Sequencing of the bilby genome opens new avenues for species conservation

The greater bilby, often identified with the Australian Easter Bunny, is the only surviving marsupial member of its family. Omnivorous, with large ears and a rear-facing pouch, it inhabits the Australian desert and has significant cultural and ecological value. However, it is found in only 20% of the range it originally occupied. Its decline is also reducing knowledge of the marsupial among the indigenous community, as well as the practices for its maintenance. Greater bilby populations living in wild habitats are often managed by indigenous rural agents, while some 6,000 individuals live in fenced sanctuaries, islands and zoos.

An international team has sequenced the genome of two species of bilby marsupials, one of which is now extinct. The data have enabled the development of a tool to more quickly and efficiently assess the natural populations of the species that still persists, in order to prevent its extinction. The results of the study represent an important advance in the fields of genomics and evolution, as well as for the conservation of the species.

The study was led by the University of Sydney in Australia, in collaboration with various research centres, mostly Australian, and was carried out in collaboration with researchers, Australian indigenous rangers and conservation managers. Aurora Ruiz Herrera and Laia Marín Gual, researchers from the Department of Cellular Biology, Physiology and Immunology and the Institute of Biotechnology and Biomedicine (IBB), part of the Autonomous University of Barcelona (UAB), also participated in the international research team.

The research has focused on the greater bilby (Macrotis lagotis), a marsupial also known as ninu by the Australian indigenous community of Kiwirrkurra, to which it is closely linked.

The study has sequenced the first genome of the greater bilby at the chromosomal level and also a large part of the genome of the lesser bilby, a species that became extinct in 1931. The first was obtained from a specimen from a zoo and the second from the skull of a specimen from 1898.

The researchers highlight that the greater bilby reference genome is one of the highest quality marsupial genomes to date.

Specimen of greater bilby (Macrotis lagotis). (Photo: Emma Peel / The University of Sydney)

Comparison of the genome with the DNA sequence of multiple individuals from different regions and habitats has provided detailed information about their unique biology, such as understanding what gives them their unique sense of smell and how they survive in the desert without drinking water, and has allowed us to see the genetic benefits of mixing different populations (in captivity and in the wild). This measure, which was taken to increase the genetic variability of the greater bilby, has been shown to ensure its adaptive potential and long-term survival.

Genomic data has also helped researchers develop and fine-tune an innovative tool based on SNPs (single nucleotide polymorphisms, i.e. small variations in the DNA chain). This tool makes it possible to determine the distribution and movement between populations of the marsupial or the relationship between individuals with the aim of supporting indigenous communities in the conservation of this species.

Unlike previously used measures, which relied on capturing and collecting tissue directly from animals, this new approach allows for the analysis of genetic variations in each individual from their excrement, which makes sample collection considerably easier and less expensive.

“The application of this new tool facilitates an appropriate ecological assessment of both captive and wild populations and a better understanding of the genetic diversity of the various populations,” says Aurora Ruiz Herrera, director of the Animal Genomics Group at the UAB. “This advance represents a major step towards the effective conservation of the greater bilby and demonstrates the power of genomics in the protection of endangered species,” highlights the researcher.

The research team was led by specialists from the University of Sydney, including Carolyn J. Hogg and Emma Peel. Specialists from the University of New South Wales (UNSW), the University of Western Australia, the University of Adelaide, the South Australian Museum in Adelaide and the Australian Museum in Sydney, as well as the University of California at Santa Cruz in the United States and the Autonomous University of Barcelona also participated.

The study is titled “Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial.” It has been published in the academic journal Nature Ecology & Evolution. (Source: UAB. CC BY-NC 4.0)