Scientists Release World’s First DNA Map of Endangered Australian Mouse, and It Will Help Save Her

The native Australian rodent Pseudomys fumeusnamed smoky mouse for its color, was already battling extinction when the 2019-2020 bushfire season broke out.

The Black Summer bushfires, which burned more than 24 million hectares, are believed to have killed an estimated 1 billion animals and endangered more than 100 endangered species. The fires have also destroyed more than 90 per cent of the smoker mouse’s habitat, with nine mice even dying at a captive breeding facility near Canberra from inhaling bushfire smoke.

But all is not lost – a newly sequenced reference genome will now aid ongoing conservation efforts for this native Australian species.



Read more: ‘Death by irony’: The mystery of the mouse who died of smoke inhalation, but didn’t go near a fire


Precious Mouse Pockets

We haven’t seen any wild smoke mice in the Australian Capital Territory since 1987. In Victoria, the species occurs only in the Grampians, central highlands and alpine regions, and in New South Wales in the alpine regions of Kosciuszko National Park and the southeastern forests near Nullica.

An active recovery plan was drawn up for the mouse in 2006. As part of this, conservationists created two captive populations, with current outings in the southeastern forests near Nullica, and a predator-proof reserve in the ACT.

These small native mice are more than cute, about twice the size of the introduced house mouse (Mus musculus). Their charcoal fur is soft and silky, and they smell great too. The males especially smell a bit like smoky burnt vanilla; these animals have a charming and calm temperament.

Over the past 12 months, a team from Museums Victoria Research Institute has been undertaking surveys to search for surviving pockets of the endangered mouse population, in preparation for future captive-bred mouse reintroduction efforts.

To support these ongoing conservation efforts, DNA Zoo at the University of Western Australia has partnered with Victoria Museums Senior Mammalian Curator Kevin Rowe will sequence a world’s first full chromosome-length reference genome for the animal.

Conservationists have been working to save the smoker mouse with an active recovery plan since 2006.
David Paul, Museums Victoria, CC BY

Protect what we have

We can now use this reference genome to inform conservation strategy. The researchers will map 70 individual DNA sequences of smoke mice from across the animal’s range of habitats – from the Grampians in western Victoria to the southeast of the New South Whales.

Increasing our understanding of living wildlife and responsibly managing available resources are among the most crucial scientific and social challenges we face today.

Despite great advances in technology, there are many things we don’t know Australia’s native biodiversity. At the same time, it is increasingly threatened by forest fires, climate change, habitat destruction, species exploitation and other human-related activities.

Fortunately, we can use genomics to help formulate an informed conservation strategy. Indeed, sampling for genomic diversity can give us a basic understanding of the health status of the species (what biologists call “population shape”). With this knowledge in hand, we can better design conservation programs.

For example, in endangered species with greatly reduced populations, we can avoid inbreeding if we use genomic data to help design breeding programs. In this way, animals will have fewer genes that lead to premature death and will have increased resistance to disease.



Read more: We’ve decoded the numbat genome – and it could bring the resurrection of the thylacine closer


Consult the genetic plans

Obtaining the genetic blueprints of Australian wildlife will create a powerful source of discoveries to improve and increase ecosystem services. A well-designed monitoring framework is crucial for the success of conservation programs on the ground.

As part of the Smoking Mouse Recovery Plan, we have DNA sequences from individuals in the Grampians, as well as historical samples dating back to 1934 from extinct populations in the Otways and Far East Gippsland.

The samples from the Grampians are particularly interesting. This is because this population is the most isolated, approximately 350 kilometers away from the nearest known population in the Yarra Ranges of the Central Highlands.

Since 2012, Museums Victoria and its partners have trapped, tagged and collected samples – ear biopsies and poop pellets, which are neither harmful to animals – from more than 200 smoker mice in the Grampians. Thanks to this work, we now have the most numerous and continuous record of the species in Victoria.

An adorable rat-like animal with a soft gray coat and a cute pink nose
Some smoking mice have been discovered in the Grampians, far removed from others of their species.
David Paul, Museums Victoria, CC BY

In addition, trapping and photographic surveys of wildlife over 100 sites revealed localized smoke mouse populations in two areas within 10 km of the Victoria Range and Mt William Range, respectively.

Researchers will now look for genetic clues as to how these animals persisted despite drought, invasive predators and large fires.

What is encouraging is how powerful technology – like genome sequencing, bioinformatics and many more combined – is now helping us to understand and conserve biodiversity. For the first time in history, we can efficiently accelerate and sequence the genomes of our only native Australian species.



Read more: It’s not too late to save them: 5 ways to improve the government’s plan to protect endangered wildlife


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