure the organic molecules, and a number of methods will be examined. Mitochondrial DNA will be examined to investigate the impact of previous climatic changes, environments associated with mass extinctions, and the consequences of human impacts and introductions. Interests in evolution, environmental change, and ancient DNA would all be an advantage. There is the potential for fieldwork at cave sites in several areas of Australia. |
|
|
| Applying Ancient DNA techniques to Forensics | Recent methodological advances at ACAD have permitted some of the first in-depth analyses of how preserved DNA is damaged over time, and the likely impacts on the accuracy of retrieved genetic information. These new methods circumvent current limitations of the traditional PCR method, and allow the length and quality of DNA templates to be measured with great accuracy. This project will apply these methods to examine how burial and preservation under a variety of conditions alters DNA templates retrieved from hair, bone, teeth and tissue. The samples analysed will include animal specimens buried under controlled circumstances, South American mummies, and permafrost animal bones over 40,000 years old. The key issues to be examined will be the types and extent of DNA damage, and the rate at which templates degrade under different burial conditions. The research will require good molecular biological skills, and an interest in forensics, ancient DNA, and DNA damage. Project supervisors will be Prof. Alan Cooper, Dr Dean Male and Dr Jeremy Austin. |
|
|
| Using ancient DNA to examine the evolution and genetics of permafrost mammal populations: Wild sheep species from Europe to Canada | Hundreds of thousands of mammal bones and teeth are preserved in permafrost deposits found across Siberia, Alaska, and the Canadian Yukon, and contain detailed genetic records of evolutionary processes spanning more than 100,000 years - including the impacts of dramatic periods of climate change. Previous studies on bison, horse and saber-tooth cats (above) have revealed surprising patterns of evolution and demographic change leading up to the mass extinctions of mammals around 12,000 years ago in the New Wold, which is commonly associated with the arrival of human populations. Strangely, one of the less commonly depicted Ice Age genera is the mighty sheep, Ovis sp. which existed as more than 8 species distributed from western Europe to Eastern Canada. Cytogenetic studies have shown that this distribution is characterised by frequent chromosome reduction (Robertsonian fusion), with the most ancestral living form (Urial sheep, O. vignei) having 2n=58 and occupying areas not influenced by Pleistocene climate changes. O.ammon (argali) have 2n=56, European and Asiatic mouflon (O. musimon and O. orientalis) have 2n=54, Siberian snow sheep, O. nivicola,2n=52. In contrast, the American Dall's sheep, O.dallii (Alaska) and bighorn, O. canadensis, have 2n=54. There is also an isolated population of snow sheep, O. borealis, in Taimyr (the Russian far north) with unkown chromosome number. Two theories have been proposed to explain this distribution, i) alternating migrations and allopatric speciation across the Beringian land bridge joing Siberia and Alaska, or ii) a rapid radiation from a putative center of species radiation, in northeastern Russia. This project will retrieve mitochondrial DNA from permafrost bone samples and investigate the evolutionary history of wild sheep species, and the impact/role of major climate changes. The laboratory techniques involved will use advanced variants of PCR, basic cloning and DNA sequence analysis. Interests in evolution, population genetics/phylogenetics, environmental change (and sheep) would all be advantage. |
|
| Genentic studies of Beringian megafauna. | This project will take advantage of the large ACAD database of DNA and bone samples of bison from across Russia, Siberia, Alaska Yukon and the lower 48 States. An initial study of the mitochondrial control region revealed strong phylogeographic and temporal structures (Shapiro et al. 2004), and indicated that climate change during the peak of the last Ice Age had an extremely negative effect on genetic diversity of this group, prior to any impact from human hunting. This important finding has created a follow-up opportunity for similar studies of both mitrochondrial and nuclear protein-coding genes. Other taxa for which large datasets are available include the narrow-faced peccary (Platygonus), American camels, and mountain sheep and goats. Samples of many taxa have also been obtained from the Grand Canyon area and eastern Russia/Europe and these contain data about climatic effects on biodiversity at the margins of the Beringian populations. |
|
|
|
Ancient DNA studies of Permafrost-preserved ecosystems across a complete glacial cycle. Contact: |
The Yukon Territory(northwestern Canada) preserves a unique frozen record of plants, animals and microbes dating from more than 130 kyr to the modern day. This time span covers the last glacial cycle from the Last Interglacial warm period 130 kyr, through to the last glacial maximum around 20kyr, and onto the Holocene. The frozen biotic remains record the migrations, extinctions and evolution of various organsims druing this period in the arcitc refugium of Beringia, and allow a detailed real-time investigation of ecosystem responses to climate change. Ancient DNA will be used to record the changes in genetic diversity, heterozygosity and speciation events that have taken place as a result of these events, allowing many evolutonary models and processes to be examined. The research will concentrate on plant records, including the large numbers of frozen seeds, fruits and leaves (plant macrofossils) recovered from sub-fossil ground squirrel burrows throughout the area. Other exceptional remains recovered form frozen contexts include buried, in situ sub-fossil vegetation, mammalian coprolites (faeces) and paleosols. The project will be performed with leading Quaternary scientists from Canada (Dr G. Zazula and Prof D. Froese) and members of ACAD, and will involve fieldwork in remote areas, and challenging laboratory work. This research will be integrated with ongoing Quaternary geological and multi-prozy paleoenvironmental research in the region. This project is available to international graduate students with strong research and/or publication records. |
|
|
| Genetic analyses of the paleoecology of the Homo floresiensis
site of Liang Bua, Flores Contact: Prof Alan Cooper, Australian Centre for Ancient NDA Dr Kira Westaway, University of Wollongong |
The cave site of Liang Bua, western Flores records the only known specimens of Homo floresiensis, informally known as 'hobbits'. This project will use anient DNA to examine the paleoecology of the site through plant and animal DNA preserved in sediments (cave, terrace and lake), skeletal remains, on stone tools, and in other records such as speleothems. The ancient DNA records offer a new approach to studying the diversity and composition of local Flores plant communities through time and, hence, the prevailing climatic and environmental conditions. These will be directly compared to established rainfall records inferred from stable isotope analysis of speleothems, and used to reconstruct the climates and environments of western Flores. These reconstructions will identify periods of extreme or abrupt environmental change or major environmental turning points, such as rainforest expansion and contraction and changes in floral composition and diversity, which may have influenced the course of faunal (and human) evolution, dispersals and extinctions. The project is part of a largesclae Quaternary dating and landscape evolution analysis performed by Dr Kira Westaway and Prof Mike Morwood at the University of Wollongong, in collaboration with archaeological investigations performed by Indonesiam archaeologists from ARKENAS, Jakarta. The ancient DNA research will involve both fieldwork at the site, and challenging laboratory research at ACAD. This project is available to international graduate students with strong research and/or publication records. |
| Examining the causes and implications of differences in long- and short-term evolutionary rates | Recent studies have shown that molecular evolutionary rates
appear to change according to the time period over which they are measured
(Penny 2005, Ho et al. 2005). This surprising finding is most pronounced
in the recent past, and suggests that molecular clock calculations could
be seriously inaccurate. The apparent curve in evolutionary rates explains
the discrepancy between extremely fast rates observed in family pedigrees
or within-individual viral populations, and those calculated between species
or populations using fossil calibration points. This difference is suggested
to be caused by the removal of many mutations that exist at the population-level,
but which disappear over time because they are slightly deleterious, or
via genetic drift. However, these processes have not yet been examined in
detail. Datasets of mitochondrial and viral sequences with time series measurements will be used to examine how evolutionary rates at individual sites decline over time. Differences in the effect will be used to infer the amount of selection acting at sites, and related to functional constraints. A variety of bioinformatics approaches will be used, and the project will use computer-based population genetics and phylogenetic packages. The project will have both practical and theoretical implications: For example, the rate curve implies that many studies involving molecular clock estimates of less than around 1 million years will need to be re-assessed. This period encompasses a number of key evolutionary events such as recent human evolution (Neandertals, Out of Africa, colonisation of Europe etc), domestication (cows, dogs, horses, crops etc) as well as conservation biology issues (isolation of populations, species etc). The project will use Genbank sequences to construct phylogenetic trees and examine changes in variability at individual sequence positions. A key aim will be to characterise the shape of the 'lazy-J' curve identified in preliminary studies of several mitochondrial datasets (Ho et al. 2005 Penny 2005). Knowlege and interest in broad scale evolutionary processes and sequence analysis/computing would be very helpful, and there is room for considerable individual input into the research direction. References: Penny, D. Relativity for molecular clocks. Nature
436: 183-4 (2005).
Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular
rate estimates and systematic overestimation of recent divergence times.
Mol. Biol. Evol. 22: 1561-1568 (2005). Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C. The Pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet 72: 659-70 (2003). Garcia-Moreno J. Is there a universal mtDNA molecular clock for birds? J Avian Biol. 35: 465-468 (2004). Shapiro B, Drummond A, Rambaut A, Wilson MC, Matheus P, Sher A, Pybus O, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A. Rise and fall of the Beringian steppe bison. Science 306: 1561-1565 (2004). Da Silva J. The fitness effects of amino acids. Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20: 1318-1325 (2003). |
|
| The thylacine - using ancient DNA
preserved in fossil bones and museum specimens. 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. |
Dr Jeremy Austin |
|
|
| Retrieving and analysing genetic records from Australian
sediment cores: This project is investigating the use of DNA preserved in sediments, and other long term records such as stalactites and corals. Sediment samples from caves, freshwater and marine situations, and a variety of terrestrial sites are being examined using a variety of extraction methods. This research involves geo/biochemical and microbiological input, and close collaboration with physical and earth scientists. We are looking for both Hons and PhD students interested in this research area. |
Prof Alan Cooper Dr Marta Kasper Dr Jeremy Austin A/Prof David Chittleborough Dr Peter Gell |
|
|
| Hobbits & Neandertals: We are developing new methods to recover and analyze trace amounts of highly degraded DNA (down to 20-30bp in size) with great accuracy. These approaches use cutting edge molecular biology approaches, and mass sequencing approaches such as the 454 analyzer. We are keen to involve molecular biologists, geochemists/biochemists and other fields in our attempts to improve all aspects of ancient DNA research. |
Prof Alan Cooper Dr Paul Brotherton Carles Lalueza David Caramelli Dr Juan Sanchez Ludovic Orlando |
| Phylogenetics and evolution of mammals and birds:
Rates, timing and processes: We have a variety of evolutionary studies involving phylogenetics and population genetics (especially of extinct taxa) from Beringia, North and South America, and across the Old World and Africa. Current projects include a focus on the evolution, domestication, and human transport of bovids, pigs and rats using a variety of novel molecular and analytical methods and samples from caves, sediments, museums and modern samples. Another major area of research is the study of the tempo and mode of evolution, especially over the recent past and the reason for apparent changes in the speed of the molecular clock. This work involves population genetics and computational work, and has generated a number of significant new research areas. |
Prof Alan Cooper Dr Jack da Silva Dr Michael Lee, SA Museum Andrew Hugall, PhD Laura Frank, Honours |
|
| Copyright ©
2009
The University of Adelaide Last Modified 21/11/2009 ACAD CRICOS Provider Number 00123M |
