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

Reptile profile

The green anole, Anolis carolinensis, is one of over 400 species in the genus Anolis (anoles) and one of over 11,000 species in the group Squamata (squamates). Squamates (lizards and snakes) are the most speciose groups of terrestrial vertebrates on earth. Native to the south-eastern United States, the green anole is known and loved for its vibrant green color and charismatic behavioral displays: during the summer months, male green anoles can be seen walking up walls using their sticky toe-pads, or elsewhere prominently perched in gardens and foliage, furiously doing pushups and extending a flag-like flap of bubblegum pink skin under their chin called a “dewlap.”

Green anole, photo by Bonnie Kircher

These characteristic displays are directed at any males that have invaded their territory, as well as any receptive females that catch their powder-blue eyes. Though males are most likely to be spotted displaying, females also perform these displays. Male and female anoles can be differentiated by differences in overall adult body size but also by the size of their dewlap, (males being larger in both cases). Though named for their gorgeous green hue, green anoles also change color to a silver-y brown. Likely not a camouflage technique, this behavior may correspond instead with environmental or social cues.

Anoles are particularly well studied because of their interesting evolutionary quirks. The genus is often described in textbooks as an example of convergent evolution, a process in which similar traits evolve in different species as a result of similar environmental conditions and not due to evolution from a shared common ancestor. Convergent evolution of morphology, physiology, and behavior has been well characterized in anoles and this group is an important model for understanding evolutionary processes. Anoles thrive in a lab setting, making it easy to adapt modern scientific tools and techniques for use in this system. Recently, CRISPR genome editing was used for the first time in a closely related species, the brown anole (Anolis sagrei), making it the first non-avian reptile to have genome editing capabilities be made available.

The genome for green anole, Anolis carolinensis, was first published in 2011 by Jessica Alföldi et al., and was the first non-avian reptile genome to be sequenced. Since its publication and re-annotation in 2013, the genome has been used widely for studies in evolution, genetics, and development. With over 600 citations, the original publication of this genome transformed the ability of researchers to study the evolution vertebrates.

Today, we share a few tweaks to the existing green anole assembly (AnoCar2.0) including anchoring suggestions for 4 microchromosomes missing in AnoCar2.0. We also share the Hi-C data generated using a fibroblast cell line from a female anole individual, originally frozen back in 1981! We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for sharing this cell line.

This is the 6th member of the Squamata family we've released here on the DNA Zoo Blog, see others here! Browse the 18 chromosomes of the green anole in the interactive JuiceBox.js session below. Note an inversion polymorphism in HiC_scaffold_1: stay tuned for more data to find out if this is a culturing artifact or a primary sample polymorphism.

Space poddity

The short-beaked common dolphin, Delphinus delphis, is one of the most wide spread and abundant dolphin species in the world. They're known to be especially social, energetic, and may live in large groups (pods) of a few hundred individuals. The common dolphin will sometimes form "mega-pods", in which thousands of individual dolphins will band together for a time [1]. The short-beaked common dolphin is known to go "bow-riding" alongside waves made by boats, and even some large whales [2].

Short-beaked common dolphin (Delphinus delphis) in Portugal by Alexandre Roux, [CC BY-NC-ND 2.0], via flickr.com

Today we share the chromosome-length genome assembly for the short-beaked common dolphin, Delphinus delphis! This genome assembly was generated using the $1K strategy with a contig N50=50Kb and a scaffold N50=89Mb. The sample for this genome assembly was provided to us by Barbie Halaska, from The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center prides itself on gathering and providing open research data that is free to access, reuse, repurpose and redistribute in service to ocean conservation and marine mammal health. Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the Center's website.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

Browse the 22 chromosomes, (2n=44), of the common dolphin in the interactive Juicebox.js session below. This is the 15th dolphin species we've released here on the DNA Zoo, check out our other assemblies here!