Genetic diversity assessment of the koala: applying novel genomic methods and assessing genetic exchangeability across the species range
The Reprogen Animal Bioscience group in the Faculty of Veterinary Science in collaboration with James Cook University, Australian Ecosystems and San Diego Zoo is offering 3 exciting PhD opportunities in Koala conservation management, genetics and genomics. PhD number 1 is outlined below along with the overall scope of the project.
One of Australia's most iconic species, the koala, is under threat. Factors responsible for significant population decreases are multifactorial in nature. Underpinning this is a lack of understanding of the genetic diversity of populations across the species range, resulting in an inability to identify populations most at risk of local extinction. This information is needed for effective management of population viability, and for the setting of conservation management units. In order to develop sound management strategies and prioritise active intervention and management of populations at greatest risk three unique PhD opportunities offer you the opportunity to participate in frontline scientific discovery and ensure survival of this iconic species. You will be working with a team of researchers and industry partners to develop new tools for the scientific management of the Koala (Phascolarctos cinereus) which will assist the Koala Species Survival Plan (SSP)Furthermore you will engage with wildlife conservation biologists at the Australian Ecosystems Foundation, national and statewide conservation groups and visit the frontline research unit in Koala genetics at San Diego Zoo. The Zoo's Institute for Conservation Research was established in 1975 and has a worldwide reputation for research and conservation of biodiversity. Their contributions in koala conservation are complemented by extensive ex-situ breeding programs, species recovery programs and reintroductions, and field conservation programs many of which are achieved through partnerships and collaborations. Their vision includes an emphasis on utilising the latest advances in science and technology to help conserve species worldwide and the work of the Institute for Conservation Research already incorporates an emphasis on the management of populations based on sound genetic information. San Diego Zoo holds the largest ex-situ collection of koalas outside of Australia and this collection has generated funds for in-situ conservation and research in Queensland Australia for the last 30 years through the Koala Ecology Group. The research group at The University of Sydney and James Cook University hold world edge capability in molecular genetics, animal genomics and molecular diversity and ecology across a wide range of species. You will be well supported with access to leading technologies and research capability. The three projects on offer are briefly described below.
This project will use new whole-genome technology to provide a foundation for the development of conservation management units for the koala. It aims to develop new high-density genome-wide markers using Restriction-site Associated DNA (RAD) tags to provide information for defining national conservation priorities for the koala, including sub-species delineation and the setting of management units. Secondly, the project will use the same technology to undertake a specific assessment of replicate southern populations to assess their conservation value and likelihood of persistence. Thirdly, it will provide low cost tools for ongoing individual and population characterisation based on low density SNP marker panels. While a limited number of studies of genetic diversity and population structure in koalas have been undertaken using neutral genetic markers from limited regions of the genome, subsequent technological advancements now permit whole-genome studies which offer a wealth of information for species conservation within affordable budgets and achievable timeframes. Single Nucelotide Polymorphism (SNP) DNA markers have been shown to be the new marker of choice since they are highly abundant across the genome and are amenable for analysis using high-throughput, low-cost technologies. In comparison to the widely used microsatellite and mitochondrial DNA (mtDNA) loci, the use of SNPs gives much broader coverage of the genome and for conservation purposes SNPs not only offer better quality information at a higher density for population studies and population relatedness, but also have the potential to provide information on natural selection, adaptation and fitness, which limited numbers of assumed neutral markers cannot readily provide.At the species level, the quality of current information being used to define koala sub-specific taxonomy is limited. Koalas are tenuously divided into three allopatric subspecies: Phascolarctos cinereus victor (Victoria and South Australia) (Troughton 1935); Phascolarctos cinereus cinereus (New South Wales) (Goldfuss 1817); Phascolarctsos cinereus adustus (Queensland) (Thomas 1923). However these classifications are based on political state boundaries and have little biological meaning or application for management. This means that to date, the sub-specific taxonomy of the koala remains unresolved. A second aim of this project is to remedy this situation by providing clear population taxonomy on a genomic level. The sample collection being accessed is the most comprehensive sample repository of Koala samples in the world. The samples are highly descriptive in terms of location, age sex and other biophysical data pertaining to each animal. You will use standard population diversity analytical methods, as well as for the first time a novel unsupervised clustering methodology and network visualization method (NETVIEW) to obtain between and within population characteristics.This project offers an Australian Industry Postgraduate Award (AIPA) with a stipend of $28,000 per year for three years.
For further details and initial discussion of project opportunities
Prof Herman Raadsma Reprogen Animal Bio-Science group, Faculty of Veterinary Science University of Sydney. Tel 02 9351 1603 e:email@example.com
Dr Kyall Zenger, Senior Lecturer James Cook University, Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, 4811 QLD, Australia. Ph: +61-7-4781 6532 e: firstname.lastname@example.org
Dr Kellie Leigh, Executive Officer, Australian Ecosystems Foundation, www.ausecosystems.org.au Ph: 02 6351 4515 35 Crane Road Lithgow NSW 2790 Australia
Want to find out more?
The opportunity ID for this research opportunity is: 1642
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