The Oz Mammals Genomics initiative: developing genomic resources for mammal conservation at a continental scale

Abstract

The Australo-Papuan region has a unique mammal fauna, which faces unique threats and poses important evolutionary and ecological questions. Genomics has great potential to advance our understanding of the region's mammals and their conservation. The Oz Mammals Genomics Initiative brings together museum collections, researchers, data specialists and wildlife management agencies to comprehensively tackle rodent, bat and marsupial genomics at a continental scale.

There are few published whole genomes for Australian marsupials. We are developing well-assembled genomes from a broadly representative range of marsupial taxa, to facilitate new insights into evolution and to provide reference data for conservation studies. Genome projects are now underway for seven priority species: the fat-tailed dunnart, brush-tailed rock-wallaby, eastern bettong, mountain pygmy possum, Leadbeater's possum, bare-nosed wombat and eastern barred bandicoot.

Our current understanding of evolutionary relationships among many mammal taxa remains incomplete. To improve resolution of genus and species boundaries, we are generating comprehensive phylogenies of all extant and recently-extinct terrestrial mammals native to the Australo-Papuan region. We are using exon capture methods to sequence over 1000 genes from around 500 species of marsupial, rodent and bat, including samples from vouchered museum specimens wherever possible. This work will clarify taxonomic boundaries for several species of conservation concern, such as the Christmas Island flying-fox.

Finally, the availability of reference genomes and phylogenies will provide a solid base for population-level studies. We are developing conservation genomic datasets for a selection of threatened mammal species. Using exon capture and genotyping-by-sequencing methods, we will measure genetic diversity and inbreeding, determine population structures, and identify adaptive variation. The inclusion of museum specimens as well as recently-collected samples will enable comparisons of modern and historic levels of genetic diversity. Conservation projects have been prioritised so that genomic data are contributing directly to urgent management decisions, for example to inform translocations, reintroductions and captive breeding.