KOALA CONSERVATION MANAGEMENT; USING GENETICS, GENOMICS AND INTEGRATED ECOLOGICAL MODELLING PHD SCHOLARSHIPS OPPORTUNITIES

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1 FACULTY OF VETERINARY SCIENCE KOALA CONSERVATION MANAGEMENT; USING GENETICS, GENOMICS AND INTEGRATED ECOLOGICAL MODELLING PHD SCHOLARSHIPS OPPORTUNITIES

2 THREE PHD SCHOLARSHIP OPPORTUNITIES FOR 2013 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. IN ADDITION, THE GENOMICS PROJECT OFFERS AN AUSTRALIAN POSTGRADUATE TRAINING SCHOLARSHIP WITH A STIPEND OF $28,000 PER ANNUM FOR 3 YEARS.

3 3 PROJECTS ON OFFER 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) 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 following. 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 exsitu 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

4 GENETIC DIVERSITY ASSESSMENT OF THE KOALA: APPLYING NOVEL GENOMIC METHODS AND ASSESSING GENETIC EXCHANGEABILITY ACROSS THE SPECIES RANGE. 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 genomewide 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 wholegenome 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.

5 5 CONSERVATION GENOMICS AND THE SIGNIFICANCE OF ADAPTIVE VARIATION IN THE KOALA AIMS: a) Use a conservation genomics approach to identify regions of the genome which may have been under selective pressure and thus may represent functional adaptive variation amongst populations. b) Based on molecular data calculate molecular inbreeding coefficients and for animals with known pedigree, degree of relatedness can be calculated as well as conventional inbreeding coefficients. c) Develop a simple identity and parentage testing SNP panel of the 96 most informative markers. Using SNPs that have been identified as neutral and adaptive we will develop a highly informative SNP array for continued use and evaluation on new koala populations. Despite a general decline in the range of koalas across Australia since European settlement there is great variation in population dynamics such as growth and mortality rates, and in morphological traits such as animal size and fur length across the species range. These ecological and morphological differences may represent an adaptation to climate over an extensive range and with further contraction of the species range predicted due to a reduction in the climate envelope, the consequences will be reflected in the ability of individuals and populations to adapt to changed environments. In addition to many direct applications to conservation of the koala, comparative population genomics can now reveal information about selective forces which determine divergence between populations. Using new technologies it is possible to isolate genomic regions which may have been under diversifying or stabilising selection pressure by identifying regions with significantly increased or decreased differentiation among populations. These areas of the genome may code for functional variation in life-history traits. Increasing our understanding of genomic variation within and between populations and across the species range will assist us to better manage this functional variation and help us to better define conservation management units. The koala is listed for whole genome sequencing in the Genome 10K project and, once complete, the RAD tag genomic maps created in this project can be aligned with the sequence to determine the marker locations on the genome. Downstream applications of this project therefore include subsequent assessments of the functional aspects for any candidate genes and alleles which this project identifies as having been under selection pressure. Using information on SNP important for adaptive fitness, and those neutral loci with high polymorphic content, a sub-panel of 96 SNP will be identified for low cost identity and parentage testing. Such SNP will allow tracking/ verification of captive and wild animals, as well as pedigree ascertainment for pedigree relationships and management of captive populations. KOALA CONSERVATION MANAGEMENT AND INTEGRATED ECOLOGICAL MODELLING. The sample collection being accessed is the most comprehensive sample repository of Koala samples in the world. Many of the samples are highly descriptive in terms of location, age sex and other biophysical data pertaining to each animal. This project will combine genetic and ecological data to describe ecological exchangeability and assign conservation management units to the koala across the species range. AIMS: 1. Undertake population viability assessments for critical southern koala populations based on levels of genetic diversity, demographic and ecological data and conservation value.

6 2. Using integrated genetic data (from PhD s 1 and 2) and ecological data, perform assessments of viability and connectivity within and between local and regional populations of koalas in each state and across the species range. Assess ecological exchangeability and prioritise koala populations most at risk of local extinction. Using this information assign conservation management units for the species. 3. Integrate predictive data on climate change effects and using Geographical Information Systems model landscape corridors to restore gene flow and connectivity for koala populations, and to reduce edge effects on populations. Outline management recommendations for key populations at risk. Sampled populations will include those containing reintroduced French Island individuals with low levels of genetic diversity, as well as those containing original Victorian remnant populations. Ecological data will be used to assess populations with indications of low ecological exchangeability (eg., differences in morphology, fecundity) that may have been under selective pressure. Additionally, ecological data from the southern populations will be used to perform intra-population and inter-population viability analyses. A review of ecological data from populations and habitats in NSW, QLD, VIC and SA will be used for integrated assessments of connectivity within and between regions using GIS, for practical application to management including the identification of high priority conservation areas. This will be an adjunct to genotypic classifications derived from the population diversity analyses provided through NETVIEW where genetically distinct populations which are geographically separated will be deemed to be of low ecological exchangeability. Furthermore, genetic population substructures within a defined population can be used to maximize genetic diversity with populations to manage exchange and relocations. FURTHER DETAILS For further details and initial discussion of project opportunities Contact: Prof Herman Raadsma Reprogen Animal Bio-Science group, Faculty of Veterinary Science University of Sydney. Tel camden.usyd.edu.au Dr Kyall Zenger, Senior Lecturer James Cook University, Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, 4811 QLD, Australia. Ph: e: kyall. Dr Kellie Leigh, Executive Officer, Australian Ecosystems Foundation, Ph: Crane Road Lithgow NSW 2790 Australia

7 Faculty of Veterinary Science T F E sydney.edu.au/vetscience/research/programs/opportunities. shtml FACULTY OF VETERINARY SCIENCE Produced by Faculty of Veterinary Science, the University of Sydney, October The University reserves the right to make alterations to any information contained within this publication without notice. 10/2012 ABN CRICOS 00026A

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