Oz Mammals Genomics Initiative

Introduction

The Oz Mammals Genomics Initiative is a collaborative project that is developing genomic resources for Australia’s mammals, tackling wildlife genomics at a continental scale. The availability of such resources for marsupials, rodents, and bats will underpin new studies of mammal evolution and guide conservation of the Australian mammal fauna.

Australia is famous for its unique terrestrial mammals, with most species found nowhere else. In the last 200 years approximately 30 Australian mammals have become extinct, including the thylacine, pig-footed bandicoot, eastern hare-wallaby and long-tailed hopping mouse. Many others are now threatened and there is an urgent need for effective conservation management. Genomics can contribute to this, for example by helping us to understand breeding systems and dispersal patterns of threatened species, and by improving our understanding of extinction risks.

Australian marsupials are genetically distinct and developmentally unique. This means that marsupial genomes are especially important comparative resources for understanding mammalian diversity worldwide. At this stage, very few marsupial or monotreme genomes have been studied in detail (the koala genome is one example), but these have led to some spectacular, globally significant discoveries about evolution. Given the unique history and biology of Australian mammals, these discoveries are just the tip of the iceberg. Future insights from marsupial DNA may include the development of novel antimicrobials, or an improved understanding of sex chromosome evolution.

Museum collections will be vital to the success of the Oz Mammals Genomics Initiative. DNA analysis of museum specimens will allow us to compare recent and historic levels of genetic diversity, and will improve our understanding of recently extinct species.

Aims

The consortium objectives are to:

  • Build a foundation of genomic data to advance our understanding and conservation of Australia’s unique mammals
  • Establish genomics as a key capacity across Australian museums and government agencies, build the community to sustain this
  • Increase awareness among the public and conservation managers of the diversity of Australian mammals and how genomics can aid in their protection

The Initiative has three key aims:

  1. Develop well-assembled marsupial genomes. By sequencing whole genomes (and transcriptomes as needed) from at least five different species, this project will generate representative marsupial genomes from a broader phylogenetic range than previously available. Candidate species have been selected based on their potential to (i) enable new insights into evolution and (ii) provide high resolution whole-genome scanning of threatened species.

  2. Generate a comprehensive phylogenetic framework for Australian mammals. High quality sequence data will be generated for around 1000 orthologous genes, using exon capture, from all mammals native to the Australo-Papuan region (around 500 taxa). Representatives of some subspecies and some species that have recently become extinct will be included. Samples will be obtained from tissue and specimen collections already in Australian and international museums, including type specimens where possible. This project will provide highly resolved phylogenies of rodents, bats and marsupials.

  3. Build reference genomic datasets for threatened species. Many Australian mammals are threatened with extinction or decline. This project will generate population genomic datasets for a selection of threatened mammals for which knowledge of genetic diversity and structure is needed urgently for conservation management. Genome scans and related data will be used to understand risks of inbreeding or outbreeding depression, put current population sizes into historical context and identify adaptive variation that should be preserved.

The OMG Consortium

The Oz Mammals Genomics Initiative is an Australia-wide collaboration involving researchers from more than 30 institutions. Core consortium members include:

See our collaborators page for more.

We also have ongoing international collaborations, including with the Natural History Museum, London (UK), the University of Otago, Dunedin (NZ) and the Museum of Vertebrate Zoology, Berkeley (USA), and we are involved with the Genome 10K project, EDGE and the IUCN Conservation Genetics Specialist Group.

Project pages

Links

Acknowledging the consortium

When using Oz Mammals Genomics Initiative data, please acknowledge the Consortium and Bioplatforms Australia support using the following wording:

"We would like to acknowledge the contribution of the Oz Mammals Genomics Initiative consortium (https://data.bioplatforms.com/organization/pages/bpa-omg/collaborators) in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia through the Australian Government National Collaborative Research Infrastructure Strategy (NCRIS)."