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Australian Centre for Ancient DNA
School of Earth & Environmental Sciences
Darling Building
THE UNIVERSITY OF ADELAIDE
SA 5005
AUSTRALIA
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Telephone: +61 8 8313 3952
Facsimile: +61 8 8313 4364

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New Postgraduate Projects currently available

Permafrost Bison bone, 20kyr
Permafrost Bison bone, 20kyr

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.

Research in permafrost areas of northern Canada, and the 'hobbit' site of Liang Bua, Flores.
Ancient DNA studies of permafrost-preserved ecosystems across a complete glacial cycle.

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 organisms during this period in the arctic 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 evolutionary 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 from 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-proxy paleoenvironmental research in the region. This project is available to international graduate students with strong research and/or publication records.

Contact:
Prof. Alan Cooper, Australian Centre for Ancient DNA; alan.cooper-at-Adelaide.edu.au
www.adelaide.edu.au/acad
Dr. Grant Zazula, Yukon Paleontology Program; grant.zazula@gov.yk.ca / www.yukonheritage.com

Genetic analyses of the paleoecology of the Homo floresiensis site of Liang Bua, Flores

The cave site of Liang Bua, western Flores records the only known specimens of Homo floresiensis, informally known as 'hobbits'. This project will use ancient 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 largescale 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 Indonesian 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.

Contact:
Prof. Alan Cooper, Australian Centre for Ancient DNA; alan.cooper@Adelaide.edu.au
www.adelaide.edu.au/acad
Dr Kira Westaway, University of Wollongong; kira@uow.edu.au
www.uow.edu.au/science/eesc/student/Postgr/westa/profile.html

PhD Students wanted,
contact: Prof Alan Cooper

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Specific projects for Honours/PhD Projects, 2007

First Nation artefacts from Whitehourse,  Yukon, Canada
First Nation artefacts from Whitehourse,
Yukon, Canada

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

Deposits of sloth dung,  Mylodon Cave, Patagonia
Deposits of sloth dung,
Mylodon Cave, Patagonia

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 World, 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 unknown chromosome number. Two theories have been proposed to explain this distribution, i) alternating migrations and allopatric speciation across the Beringian land bridge joining 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.

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 this 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). Knowledge 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. Submitted.
  • Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20: 1318-1325 (2003).