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The Smoky Mouse - Edging towards extinction

The native Australian rodent the smoky mouse Pseudomys fumeus, also known by the First People’s name ‘Konoom’ (the name is from the Wadawurrung people of Victoria), was already fighting off extinction when the 2019-2020 fire season hit. The bushfires torched 13.6 million acres, killing an estimated one billion animals and putting more than 100 threatened species at risk. More than 90 percent of the mouse’s habitat was razed by the conflagration. The fires even came for the mice in captive breeding facilities: nine mice died by smoke inhalation at a captive breeding facility near Canberra in February 2020.

The smoky mouse, Pseudomys fumeus. Photo by David Paul, Museums Victoria [CC-BY 4.0]

The smoky mouse is a gentle little mouse with a two-toned pink and grey tail and very soft blue-grey fur which gives them their name. It was described from two specimens first collected in the Otway Ranges, Victoria, in 1933; specimens were later found in the Grampians in 1963, Gippsland in 1971, the Australian Capital Territory (ACT) in 1985 and in New South Wales (NSW) in 1993.

Despite once being widespread, populations of the smoky mouse now tend to be small and fragmented. The species has not been seen in the ACT since the initial capture of two individuals in 1985 and 1986. In Victoria, smoky mice were once found in the Otways and Far East Gippsland but since the 1980s have only been recorded in the Grampians, Central Highlands and Alpine regions of the state. In NSW, the species occurs in alpine regions of Kosciusko National Park and southeastern forests near Nullica.

An active recovery plan was established for the species in 2006. As part of this plan, two captive populations have been established from NSW sources. The first releases from these captive populations are happening into southeastern forests and into a predator proof reserve in the ACT.

To support ongoing conservation efforts, DNA Zoo teamed up with Museums Victoria Senior Curator of Mammals Kevin C. Rowe to release the chromosome-length assembly for the species.

The genome draft was generated with short-insert size Illumina reads [500 PE reads] and scaffolded to chromosome length genome with Hi-C [450 PE reads]. See our Methods page for more detail on the procedure.

The chromosomal-length reference genome will be used to map genomes from 70 smoky mouse individuals from across the species distribution range in the Grampians in western Victoria to southeastern New South Whales (see map below). The data will include historical samples from the holotype specimen (1933) and extirpated populations in the Otways, eastern Victoria, parts of the Grampians as well as contemporary samples.

Geographical distribution of smoky mouse resequencing data by Museums Victoria. Samples include specimens from 1933 (the holotype) as well as contemporary samples from to 2020. Inset map shows details of sampling in Grampians National Park. Geographic centroids of sample clusters are indicated with yellow stars. Each circle represents data from an individual smoky mouse. Shading of circles indicate decade of collection from the 1930s to 2010s.

Samples from the Grampians population are of particular interest. The Grampians population is the most isolated, removed by about 350 km from the nearest extant population in the Yarra Ranges of the Central Highlands. Since 2012, Museums Victoria and partners have trapped, marked, and collected samples (ear biopsies and faecal pellets) from over 200 smoky mouse individuals in the Grampians providing the most numerous and continuous record of the species in Victoria. Trapping and wildlife camera surveys at more than 100 sites revealed populations of Smoky Mouse are localised to two areas spanning <10 km of the Victoria Range and Mt William Range, respectively. Stay tuned for more information about this population as well as genetic clues on how it persisted despite drought, invasive predators and significant fire.

Detections and non-detections of Smoky Mouse in the Grampians based on Museums Victoria surveys from 2012-2021.

This work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Blog post by Parwinder Kaur and Kevin C. Rowe

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