PhD projects available now
Postgraduate divisional scholarships (FOR AUSTRALIAN OR NEW ZEALAND RESIDENTS
ONLY) commencing in 2011, Semester 2, now open. For expression of interest in any
of the following projects, please apply here
and include your CV/resume. International students should consult the International
Student website for tuition fees and associated costs for PhD Candiature before
applying. [ Visit
website here] ·
Both the Australian Department of Immigration and University of Adelaide expect international applicants to meet English Language Proficiency (ELP) requirements. The ELP is based on high scores in IELTS (International English Language Testing System) or TOEFL (Test of English as a Foreign Language). For further information please refer to http://www.international.adelaide.edu.au/admission/ or http://www.adelaide.edu.au/publications/pdfs/inter_pgcw_en10.pdf.
Applicants will also be encouraged to apply for Australian postgraduate awards (closing date is Oct 31st) where applicable, refer to this website for the application process >> http://www.adelaide.edu.au/graduatecentre/scholarships/postgrad/pgresearch/apa.html. International students are also invited to apply, although international course fees are likely to apply and you should consult the following International webpage before making enquiries. Closing date for International Scholarship applications is August 30th and you should note the selection process is extremely competitive. Recent successful applicants for the research awards have usually had a research Masters, or a coursework Masters with a substantial research component, and an outstanding academic performance at an internationally recognised university. Projects are open to Australian and NZ citizens/permanent residents with a 1st class Honours degree.
Enquires to Ms Maria Lekis or Prof. Alan Cooper for further details.
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Application of computational methods in the analysis
of human evolution
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The study will use both ancient and modern sequence data produced as
part of the National Geographic Society 'Genographic
Project'. The project will investigate the impact and applications
of recent advances such as the rates curve (Ho et al. MBE 2005), paleodemographic
reconstructions (Atkinson et al. MBE 2008) and other issues involved in
the molecular dating of human migrations and population movements, and
the relationship to environmental and climatic changes over the past 100-200
Kyr. The work will involve collaborations with archaeologists, palaeoenvironmentalists
and other members of the Genographic Project. |
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aDNA studies of Liang Bua Cave, Flores
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Genetic studies of sediments, rodent bones, and other biological signals
such as stalactites from the home of the hobbits, Homo floresiensis, and
surrounding sites on Flores and Sulawesi. In collaboration with Kira Westaway
and Mike Morwood (U. Wollongong), Mike Gagan (ANU) and Jian-xin Zhao (UQ). Desirable background. Evolution, ecology, climate/environmental change, sedimentology, stratigraphy, paleontology, fieldwork. |
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Naracoorte caves
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A unique deposit of preserved rodent bones and possum droppings has been found in Blanche Cave, Naracoorte, which provide a detailed record of environmental changes in SE Australia over a 40 Kyr time period, recording the impacts of climate change, Aboriginal landscape use, the Last Glacial Maximum, Holocene warming and the impacts of Europeans and introduced pests. Desirable background. Evolution, ecology, climate/environmental change, sedimentology, stratigraphy, paleontology, fieldwork. |
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Sediment DNA records of climate change and evolution
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ACAD has a large collection of sediment samples from marine, lacustrine,
and terrestrial (mostly cave) sites from around the world. This project
involves recovering plant, animal and other genetic records to analyse
climate and environmental change. It could be combined with the next project. Desirable background. Sedimentology, stratigraphy, soil chemistry, biochemistry, ecology, paleontology, fieldwork. |
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Antarctic ice
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The ultra low temperatures of Antarctic sediment and ice deposits are perfect for long-term preservation of genetic records. Working with Antarctic researchers, this project will analyse the genetic records of microbes, plants, and marine organisms from both terrestrial and marine sediment samples. New technological approaches will be used to detect extremophiles, and the full genetic diversity of these environments. Desirable background. Evolution, sedimentology, stratigraphy, polar research, fieldwork. |
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Yukon permafrost deposits
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A detailed genetic and ecological study of the impacts of climate change on a deep frozen ecosystem spanning a 130kyr time frame. The study groups will be plants and small mammals, and this project will examine the biological and genetic responses of populations to major environmental change - such as migration, glacial refugia, local extinction, and invasions. Desirable background. Evolution, sedimentology, stratigraphy, polar research, fieldwork. |
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Rates of evolution
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This project will further explore the issues of temporal dependency of molecular rates, ie changes in the speed of the molecular clock according to the time period over which it is used. This largely computer-based analysis will explore new discoveries about why this effect occurs, and how it might be corrected to allow for accurate dating of major evolutionary events within human evolution, domestication, biogeography and epidemiology. Desirable background. Evolution, computational biology, phylogenetics, population genetics |
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Using new aDNA approaches to improve forensic methods
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New methods have recently been developed at ACAD to allow finescale analysis of ancient DNA molecules - including their length and amount and type of damaged positions, which would effect the accuracy of genetic typing. This new window into the way in which DNA degrades, and is affected by different types of environmental treatment (drying, washing, temperature, humidity etc) is of major importance for forensic studies. This project is in collaboration with several forensic groups, and the Australian Federal Police. Desirable background. Molecular biology, chemistry, genetics, evolution, population genetics. |
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Studies of megafauna from the La Brea tar pits, Los Angeles
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The La Brea tar pits, in the middle of Los Angeles, hold an amazing collection of well-preserved megafauna, including hundreds of thousands of bones of carnivores (wolves, bears, lions, saber-tooths etc). Many of the bones are extremely well-preserved, with extractable collagen and perfect morphological preservation - although they are deeply ingrained with tar. Recent studies at ACAD have demonstrated that it is possible to retrieve DNA from young specimens, and this has opened the way to largescale population level analyses of megafauna on a number of levels, ranging from phylogenetics to population genetics. Desirable background. Molecular biology, chemistry, evolution, population genetics. |
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Phylogeny and age of the New Zealand Acanthisittid wrens
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The NZ wrens are the sister taxa to the passerines (song birds), which includes nearly 50% of all bird species. Their unique basal position means that they record the earliest characteristics of this group, and in addition they are one of the only large bird radiations in NZ. This project will reconstruct this phylogeny using ancient DNA, and analyse the timing of the radiation with respect to the Oligocene Drowning, a major genetic bottleneck in NZ's past. Desirable background. Evolution, molecular biology, genetics, population genetics. |
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Rodent evolution, biodiversity and human migration in
Australia and South East Asia
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This collaborative study with Dr Ken Aplin, CSIRO, will use ancient DNA
from the large numbers of rodent bones preserved in caves and archaeological
sites throughout these areas to analyse rodent evolution, biodiversity
and extinctions through time, in response to climate change and human
habitat alteration. A key project will be to analyse Rattus rattus species
complex, and to use this to trace the timing and nature of human migration
patterns during the Neolithic. The project has the potential to allow
a focus on evolution, population genetics, taxonomy, biodiversity, and
archaeology. Desirable background. Evolution, ecology, molecular biology, genetics, population genetics, fieldwork. |
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| 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. |
| 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). |
