Advanced Bioinformatics workshop dates for 2016 announced. We are pleased to advise that the Advanced Bioinformatics workship is planned for 7-11th November, 2016. Click here for details
Guest and Visiting Researcher Seminars.
The Deep History of Sea Country: Colonisation, submerged landscapes and the archaeology of Australia's coasts.
Professor Sean Ulm, ARC Future Fellow and Director of the Tropical Archaeology Research Laboratory, James Cook University.
Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin.
Anna Szecsenyi-Nagy, University of Mainz, Germany.
Western Carpathian Basin (including western Hungary or Transdanubia) was one of the key regions in the process of Neolithisation in Central Europe. The Starčevo culture, representing the earliest farmers on this region, settled down at around 5800 cal BC in western Hungary. It had a major role in the formation of the Linearbandkeramik culture (LBK). The following Sopot, Lengyel cultures of the Late Neolithic and the Early Copper Age Transdanubia show repeated cultural influences from Southeastern Europe, besides local extant cultural traditions. The focus of my PhD study is the process of these cultural changes in western Hungary, investigating mitochondrial and Y chromosomal aDNA. A total of 298 skeletons were sampled and processed, with an overall success rate of 86% for the typing of the mitochondrial DNA. Comparing the mitochondrial and Y chromosomal results with other published data and evaluating them with population genetic analyses, I gained an insight into the prehistoric population history of Western Hungary. My study may give an additional help to prehistoric archaeology, for a better understanding of the nature of cultural changes, supporting it with new types of evidence that shows that prehistoric Transdanubia was a mediating area between Southeast and Central Europe.
|16 &17 December||
Talk 1: Cultural & Ecological complexity in prehistoric South America: Things to be considered when inferring Native South American population history from palaeogenetic data: mini workshop.
Talk 2: Colonial Encounters and Climate Change: using ancient DNA to study the human population of Western South America
A/Professor Lars Fehren-Schmitz, Department of Anthropology, Biomolecular Science & Engineering
|2 & 3 December||
Talk 1: The genetic History of cattle breeds: mini workshop.
Talk 2: Identifying signatures of selection using a novel approach called Generation-Proxy Selection Mapping.A/Professor Jared Decker, Division of Animal Science, University of Missouri, USA
|Public Talk 28 November Venue: The Braggs Lecture Theatre Start: 5:30pm||
Survivors: the animals and plants that time has left behind
Professor Richard Fortey, Natural Museum of London
Despite a commonly held view that evolution moves ever onwards and upwards, there are, scattered around the globe, living survivors that tell the story of ancient worlds. Many of these organisms have come through global crises that reorganised the entire biosphere through mass extinction: several of them have outlived both trilobites and dinosaurs. I spent several years visiting these messengers from the past in their natural habitats, to find out if there was some common factor in their longevity, or whether they were simply lucky. The journey took me to Yellowstone Park, remote mountains in China - and, not surprisingly, several places in Australia. In my talk I shall describe the lives of these survivors, and explore the threats they now face to their continued existence. We need to conserve what Charles Darwin termed “living fossils” for future generations.
Advanced Bioinformatics for Early Career Researches, November 10-14, 2014.
Workshop - Computational Macroevolution: analysis and visualisation of complex dynamics on phylogenetic trees.Hosted by ACAD and sponsored by the Environment Institute, this 1 day free workshop is presented by Dan Rabosky from the University of Michigan. The workshop will provide theoretical background and a hands-on practicum in new methods for quantifying complex mixtures of macroevolutionary rate dynamics on phylogenetic trees.
The Royal Society of South Australia Seminar
The next public seminar will be held on Thursday, September 11th. The speakers will present the fascinating life of Norman Tindale who, as an anthropologist and entomologist, recorded a large number of genealogies of Aboriginal people during the 1920s and 1930s. His vast ethnographic collection, housed at the South Australian Museum, culminated in the 1974 map of ‘Aboriginal tribes of Australia, their terrain, environmental controls, distribution, limits and proper names’.
Work on StalictitesDr Silivia Frisia
University of Newcastle
|19th December 13||
Title TBAVanessa Hayes
Head, Human Comparative & Prostate Cancer Genomics
The Kinghorn Cancer Centre, NSW
Meeting the BEASTJoseph Heled (developer of *BEAST), and
New algorithms for phylogeographyby Stephane Guindon (developer of PhyML and FitModel)
from the University of Auckland, New Zealand
What we know about the BovidaeColin Groves
Australian National University
Update on molecular rates and implications for estimation of evolutionary timescales.
Simon Ho and PhD Candidates: Martyna Molak, Sebastian Duchene and Fangzhi Jia, of the Molecular Ecology, Evolution & Phylogenetics lab at the University of Sydney.
Solving challenging DNA casework with SNPs and InDels: forensic apllication of biallelic markers
Applying ancestry informative SNPs to aid identification in major criminal investigationCarla Santos
Forensics Genetics Unit, University of Santiago de Compostela
Insights into genetic variation in diverse human populations from large-scale resequencing
It is now possible to sequence whole human genomes from population samples, and I will present some analyses of this data, mostly from the 1000 Genomes Project. Each individual carries 3-4 million variants. Most of these are neutral and have no effect on our survival or evolutionary fitness, but provide insights into our past population movements and expansions. Some are harmful and we can now measure this ‘genetic burden’. We all carry around 100 loss-of-function variants that inactivate protein-coding genes; for about 20 genes, both copies are inactivated. However, this is generally not detrimental to our health. But we also carry 0-7 known disease mutations, and these are predicted to have a detectable impact on health in at least 10% of people. In addition we can identify advantageous variants and begin to understand the ways in which we have adapted to different environments
The Origin of Our SpeciesChris Stringer
Earth Sciences Department
The Natural History Museum, UK
Human evolution can be divided into two main phases. A pre-human phase in Africa prior to 2 million years ago, where walking upright had evolved but many other characteristics were still essentially ape-like. And a human phase, with an increase in both brain size and behavioural complexity, and an expansion from Africa. Evidence points strongly to Africa as the major centre for the genetic, physical and behavioural origins of both ancient and modern humans, but new discoveries are prompting a rethink of some aspects of our evolutionary origins, including the likelihood of interbreeding between archaic humans (for example the Neanderthals) and modern humans.
Applications of Single Molecule, Real-Time (SMRT) Sequencing to understand human diseases.
SMRT sequencing is a new DNA sequencing technology which is characterized by long read lengths and high consensus accuracy regardless of the sequence complexity or GC content of the DNA sample of interest. These characteristics can be harnessed to gain information about human genomic regions previously inaccessible with other technologies. These new applications are highlighted, including the study of trinucleotide repeat expansions, structural variations, large-scale deletions, and palindromic sequences.
Retention of hunter-gatherer economies among maritime foragers from Caleta Vitor, northern Chile, during the late Holocene: Evidence from stable carbon and nitrogen isotopic anlysis of skeletal remains
Empire does not strike back: glorious past, struggling present, and doomed future of the lion.
A high coverage Denisovan genome - what 30x coverage from a more than 50,000 old pinky bone tells us about her and our past.
Martin Kircher, Department of Genome Sciences, University of Washington
The last million years of horse evolution.
Ludovic Orlando, Centre for GeoGenetics, Natural History Museum of Denmark
The eukaryotic tree of life as a framework for eukaryotic community analyses.
Laura Wegener-Parfrey, Department of Chemistry & Biochemistry, University of Colorado
Application of whole genome sequencing to identify Mendelian disease candidates in dogs using a 1-case + N-control design.Bob Schnabel, College of Agriculture, food and Natural Resources
The evolving molecular clock: Current research directions.
Dr Simon Ho
|17th May, 12||
The Genome of the Black Death
A/Professor Johannes Krause
Computational Approaches for Linking Comparative Genomics to Biochemistry and Evolution
A/Professor David Liberles
Forensic genetics for human remains identification: The EAAF experience.
Dr Carlos Vulla
From falconry to farming: new ways of exploring the "Neolithic Revolution" through the fossil vertebrate recordProfessor Keith Dobney
Department of Archaeology, University of Aberdeen, UK
Natural Disaster Victims and DNA identificationKirsty Wright
University of Queenland.
Ancient Proteins: Going beyond bulk collagen isotope analysis using Liquid Chromatography Isotope Ratio Mass Spectrmetry.
Dr Colin Smith, ARC Future Fellow
Ellie Simpson, Forensic Anthropologist
|14th October, 11||
Prof Mike Wilkinson
Mapping diversity to geochemistry
Vital legacies: Indigenous DNA and posstcolonial science. 2) Towards genetic research in Aboriginal and Torrens Strait Islander
Dr Emma Kowal, NHMRC Research Fellow
Dr Stephen Bent
Aboriginal use of spinifex and spinifex collections in the South Australian Museum
Identifying Cliques of Convergent Charactoers: Concerted evolution in the cormorants and shags.
Dr Barbara Holland
Present a collection of research work on plant genomics.Dr James Breen
University of Zurich, Switzerland
|7th December, 2010||
The Neandertal in you: What have we learned from the Neandertal Genome Project?Prof Carles Laluza-Fox
Institute of Evolutionary Biology, Barcelona, SPAIN
Present collection of research work on microbial biogeochemistry to oceanography.Dr Eric Gaidos
University of Hawaii, USA
|25th November, 09||
Learning from the past - studying the effects of climate change using temporal DNA data.Stefan Prost
Department of Microbiology and Genetics, University of Vienna.
Comparative phylogeneticsProf Mark Pagel
Head, Bioinformatics Lab, University of Reading
|5th December, 08||
Salia, Biofilms and the Oral EnvironmentDr John Kaidonis
Senior Lecturer, Dental School, University of Adelaide
Phylogeography of Beringian Arctic Plants
Software demo on Geneious; its uses and future directions
Using dietary isotopes from ancient bones and teeth to study early humans, Neandertals and animals
|4th August||Dr Jennifer Cropley, Postdoctoral Fellow
Victor Chang Cardiac Research Institute, Molecular Genetics Program, Epigenetics Laboratory
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
The genetic diversity of past (equid) populations: what it tells and what it does not
Silent witness: new analytical approaches to advance and enhance the forensic value of human hairChris Lennard and Dennis McNevin
University of Canberra
Bayesian divergence time estimation using relaxed clocksSimon Ho
School of Botany & Zoology, Australian National University
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.
A biologist's need for computationAjay Royyuru
Head of IBM's Computational Biology Center and lead scientist for IBM's Genographic Project. USA
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.
Linguistic Prehistory of Australia and SahulPeter Sutton
South Australian Museum/University of Adelaide
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.
Bovine & Sheep EpigeneticsStefan Hiendleder
Dept. of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilian University, Munich, Germany.
Origin and evolution of the Fragaria polyploid genomesMathieu Rousseau-Gueutin
National Institute for Agronomical Research, Bordeaux France
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.
The past, present and future of South American camelids
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.