The Origin and Evolution of the Animal Phyla inferred from Analysis of Multiple-Gene Data. Australia has recently begun an extensive research programme in the genomics of our flora and fauna. The enormous amounts of data that emerge from such research are highly complex, but they hold the key to understanding how biological organisms change over time. Our research will untangle that data to answer fundamental, unanswered questions in modern science: How did the animal groups originate? How are ....The Origin and Evolution of the Animal Phyla inferred from Analysis of Multiple-Gene Data. Australia has recently begun an extensive research programme in the genomics of our flora and fauna. The enormous amounts of data that emerge from such research are highly complex, but they hold the key to understanding how biological organisms change over time. Our research will untangle that data to answer fundamental, unanswered questions in modern science: How did the animal groups originate? How are they related to each other? How is biodiversity changing? The answers to these questions and the new analytical tools we will develop will put Australia firmly on the international "map" of Bioinformatics.Read moreRead less
Efficient phylogenetic methods that manage the curse of genomic complexity. This project aims to develop new methods and software to infer the evolutionary history of organisms using genomic data. These new phylogenomic methods need to take account of the complexity of evolutionary processes and/or patterns in time (along the evolutionary tree) and space (along the genome). This project is significant because these methods must merge mathematics and statistics with High-Performance Computing to ....Efficient phylogenetic methods that manage the curse of genomic complexity. This project aims to develop new methods and software to infer the evolutionary history of organisms using genomic data. These new phylogenomic methods need to take account of the complexity of evolutionary processes and/or patterns in time (along the evolutionary tree) and space (along the genome). This project is significant because these methods must merge mathematics and statistics with High-Performance Computing to handle the huge quantities of genetic data and the complexity of evolution itself. An important expected outcome of this project will be the development and release of freely-available software that incorporates these new methods. This project expects to benefit scientists who need to infer phylogenies from genomic data. Read moreRead less
New Molecular Approaches to Comparative Phylogeography. Funds are requested to gather data to test new molecular and analytical approaches in the field of molecular phylogeography. We will generate phylogeographic hypotheses from mitochondrial and microsatellite DNA for six species and evaluate the utility of microsatellite data for the reconstruction of phylogeographic history. We will borrow powerful analytical techniques from the field of evolutionary ecology and use them in a completely nove ....New Molecular Approaches to Comparative Phylogeography. Funds are requested to gather data to test new molecular and analytical approaches in the field of molecular phylogeography. We will generate phylogeographic hypotheses from mitochondrial and microsatellite DNA for six species and evaluate the utility of microsatellite data for the reconstruction of phylogeographic history. We will borrow powerful analytical techniques from the field of evolutionary ecology and use them in a completely novel way to test hypotheses of microsatellite diversity. Our research is inter-disciplinary in that we will bridge the gap between molecular phylogenetics and molecular evolution and in so doing make a major advancement in this emerging field.Read moreRead less
Analysing and modelling molecular rate variation among nuclear and mitochondrial genomes. My research will have important practical benefits for bioinformaticians and evolutionary biologists, because existing analytical methods will be rigorously tested and new tools will be developed. Australia has a comparatively high concentration of researchers in this field, so my research will foster domestic collaboration and import international expertise. The research will provide important insights int ....Analysing and modelling molecular rate variation among nuclear and mitochondrial genomes. My research will have important practical benefits for bioinformaticians and evolutionary biologists, because existing analytical methods will be rigorously tested and new tools will be developed. Australia has a comparatively high concentration of researchers in this field, so my research will foster domestic collaboration and import international expertise. The research will provide important insights into the rates and patterns of genetic changes associated with domestication, and into variation in evolutionary rates among the primate ancestors of humans. In addition to developing new software, which will be made publicly available, I will develop new evolutionary models to supplement existing software packages. Read moreRead less
Dynamic evolution of mutation rates: causes and impacts on genomic analysis. This project aims to illuminate the role of variation in mutation rate in driving evolutionary change. Mutation rate is a core parameter in evolutionary analyses in essential applications including epidemiology, conservation and medicine, yet remains a “black box” given arbitrary universal values. This project will take a whole-of-biodiversity approach to understanding the forces shaping mutation rate, impact on evoluti ....Dynamic evolution of mutation rates: causes and impacts on genomic analysis. This project aims to illuminate the role of variation in mutation rate in driving evolutionary change. Mutation rate is a core parameter in evolutionary analyses in essential applications including epidemiology, conservation and medicine, yet remains a “black box” given arbitrary universal values. This project will take a whole-of-biodiversity approach to understanding the forces shaping mutation rate, impact on evolution of biodiversity and effect on accuracy and precision of phylogenetic analyses. Using Australian case studies, the expected outcome of this project will be a greater understanding variation in mutation rate between species, providing significant benefits in developing more sophisticated and reliable phylogenetic analyses.Read moreRead less
Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence. Phylogenies describe the relationships among species and provide the essential framework for understanding evolutionary processes. They are an essential tool in the identification of functionally important regions in DNA sequences. An important aspect of identifying phylogenies is measuring how DNA sequences change in time. The proposed research will develop sophisticated, practical models of sequen ....Improving the accuracy of phylogenetic reconstruction by improving models of sequence divergence. Phylogenies describe the relationships among species and provide the essential framework for understanding evolutionary processes. They are an essential tool in the identification of functionally important regions in DNA sequences. An important aspect of identifying phylogenies is measuring how DNA sequences change in time. The proposed research will develop sophisticated, practical models of sequence divergence and make them freely available in open source software. The software and models will positively impact on studies seeking to understand Australian biological diversity. The proposed resolution of the eutherian mammal orders will further significantly impact on utilisation of rodents as a model organism for human biology.Read moreRead less
Climate change and cryptic biodiversity in the Australian arid-zone: Molecular phylogeny-based assessment of conservation priorities. Australia's arid zone comprises two thirds of the country yet from a climate change, biodiversity, and conservation point of view it has received little attention relative to eastern Australia. The project will address broad questions in evolutionary biology with unique Australian systems, make a world class contribution to the fields of phylogeography, molecular ....Climate change and cryptic biodiversity in the Australian arid-zone: Molecular phylogeny-based assessment of conservation priorities. Australia's arid zone comprises two thirds of the country yet from a climate change, biodiversity, and conservation point of view it has received little attention relative to eastern Australia. The project will address broad questions in evolutionary biology with unique Australian systems, make a world class contribution to the fields of phylogeography, molecular phylogenetics and conservation genetics and contribute substantially to the continued training of high quality research students and postdoctoral fellows. The project directly addresses two National Priority Research Areas and will supply of critical information to the eight biggest of the 57 Natural Resource Management Regions. Read moreRead less
Comparative phylogeography and conservation genetics of Australia's biodiversity hotspot. Southwestern Australia has been identified as one of the world's 25 biodiversity hotspots. The project will address broad questions in evolutionary biology with unique Australian systems, make a world class contribution to the fields of phylogeography, molecular phylogenetics and conservation genetics and contribute substantially to the continued training of high quality research students. I am a foundation ....Comparative phylogeography and conservation genetics of Australia's biodiversity hotspot. Southwestern Australia has been identified as one of the world's 25 biodiversity hotspots. The project will address broad questions in evolutionary biology with unique Australian systems, make a world class contribution to the fields of phylogeography, molecular phylogenetics and conservation genetics and contribute substantially to the continued training of high quality research students. I am a foundation member of the new ARC Environmental Futures Network: Discovering the Past and Present to Shape the Future. One of its primary listed objectives is "documenting Australia's biodiversity: recognising, understanding and managing key hotspots". My research plan fits in precisely with this research agenda. Read moreRead less
Mechanisms of colour production and the evolution of animal signals. This project aims to reveal how diverse colours are produced in reptiles and the information these colours convey about individual health, condition and performance. The project evaluates how stress affects both pigment deposition and the nano-structure of cells and tissues, which together produce colour. By comparing similar colours generated by two entirely different classes of pigment (carotenoids and pteridines), this proje ....Mechanisms of colour production and the evolution of animal signals. This project aims to reveal how diverse colours are produced in reptiles and the information these colours convey about individual health, condition and performance. The project evaluates how stress affects both pigment deposition and the nano-structure of cells and tissues, which together produce colour. By comparing similar colours generated by two entirely different classes of pigment (carotenoids and pteridines), this project will provide new insights into the evolution of animal coloration, and will significantly enhance our understanding of pteridines, one of the most prevalent but least understood classes of pigment in vertebrates.Read moreRead less
Old brains, new data - early evolution of structural complexity in the vertebrate head. Of the all the complex structures biology has provided, the evolution of the vertebrate brain and its sensory organs is perhaps the most enigmatic. The fossil record occasionally provides a chance to trace this evolution, but only with the use of novel X-ray scanning techniques can these secrets be detailed in three dimensions. Exploiting the exceptional fossil record from Australia and China, this team will ....Old brains, new data - early evolution of structural complexity in the vertebrate head. Of the all the complex structures biology has provided, the evolution of the vertebrate brain and its sensory organs is perhaps the most enigmatic. The fossil record occasionally provides a chance to trace this evolution, but only with the use of novel X-ray scanning techniques can these secrets be detailed in three dimensions. Exploiting the exceptional fossil record from Australia and China, this team will for the first time collect a vast comparative data base which will yield clues on the early evolution of the ear, eye and brain. Read moreRead less