Using genetics to inform conservation of Australia’s threatened species

The Threatened Species Initiative (TSI) brings together genome biologists, population biologists, bioinformaticians, population geneticists and zoologists with conservation agencies across Australia, including government, zoos and NGOs. Our objective is to create a foundation of genomic data to advance our understanding of key threatened species in Australia, ultimately empowering conservation practitioners to leverage genomic information to tackle critical biological and conservation issues – including genetic data to inform translocations, captive breeding and their ongoing management.

This initiative, which will run over the coming 3-years, has been developed in direct consultation with government threatened species managers and non-government conservation organisations, to ensure that the project meets their needs and develops a systematic approach to integrating genomics into species recovery.

Building on existing Bioplatforms Australia investment into Oz Mammal Genomes, Genetics of Australian Plants and the Australian Reptile and Amphibian Genome Project, the TSI will:

  • develop best practice reference genomes for up to 50 key threatened species in Australia, alongside reduced representation sequencing datasets for individuals of each species;
  • generate analytical methods for routine adoption of genetic analysis for threatened species management plans;
  • develop a reporting mechanism on genetic appropriateness of breeding populations for use in species translocations and subsequent management actions;
  • develop tools for ongoing genetic monitoring e.g. genetic diversity over time, response to intervention etc.
  • ensure that genomic data is made freely available to enable iterative and ongoing analysis into the future.

Outcomes from this program will be made available through open access platforms and details on protocols and methods will be available online through the Threatened Species Initiative website (coming shortly).

To read more about the initiative please see: https://bioplatforms.com/projects/threatened-species/

THE PILOT PHASE

To ensure seamless delivery of the larger project, the TSI is running a Pilot to trial, test and bed down workflows and pipelines to ensure outputs are fit-for-purpose for conservation management and decision-making.

The TSI Steering Committee has undertaken a review of the list of species provided from the consultation with the threatened species managers; existing Bioplatforms Australia framework initiatives; and the recent Commonwealth government bushfire list of priority species.

Pilot phase scenarios

The species on these lists were grouped into the following five scenarios to enable comprehensive testing at different stages of the conservation genomics pipeline:

  1. The species has no reference genome, no population genetic data
  2. The species has closely related species with a reference genome, but no population genetic data
  3. The species has no reference genome, and population genetic data exists
  4. The species has a reference genome, or conspecific genome, some population genetic data and is subject to conservation action which mixes genetically distinct populations
  5. The species has no reference genome, but short-read data exists, and some population genetic data exists

Pilot phase criteria

Species were then assessed against the following criteria to ensure we maximise effort and resources whilst minimising duplications:

  • The species has existing data, including information produced by other Bioplatforms Australia initiatives, or genomic work proposed or already being undertaken, for the species, or a closely related species;
  • The species has genetic research listed as a priority 1 action in its National (or State) Recovery or other conservation Plan;
  • The species is listed on the Commonwealth government’s bushfire priority list of species requiring urgent management intervention;
  • The species is involved in a current or upcoming conservation translocation program (including insurance populations) and no or limited genetic data exists;
  • There are samples readily available for the species;
  • Co-investment for the species exists, or there is potential for co-investment, in generating data for the species; and
  • Together, the pilot species represent different conservation activities across Australia.

The resulting seven species that have been nominated for the pilot project are detailed below:

We note that these seven species do not represent species with the most urgent management needs, but rather those that meet our criteria for testing concepts and informing the logistics of the broader program.

With the lessons learnt from the pilot phase, and following consultation to identify a further set of priority species, the TSI will have an open program where we will engage with relevant conservation management groups to guide this process.

We welcome collaboration and parties interested in participating in the pilot phase are encouraged to get in contact with Sarah Richmond (srichmond@bioplatforms.com).

We look forward to providing the Australian genomics and conservation communities with further details as the pilot project progresses.

Carolyn Hogg, Peter Latch, Kym Ottewell

TSI Project Co-Leads

Pilot species

  • Eastern bristlebird (Dasyornis brachypterus)

    Scenario: The species has no reference genome, no population genetic data

    Lead end-user group: Victoria DEWLP & NSW Saving Our Species

    Genetics group lead: Andrew Weeks, University of Melbourne

  • Native guava (Rhodomyrtus psidiodes)

    Scenario: The species has no reference genome, no population genetic data

    Lead end-user group: NSW Saving Our Species

    Genetics group lead: Maurizio Rossetto, Royal Botanical Gardens Sydney

  • Swan Galaxiid (Galaxias fontanus)

    Scenario: The species has no reference genome, no population genetic data

    Lead end-user group: Inland Fisheries Service Tasmania

    Genetics group lead: Bruce Deagle, CSIRO Australian National Fish Collection

  • Hastings River mouse (Pseudomys oralis)

    Scenario: The species has closely related species with a reference genome, but no population genetic data

    Lead end-user group: NSW Saving Our Species & QLD Department of Environment & Science

    Genetics group lead: Kevin Rowe, Museums Victoria

  • Barred bandicoots (Perameles bougainville & P. gunnii)

    Scenario: The species has a reference genome, or conspecific genome, some population genetic data and is subject to conservation action which mixes genetically distinct populations

    Lead end-user group: WA Department of Biodiversity, Conservation and Attractions & Department of Environment, Land, Water and Planning Victoria

    Genetics group lead: Kate Farquharson, University of Sydney (P. bouganiville)

    Andrew Weeks, University of Melbourne (P. gunnii)

  • Orange-bellied parrot (Neophema chrysogaster)

    Scenario: The species has no reference genome, but population genetic data exists

    Lead end-user group: OBP National Recovery Team

    Genetics group lead: Carolyn Hogg, University of Sydney

  • Ghost bat (Macroderma gigas)

    Scenario: The species has no reference genome, but short-read data exists, and some population genetic data exists

    Lead end-user group: WA Department of Biodiversity, Conservation and Attractions

    QLD Department of Environment and Science

    NT Department of Environment and Natural Resources

    Genetics group lead: Kym Ottewell, WA Department of Biodiversity, Conservation and Attractions

Contact

  • Contact

    Science Lead – Dr Carolyn Hogg, University of Sydney (carolyn.hogg@sydney.edu.au)

    General Manager, Science Program – Sarah Richmond, Bioplatforms Australia (srichmond@bioplatforms.com)

    Chief Executive  – Andrew Gilbert, Bioplatforms Australia (agilbert@bioplatforms.com)

  • Note to editors

    Funding

    The project is supported by funding from Bioplatforms Australia through the Australian Government National Collaborative Research Infrastructure Strategy (NCRIS), with support from the University of Sydney, the Australian Government Department of Environment and Energy, the WA Department of Biodiversity, Conservation & Attractions, Amazon Web Services, NSW Saving Our Species, Australian Wildlife Conservancy and the Zoo and Aquarium Association.

Plains Wanderer Photographer: David Baker-Gabb
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