Demographic and evolutionary inferences from large, whole-genome datasets. A new data structure for genome-wide datasets has allowed great improvements in the efficiency of genomic data storage and in population genomics simulations, which are crucial to developing and testing mathematical models of population history and species evolution. We will take these advances in new directions, using efficient data structures to dramatically improve inferences about: the demographic histories of popul .... Demographic and evolutionary inferences from large, whole-genome datasets. A new data structure for genome-wide datasets has allowed great improvements in the efficiency of genomic data storage and in population genomics simulations, which are crucial to developing and testing mathematical models of population history and species evolution. We will take these advances in new directions, using efficient data structures to dramatically improve inferences about: the demographic histories of populations, rates of genome change, and phylogenetic networks, and we will develop the first inference methods for the multispecies coalescent with recombination. Outcomes will include advances in understanding the evolutionary histories of humans and other species, including pathogens of importance for global health.Read moreRead less
Australian Heritage: constructing the first Aboriginal reference genome. This project aims to use DNA sequencing technologies to generate the first complete and accurate Aboriginal genomes, along with maps of genomic variation around Australia. It will combine a range of advanced analytical methods to integrate past and present indigenous genetic diversity from human populations around the world into a new pan-human reference genome. This project will lead to a step change in our understanding o ....Australian Heritage: constructing the first Aboriginal reference genome. This project aims to use DNA sequencing technologies to generate the first complete and accurate Aboriginal genomes, along with maps of genomic variation around Australia. It will combine a range of advanced analytical methods to integrate past and present indigenous genetic diversity from human populations around the world into a new pan-human reference genome. This project will lead to a step change in our understanding of global human genomic variants and provide a range of new targets relevant to medical biology, while significantly improving our knowledge of human genetic history and its consequences in the modern day.Read moreRead less
The genomic landscape of speciation in hominins and other taxa. This project will develop a new analytical framework to build detailed genomic maps of speciation genes across different taxa, to determine whether observed speciation is the result of background selection and demography alone, or whether there are actual barriers to gene flow and introgressed DNA. The model will provide novel insights into the mechanistic basis of speciation, specifically whether a common set of genes or pathways a ....The genomic landscape of speciation in hominins and other taxa. This project will develop a new analytical framework to build detailed genomic maps of speciation genes across different taxa, to determine whether observed speciation is the result of background selection and demography alone, or whether there are actual barriers to gene flow and introgressed DNA. The model will provide novel insights into the mechanistic basis of speciation, specifically whether a common set of genes or pathways are central to the speciation process. The framework will be developed using the large genomic datasets available across a range of plant and animal species. Applying the model to a modern human population dataset will elucidate the role introgressed DNA from Denisovan and Neanderthals has played in shaping human evolutionary history and may provide novel insights into the genetic basis of disease.Read moreRead less
Challenging current dogma on the inheritance of mitochondrial DNA. Mutations in mitochondrial DNA are often used to infer genetic relationships and have been associated with the expression of human diseases. This project examines the exact mechanism of inheritance of mitochondrial genes to enhance biological interpretations and our understanding of the heritability of specific diseases.
Population dynamics and genetic variation of plants with contrasting fire responses. We combine the traditional concerns of population viability analyses with the modern techniques of DNA fingerprinting for precise genotyping of individual plants and their seeds. We expect major breakthroughs in our understanding of how fire-killed species have survived thousands of years of frequent burning by Aborigines (by identifying seeds dispersed long distances from burnt parents); how paternity of offspr ....Population dynamics and genetic variation of plants with contrasting fire responses. We combine the traditional concerns of population viability analyses with the modern techniques of DNA fingerprinting for precise genotyping of individual plants and their seeds. We expect major breakthroughs in our understanding of how fire-killed species have survived thousands of years of frequent burning by Aborigines (by identifying seeds dispersed long distances from burnt parents); how paternity of offspring changes over the lifespan of plants which retain their seeds for many years; at what age within-plant genetic variation is at a maximum as a guide to optimal fire management; and the extent that deleterious somatic mutations explain low seed set among long-lived species.Read moreRead less
Evolution and the immune system: genetic differences in immune response between human populations due to adaptation to living in different geo-climatic locations. The project, which investigates the genetics of inter-population differences in immune response, will lead to advances in immunology and population genetics research, explain present population specific differences in disease incidence and possibly forecast future population trends of diseases such as asthma and allergy. The study will ....Evolution and the immune system: genetic differences in immune response between human populations due to adaptation to living in different geo-climatic locations. The project, which investigates the genetics of inter-population differences in immune response, will lead to advances in immunology and population genetics research, explain present population specific differences in disease incidence and possibly forecast future population trends of diseases such as asthma and allergy. The study will strengthen ties with collaborators around the world, thus promoting excellence in Australian research and gain Australia prestige in the international community as a country that produces research of global significance. Understanding the immune system's 'recent evolutionary roots' has implications for the health of Australians, especially in light of Australia's increasingly multi-ethnic background.Read moreRead less
Sex, parthenogenesis and adaptation: a novel laboratory 'natural selection' experiment testing the adaptive significance of sexual and asexual reproduction. One of the greatest challenges for evolutionary biology is explaining the widespread occurrence of sexual reproduction. Many theoretical models show some inherent benefits of sex, however these models make assumptions that little or no empirical data exists for. Using a novel phenomenon found in the parasitoid wasp genus Trichogramma, I will ....Sex, parthenogenesis and adaptation: a novel laboratory 'natural selection' experiment testing the adaptive significance of sexual and asexual reproduction. One of the greatest challenges for evolutionary biology is explaining the widespread occurrence of sexual reproduction. Many theoretical models show some inherent benefits of sex, however these models make assumptions that little or no empirical data exists for. Using a novel phenomenon found in the parasitoid wasp genus Trichogramma, I will investigate the adaptive significance of sexual and asexual reproduction in a laboratory natural selection experiment and therefore directly test the theory for the evolution and maintenance of sex. This will be the first such test in a higher organism.Read moreRead less
A shipload of consequences: studying the impact of Old World diseases on native South American populations via ancient DNA. This pioneering project will give the first real-time picture of the genetic changes induced by epidemics in human populations. This will reveal important new information about the likely impact of future epidemics on the genetic diversity of the immune system in modern human populations and will be of substantial use in building epidemiological models. By proposing to comb ....A shipload of consequences: studying the impact of Old World diseases on native South American populations via ancient DNA. This pioneering project will give the first real-time picture of the genetic changes induced by epidemics in human populations. This will reveal important new information about the likely impact of future epidemics on the genetic diversity of the immune system in modern human populations and will be of substantial use in building epidemiological models. By proposing to combine state-of-the-art science with global problems of humanity, we will address Australia's interests in expanding scientific expertise beyond its borders and place Australia at the leading edge of disease impact studies.Read moreRead less
Diet influences the selective advantage of mitochondrial DNA mutations. This project aims to examine critical mechanisms that affect mitochondrial DNA variation within species. It aims to test the hypothesis that mitochondrial DNA haplotypes have the potential to be under nutritionally induced balancing selection as a consequence of cellular signalling and/or Adenosine triphosphate (ATP) production by mitochondria. Diet can vary both seasonally and geographically and is a key environmental param ....Diet influences the selective advantage of mitochondrial DNA mutations. This project aims to examine critical mechanisms that affect mitochondrial DNA variation within species. It aims to test the hypothesis that mitochondrial DNA haplotypes have the potential to be under nutritionally induced balancing selection as a consequence of cellular signalling and/or Adenosine triphosphate (ATP) production by mitochondria. Diet can vary both seasonally and geographically and is a key environmental parameter that influences the ability of a species to colonise new habitats. The project plans to characterise the functional links between specific mitochondrial DNA haplotypes, mitochondrial functions and organismal traits. The expected outcome is a more precise grasp of the processes influencing genetic variation within and among species, which would inform current issues in ecology and genetics.Read moreRead less
Why do only some exotics become invasive? Combining ecological and genomic approaches to address alternative hypotheses in a recent Australian weed. This project will specifically test alternative hypotheses about how weeds become invasive. As invasive weeds affect both agricultural and native ecosystems equally, research on understanding the mechanisms of weed invasion is critical. Outcomes will benefit Australia by allowing better prioritisation of management against exotic plants already i ....Why do only some exotics become invasive? Combining ecological and genomic approaches to address alternative hypotheses in a recent Australian weed. This project will specifically test alternative hypotheses about how weeds become invasive. As invasive weeds affect both agricultural and native ecosystems equally, research on understanding the mechanisms of weed invasion is critical. Outcomes will benefit Australia by allowing better prioritisation of management against exotic plants already in the country by providing predictive tools to estimate likelihood of spread. For formal Pest Risk Analysis by regulators (eg Biosecurity Australia), our project will provide genomic tools by which the potential weediness of a regulated plant can be assessed through genetic screening, and forms part of an international effort to identify 'weedy genes'. Read moreRead less