Visitor seminar

16th April, 09, Darling T.Rm

Comparative phylogenetics

Visitor seminar

15th April, 09, Darling T.Rm

Coalescence/SIR/ABC methods

by Christian Anderson
Scripps Institute of Oceanography, University of San Diego

Guest presenter

5th Dec 08, Darling T.Rm

Salia, Biofilms and the Oral Environment

Visitor seminar

28th Nov 08, Darling T.Rm

Phylogeography of Beringian Arctic Plants

by A/Prof Eric Dechaine
Western Washington University, USA

Visitor seminar

31st Oct 08, Darling T.Rm

Software demo on Geneious; its uses and future directions

by Shane Sturrock, Geneious, Auckland, NZ

Visitor seminar

3rd Oct 08, Darling T.Rm

Using dietary isotopes from ancient bones and teeth to study early humans, Neandertals and animals

by Mike Richards
Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig Germany

Visitor seminar

4th Augt 08, Darling T.Rm

Epigenetic variation in adaptive evolution

The epigenetic state of a locus can be affected by environmental factors such as diet. The murine Avy (agouti viable yellow) allele is one such locus: dietary supplementation of pregnant dams with methyl donors changes the epigenetic state of the locus in the offspring. At Avy, an IAP retrotransposon is inserted upstream of agouti. When epigenetically active the IAP usurps transcriptional control, driving ectopic expression of agouti signalling protein to produce the characteristic obese yellow phenotype. The epigenetic state of the IAP is unstable in the germline, so that isogenic mice show wide variation in the somatic epigenetic state of the IAP, with resultant broadly variable penetrance and expressivity. Supplementation of maternal diet with methyl donors promotes epigenetic silencing of the IAP, shifting the spectrum of offspring phenotypes away from obese yellow. We have previously shown that methyl donors can affect the germline epigenetic state of the Avy IAP. Here we show that continual supplementation of Avy mice over five generations leads to progressive germline stabilisation of the IAP epigenotype, so that the silent state becomes more strongly heritable and thus significantly more prevalent in the population. In unsupplemented populations the IAP is completely silent in 13% of mice. In a supplemented population, successive breeding of males carrying a silent IAP increases the prevalence of the silent allele almost three-fold (to 31%) by the fifth generation. These results suggest that long-term exposure to an environmental stimulus can effect epigenetic changes throughout a population. Such mechanisms may contribute to adaptive evolution via stable epigenetic silencing in the germline.

Visitor seminar

25th July 08, Darling T.Rm

The genetic diversity of past (equid) populations: what it tells and what it does not

by Ludovic Orlando
Paléogénétique et Evolution moléculaire, Institut de Génomique Fonctionnelle de Lyon, FRANCE

Visitor seminar

18th July 08, Darling T.Rm

Talk on Linkage project - Silent witness: new analytical approaches to advance and enhance the forensic value of human hair

Visitor seminar

4th July 2008, Darling T.Rm

Bayesian divergence time estimation using relaxed clocks

Simon covered aspects of the origins of the molecular clock hypothesis, the support for the clock from the neutral and nearly neutral theories, including a summary of various methods that can be used to deal with rate variation among lineages, and provided an overview of the latest methods that are available in the Bayesian software BEAST.

Public Seminar

10th June 08, Benham LT

A biologist's need for computation

Information technology plays a vital role in enabling new science and discovery in biology. Advances in high throughput and platform technologies in biology present an unprecedented challenge in scale, management, and analysis of biological data. Advances in computing architecture and scale are enabling simulations of complex biological processes at various organizational levels from atomic to cellular and beyond. High performance computing that takes full advantage of massive parallelism is a necessary means to obtain the performance needed to tackle this complexity.

This talk will examine the trends in biology driving new needs of information technology and provide examples of research at the intersection of these two disciplines, including the Genographic Project, where it seeks to chart new knowledge about the migratory history of the human species and answer age-old questions surrounding the genetic diversity of humanity. A group of the world's leading scientists are working to collect and analyse more than 100,000 DNA samples from people all over the world and The Australian Centre for Ancient DNA at the University of Adelaide is analysing ancient human specimens from around the world as part of this project.

Short bio: Ajay Royyuru heads the Computational Biology Center at IBM Research, with research groups engaged in various projects including bioinformatics, structural biology, protein science and applications on Blue Gene, functional genomics, systems biology, and computational neuroscience. Ajay joined IBM Research in 1998, initiating research in structural biology. He obtained his Ph. D. in Molecular Biology from Tata Institute of Fundamental Research, Mumbai and B. Sc. (Hons.) in Human Biology and M. Sc. in Biophysics from All India Institute of Medical Sciences, New Delhi. Ajay
did post-doctoral work in structural biology at Memorial Sloan-Kettering Cancer Center, New York. Currently, his work focuses on collaborative research at the interface of information technology and biology. Working with biologists and institutions around the world, he is engaged in research and development of computer and software systems that will advance personalized, information-based medicine. Ajay leads the IBM Research teams working with National Geographic Society on the Genographic Project.

Personal page: http://www.research.ibm.com/people/r/royyuru
Research page: http://www.research.ibm.com/compsci/compbio

Guest seminar

30th May 08, Darling T.Rm

Linguistic Prehistory of Australia and Sahul

Over the last 40 years there has been enormous progress in our understanding of Australia's and Sahul's prehistory, both archaeologically and linguistically. On the other hand the human biological prehistory of the region saw a burst of research activity in the 1930s-1960s followed by a slow-down. Recent advances in DNA studies have reinvigorated activity in this field, and since the 1990s indigenous people have engaged in several collaborative DNA projects with researchers. In this paper we sketch out the state of play in Sahul's prehistory and the linguistic prehistory of mainland Australia, including the debate on whether or not Australian linguistic prehistory can be reconstructed to any significant time-depth. We also discuss the evidence for the role of climate change and technological change in the huge and explosive expansion of the linguistic family known as Pama-Nyungan, which obliterated most other languages of the Australian mainland in the mid-Holocene.

Guest seminar

23rd May 08, Darling T.Rm

Bovine & Sheep Epigenetics

Guest seminar

18th Apr 08, Darling T.Rm

Origin and evolution of the Fragaria polyploid genomes

Polyploidy or whole genome duplication has long been recognized to be a major force in evolution. This process has been observed in plants, invertebrates, lower vertebrates and even in human (paleopolyploidy). Polyploidy is especially prevalent in plants, where it is known as a major speciation process that has recurrently affected various lineages. Most of the cultivated species, as the cultivated strawberry Fragaria x ananassa (2n = 8x = 56), are polyploid species. The objective of my PhD was to obtain a better knowledge of polyploidy within the Fragaria genus by studying the origin and evolution of its polyploid species.
We first explored the contribution of two low-copy nuclear gene phylogenies (GBSSI and DHAR) to clarify the evolutionary relationships within the small Fragaria genus (11 diploid and 9 polyploid species). After orthology assessment, the finding of almost identical phylogenetical relationships with two independent datasets gives strong support of the hypothesis proposed for the origin of the polyploid species. Our results provided new insights into the evolutionary history of Fragaria, demonstrating the occurrence of independent events of polyploidization, suggesting new hypothesis on the origin of the tetraploid species and demonstrating hybrid speciation (allopolyploidy) in the hexaploid and octoploid species.
At a second time, we were interested by the evolution of the octoploid Fragaria genome structure along the events of polyploidization and hybridization. To that purpose, comparative genetic mapping was conducted using two Fragaria populations with different levels of ploidy, 2x and 8x. Results showed high levels of macrosynteny and colinearity suggesting that polyploidization and hybridization were not accompanied by major structural rearrangements.
In conclusion, the main results of this work provide evidence of the reticulate evolution of the hexaploid and octoploid species and highlight the absence of important genome reorganization after the polyploidization events and during evolution.

Guest seminar

4th April 08, Darling T.Rm

The past, present and future of South American camelids

by Jane Wheeler, Conopa Peru

Guest seminar

5th Feb 08, Darling T.Rm

Sahultime

Imagine we could turn back time and view Australia's ancient past. What would we see? SahulTime is a Monash University research projet that presents an interative model of the Australian/PNG continent over the last 100,000 years.

ACEBB Guest seminar

24th Sep 07, Mawson LT

Disentangling the complex web of climatic change and human colonization on the flora and fauna of Pleistocene Australia

Australia rifted from Antarctica some 50 Ma, allowing ecosystems to evolve along a separate pathway from the rest of the planet. Lacking placental mammals, marsupial mammals evolved to fill most familiar niches. As the continent drifted into the subtropics in the late Cenozoic, rainfall decreased, and monsoonal circulation dominated the moisture regime of northern Australia. The flora and fauna of the continent evolved to meet these new conditions. At the onset of the Quaternary, short term, high-magnitude oscillations began between relatively warm, wet conditions during global interglacials trading dominance with cold, arid conditions during global glaciations, resulting in additional ecosystem adjustments. Recent studies have shown that large vertebrates were able to adjust to these changing conditions without dramatic loss of species diversity. In this larger context, the loss of all large and many smaller marsupials as well as several other large vertebrate species in the Late Pleistocene has challenged our community for over 150 years to develop a coherent explanation for the extinction based on solid evidence with a consistent theoretical underpinning. Climate reconstructions at both global and continental scales suggest that primary resources should have varied markedly on millennial timescales for most of the Quaternary, possibly amplifying in the mid Quaternary, although there is little evidence to suggest the late Quaternary was significantly different, other than the colonization of the continent by humans about 50 ka. Our research has focused on teasing apart the impacts of climate change and human colonization on the flora and fauna of Pleistocene Australia. We rely on isotopic tracers of diet, drinking water, and moisture stress preserved in the eggshells and teeth of large vertebrates to compare ecosystem response to climate change prior to human colonization with changes following a human presence on the landscape. This requires developing continuous time-series of paleoecological proxies that extend from the present back 50 to 100 ka before human colonization. Our results from four large and widely separated regions representing arid to semi-arid climates provide compelling evidence for an unprecedented and irreversible decrease in plant diversity between 50 and 45 ka, shortly after humans colonized Australia and about the same time that most megafauna became extinct. Independent climate reconstructions indicate an intermediate climate regime without rapid oscillations 60 to 40 ka, minimizing the possibility of a climate-mediated impact. Dietary intake exhibits only minor variability in response to climate changes over the 100 ka prior to human colonization. With a climate driver for ecosystem change and megafaunal extinction no longer tenable, the core question centers around what exactly did humans do to result in the unprecedented changes to Australia's flora and fauna preserved in the geological record.