The genetics of four ancient 'Kings' of Sahul and Sunda. This project aims to recover all the genetic information from four ancient humans. Two of these iconic specimens come from Australia and two from Malaysia. We will sequence the entire DNA (genomes) and proteins (proteome) of Mungo Man (Willandra), the Yidinji King (Cairns), the Deep Skull (Borneo) and the Bewah specimen (Malaysian Peninsula). This will provide a better understanding of the settlement of Australia and new knowledge about th ....The genetics of four ancient 'Kings' of Sahul and Sunda. This project aims to recover all the genetic information from four ancient humans. Two of these iconic specimens come from Australia and two from Malaysia. We will sequence the entire DNA (genomes) and proteins (proteome) of Mungo Man (Willandra), the Yidinji King (Cairns), the Deep Skull (Borneo) and the Bewah specimen (Malaysian Peninsula). This will provide a better understanding of the settlement of Australia and new knowledge about the ancient people of Australasia and their relationship to other human populations worldwide. The research will use cutting-edge methods of DNA and protein sequencing of ancient human material and will provide critical reference genomes / proteomes that will anchor future research.Read moreRead less
The origins of Australia's non-Pama-Nyungan speaking people. This project aims to test the likelihood of multiple migrations into Australia before European arrival and determine if the phylogenetic relationships among non-Pama-Nyungan languages is mirrored by their speakers’ genomic phylogenetic relationships. The non-Pama-Nyungan First People of Australia speak an extraordinary number and diversity of Aboriginal languages, but the origins of these languages and the genomic diversity of the peop ....The origins of Australia's non-Pama-Nyungan speaking people. This project aims to test the likelihood of multiple migrations into Australia before European arrival and determine if the phylogenetic relationships among non-Pama-Nyungan languages is mirrored by their speakers’ genomic phylogenetic relationships. The non-Pama-Nyungan First People of Australia speak an extraordinary number and diversity of Aboriginal languages, but the origins of these languages and the genomic diversity of the people who speak them are only now starting to be understood. There is a remarkable concordance between the Pama-Nyungan languages and the genomic diversity of their speakers. This research could show whether genomes change languages or vice versa, or whether they evolve together over time.Read moreRead less
Postgraduate Funding - Population Biology And Dynamics Of Yellowfin Whiting
Funder
Fisheries Research and Development Corporation
Funding Amount
$75,000.00
Summary
The South Australian Marine Scalefish Fishery (MSF) is the most complex fishery in South Australia and is currently undergoing transition through structural reform, development of new harvest strategies and review of the Management Plan. Changes in the dynamics of the fleet have resulted in redirection of effort from primary species such as garfish, snapper and King George whiting towards secondary species including yellowfin whiting.
Yellowfin whiting Sillago schomburgkii is the second ....The South Australian Marine Scalefish Fishery (MSF) is the most complex fishery in South Australia and is currently undergoing transition through structural reform, development of new harvest strategies and review of the Management Plan. Changes in the dynamics of the fleet have resulted in redirection of effort from primary species such as garfish, snapper and King George whiting towards secondary species including yellowfin whiting.
Yellowfin whiting Sillago schomburgkii is the second most valuable Sillaginid after King George whiting and one of the most valuable secondary species in the MSF fishery with most catches from Northern Spencer Gulf, and smaller catches from the West Coast, Southern Spencer Gulf, and Gulf St Vincent. There are also significant recreational catches (31.5% of State catch in 2013/14).
There is a need for improved understanding of the life-history of yellowfin whiting with quantitative estimates of population dynamics including reproduction, growth performance and stock structure. Oceanographic separation of Spencer Gulf and Gulf St Vincent suggests that yellowfin whiting may constitute separate stocks in these regions while possible population sub-structuring occurring at smaller scales has implications for fishery management. There is potential to compare results of the proposed study with previous work to investigate whether decadal changes in the demography and population dynamics of yellowfin whiting have occurred in the South Australian Gulfs, as well as potential factors driving any change.
This project proposal aims to (i) build the capacity for scientific investigation of finfish species in South Australia by providing an opportunity for a science graduate to develop skills in fishery science, (ii) improve the understanding of life-history and population dynamics of yellowfin whiting, and (iii) improve understanding of the stock structure of yellowfin whiting. This project will have linkages to another FRDC funded project (2017/023), “ESD risk assessment for under-utilised species to facilitate structural reform of South Australia’s commercial Marine Scalefish Fishery”.
Objectives: 1. Define the stock structure of yellowfin whiting in South Australia and the relationship to Western Australian stocks using genomic approaches. 2. Define finer scale population structure of yellowfin whiting in the South Australian gulfs using otolith chemistry. 3. Examine spatial and temporal trends in catch among yellowfin whiting and other species in the marine scalefish fishery and how representation among different life-history strategy groups has changed. 4. Investigate size and age structures of yellowfin whiting in the two gulfs of SA and how these have changed over a 22 year period. 5. Increase fisheries science capacity in South Australia through training of the next generation of researchers. Read moreRead less
Assessment Of The Utility Of Genomics For Sydney Rock Oyster Breeding
Funder
Fisheries Research and Development Corporation
Funding Amount
$620,000.00
Summary
Genomics is routinely used across many livestock and plant breeding industries. It is now practical, within certain considerations, to consider applying genomic selection to aquaculture breeding programs due to significant cost reductions in the last decade. Its use in aquaculture breeding programs is increasing and genomics has already been researched for oyster breeding by USC (Vu et al. 2021a; Vu et al. 2021b).
Genomic selection has the potential to reduce the cost of estimating bre ....Genomics is routinely used across many livestock and plant breeding industries. It is now practical, within certain considerations, to consider applying genomic selection to aquaculture breeding programs due to significant cost reductions in the last decade. Its use in aquaculture breeding programs is increasing and genomics has already been researched for oyster breeding by USC (Vu et al. 2021a; Vu et al. 2021b).
Genomic selection has the potential to reduce the cost of estimating breeding values, which presently is a costly and challenging exercise with SROs and also may potentially increase genetic progress and selection accuracy for the SRO BP. The research proposed in this application will evaluate if it is possible to increase genetic progress for the productivity traits of QX disease resistance and growth as well as the product quality trait of meat condition. Increased QX survival and growth are particularly important traits for the SRO industry at this current time due to Port Stephens, the second largest SRO producing estuary in NSW, reeling from the impact of QX disease outbreaks. Climate change resilience is a new trait being investigated for incorporation into the breeding program for industry to respond to this threat. We would also like to assess whether genomics can provide a pathway to increase selection for resilience.
This project has been developed in line with the Oysters Australia Strategic Plan 2020 and the FRDC R&D Plan 2020-2025. The outcomes from this project will assess the feasibility of increasing selection accuracy for traits that improve productivity (growth and meat condition) as well as reduce impacts caused by QX disease and climate change through breeding for resilience. The outcomes will assess the possibility to improve genetic selections for multiple traits such that oysters can be selected on their ability to adapt to new climate conditions, survive QX disease whilst having faster growth and better meat condition. Additionally, this project will build new knowledge skills and networks through a NSW DPI, The University of the Sunshine Coast and The University of New South Wales alliance as well as create post-doctoral study opportunities. These meet the goals in Program 1, 2 and 3 outlined in the 2020-2025 Oysters Australia Strategic Plan.
With respect to the FRDC R&D Plan 2020-2025, this project will build capacity and create knowledge through developing skills and networks between NSW DPI, The University of the Sunshine Coast and The University of NSW to breed oysters that offer oyster businesses greater profitability, reduced risk and that can adapt to changing environments.
This project will explore alternative methods to what is presently used for SRO breeding to assess feasibility of genomic selection and what might be required today to move towards genomic selection in the future. This project will start compiling a reference library for SROs that can be used in the future and promote innovation in SRO breeding to integrate the technology developed from this project. Moreover, costs associated with genomic selection are reducing which increases the value proposition for incorporation into the future. The ultimate success and transfer of outcomes from this project to end user beneficiaries will be through incorporation of these new technologies into the SRO breeding program. Objectives: 1. Collect tissue samples using non-lethal methods and tagging to identify oysters 2. Sequence the whole genomes of selected individuals at high read depth, which will serve as the genotype resource for the project 3. Identify the associations between genotypes and phenotypes and compile a list of genetic markers and the genes associated with QX survival, whole weight and meat condition to then use modelling (for genomic predictions) to give individuals breeding values Read moreRead less
Unlocking the genetic and biochemical potential of kangaroo paws. Using cutting-edge gene technology and an interdisciplinary approach, this project aims to uncover the genes responsible for flower colour in the iconic kangaroo paws of Western Australia, and identify the compounds that produce the colours. The project expects to produce the first entire kangaroo paw genome and identify unique genetic variants and biochemicals underlying colour differences. This new knowledge should help horticul ....Unlocking the genetic and biochemical potential of kangaroo paws. Using cutting-edge gene technology and an interdisciplinary approach, this project aims to uncover the genes responsible for flower colour in the iconic kangaroo paws of Western Australia, and identify the compounds that produce the colours. The project expects to produce the first entire kangaroo paw genome and identify unique genetic variants and biochemicals underlying colour differences. This new knowledge should help horticultural programs to more easily breed varieties with desirable and highly marketable new colours, and could assist in conserving these amazing Australian plants.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
Precision Epigenetics: Targeting The Epigenome To Treat Disease
Funder
National Health and Medical Research Council
Funding Amount
$1,940,576.00
Summary
Epigenetic marks are changes made to the DNA that allow genes to be switched off in some cells and switched on in others. These marks are critical to normal development and often go wrong in disease. We aim to find genes that add epigenetic marks to the DNA and understand how they co-operate at the molecular level to switch genes off. Our focus is on one such gene, SMCHD1. We are developing new drugs against SMCHD1 to treat incurable neurodevelopmental disorder PWS and muscular dystrophy FSHD.
Overcoming The Barriers To Treatment Of Multi-drug Resistant Gram-negative Bloodstream Infections In Australian Children
Funder
National Health and Medical Research Council
Funding Amount
$447,603.00
Summary
There is a critical need to develop new treatments for children with antibiotic resistant infections. The most important bacteria causing resistant infections are known as Gram-negative bacteria. Doctors treating children with resistant Gram-negative infections are faced with few antibiotic options. This project will discover the most important resistant infections in Australian children, and trial a new antibiotic to help doctors to use it in the right children and at the right dose.