The Australian alpine canine

The dingo is the Australian canine, which is thought to be introduced to Australia by seafarers from Asia around 5000 year ago (1). Since then the dingo has become Australia’s apex predator on land and has integrated into local ecosystem. By controlling populations of native and introduced herbivores including introduced mesopredators such as red foxes and cats, dingoes are fundamental for maintaining balance in the ecosystem. Additionally, by controlling populations of herbivores, dingoes benefit plant communities and other smaller native prey such as small marsupials and rodents (2).

Cooinda the Alpine dingo; Photo: Bargo Dingo Sanctuary.

The dingo is a medium-sized canine, with males being slightly larger than females. The dingo breeds once a year and usually produces a litter of four to six pups. The dingo may have multiple coat colours: ginger with white feet, darker tan to black, white, and golden yellow. Interestingly, like wolves, dingoes howl to communicate. The extensive hybridisation with domestic dogs has raised concerns over the persistence of pure dingoes in the wild.

Morphological and genetic studies have indicated a subgrouping in dingoes – Desert, Alpine and Tropical, primarily based on their geographical distribution. Skull shape differ between dingoes from different climatic zones, where the skulls of dingoes from the southeastern alpine regions of Australia are wider than the skulls of dingoes from the northwestern desert parts of Australia (3). Genetic studies however have supported the presence of only two lineages: Desert and Alpine (4). Alpine dingoes are found in the high elevation Australian alps and grow a thicker fur during late autumn. Alpine dingoes are typically larger than desert dingoes (5).

Here we release a chromosome-length genome assembly of the Alpine dingo - Cooinda. Cooinda is a pure dingo and was raised in the Bargo dingo sanctuary. Unfortunately, she has now passed, but it is expected she will go on display at the Australia Museum, Sydney as the type representative of the Alpine dingo. This assembly has a contig N50 = 23,108,747bp and scaffold N50 = 64,752,584bp. See Dudchenko et al., 2018 for details on the procedure. Thank you to Bargo Dingo Sanctuary for providing the sample for this assembly.

The assembly is now available on NCBI as UNSW_AlpineDingo_1.0:

Basenji – the African hunting dog

Basenji’s are an ancient dog breed, originally indigenous to central Africa. Basenji-like dogs are depicted in drawings and models dating back to the Twelfth Dynasty of Egypt [1] and they sit at the base of the currently accepted dog phylogeny [2]. Basenjis share many unique traits with pariah dog types. Like dingoes and New Guinea Singing dogs (NGSD), Basenji’s come into oestrus annually—as compared to most other dog breeds, which have two or more breeding seasons every year. The annual oestrus of Basenji is possibly an adaptive response to protect puppies from higher temperature and humidity of the equatorial summer. In the rainforests the key factor affecting breeding is the availability of food [5].

They are often referred as “barkless” dogs of Africa. Basenji, dingoes and NGSDs are prone to howls, yodels, and other vocalizations over the characteristic bark of modern dog breeds. One explanation for the unusual vocalisation of the Basenji is that the larynx is flattened [3]. Basenji’s have short, fine chestnut red and black coat colour with white feet, chest and tail tip.

China striking a pose; Photo: Zanzipow Kennels

The Basenji made its debut in the western world in 1895 when a brace of the dogs was exhibited at the Cruft's show as African Bush dogs or Congo Terriers. Unfortunately, all contracted distemper shortly afterward and died. In England, the breed traces back to six dogs that were transported from Africa by Mrs. Olivia Burn in the 1930’s. The dogs were passed as pure breed by Kennel Club and zoological experts, and placed into the hound group.

Prior to 1987, a total of 28 Basenjis were exported directly from Africa to Europe or the United States [4]. Most of the imports went to England. Six were imported to the United States including one that came as a stowaway in a coffee shipment and two that came with a shipment of baby gorillas. In the 1970s and in the 1980s five Basenjis were imported into Germany. Subsequently, the American Kennel Club re-opened its stud book on multiple occasions so that additional Basenji’s from Africa could increase the genetic diversity of the breed.

Here we release a chromosome-length genome assembly of the Basenji – China or more formally Australian Supreme Champion Zanzipow Bowies China Girl. The genome assembly (Oxford Nanopore + BGISEQ + Illumina Hi-C) is of high quality with the contig N50 of 23,108,747 Mb and scaffold N50 of 64,752,584 Mb. See Dudchenko et al., 2018 for details on the procedure. Thank you to Jennifer Power for providing the sample for this assembly.

The genome is now available on NCBI as UNSW_CanFamBas_1.0:

References:

1. Dollman, G. The Basenji Dog. Journal of the Royal Africa Society 36, 148-149 (1937)

2. Parker, H. G. et al. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development. Cell Rep 19, 697-708 (2017)

3. Ashdown, R. R. & Lea, T. The larynx of the Basenji dog. J Small Anim Pract 20, 675-679 (1979)

4. America, B. C. o. Foundation stock sorted by year of import, 2017)

5. Johannes, J. E. (2003). The Basenji Annual Estrus: The impact of the rainforest ecology on its development.

Something fishy

The Macquarie perch (Macquaria australasica) is an Australian native freshwater fish. The Macquarie perch derives its scientific name from the Macquarie River where the first scientifically described specimen was collected (Macquaria) and a derivation of the Latin word for "southern" (australasica).

Photo Description - Macquarie Perch (Macquaria australasica). Photo Credit and acknowledgement - Victorian Fisheries Authority.

At least three genetic lineages of this species once existed in Eastern Australia. The most ancestral one from Shoalhaven Basin is now presumed extinct (1). The remaining two lineages- from Hawkesbury-Nepean and Murray-Darling Basins, diverged in mid-Pleistocene, are so different in appearance and genetics that there are calls to recognize them as separate species (1,2).

The Macquarie Perch is a long-lived (>25 years) moderate-sized fish with an elongate-oval laterally compressed body. It feeds upon aquatic insects and crustaceans (shrimp and crayfish), but also preys upon molluscs and small fish (3).

This riverine species prefers clear water with deep, rocky holes with lots of cover (3). Males reach maturity at as early as two years of age when they are about 210 mm in length, but females do not spawn until three years of age when they are about 300 mm in length (4). Spawning occurs just above riffles (shallow running water), where fish form annual spawning aggregations (5). A large 3.5kg female can produce up to 110,000 eggs, although few survive to adulthood.

The species is endemic to NSW, ACT and Victoria. It was once common in upland and slope zones in New South Wales, but in Victoria it was also abundant in lowland zones of the major tributaries of the Murray River (6).

Like many native Australian fish, this species lost 90% or more of its former numbers and geographic range, through a variety of human impacts including overfishing, changing the flows of rivers, removing fallen wood from them (important habitat), and the introduction of competitors, predators and diseases (7). The few remaining populations occur mostly in headwaters of their river systems and are genetically and demographically isolated from each other (1). This puts them at the high risk of extinction through inbreeding and environmental disasters, such as drought and fires (8).

The Macquarie perch is now listed as endangered under state and Commonwealth legislation. The national recovery plan for this species has been developed under the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) to guide species recovery (9).

A great body of work over many years through collaborations across universities and wildlife agencies in VIC, ACT and NSW, has shown that genetically mixing populations from throughout the Murray Darling Basin through assisted gene flow would improve their health and capacity to adapt to changing environments (8). Collaborative work by Monash University with the Department of Environment, Land, Water and Planning (DELWP), and Victorian Fisheries Authority, in the Ovens River in Victoria, where the species was previously extinct, showed that mixing fish from different populations makes a reintroduced population genetically and demographically healthier (10). Such genetic management of wildlife benefits greatly from genomics (11).

To support ongoing conservation efforts by many agencies including DELWP and NSW Department of Primary Industries, DNA Zoo has been working with Alexandra Pavlova and Paul Sunnucks at Monash University to obtain a chromosome-length assembly genome for the Macquarie perch.

The chromosome-length assembly we share today is based on the draft assembly available on NCBI generated by Han Ming Gan, Deakin Genomics Centre, and the Monash University team, with funding from Australian Research Council-funded projects LP110200017 and LP160100482. The draft genome assembly of the Murray Darling Basin Macquarie perch lineage was created using MaSuRCA v. 3.2.4 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads.

The above draft was scaffolded to 24 chromosomes with 179M PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

The sample for Hi-C was kindly provided by Tim Curmi (Native Fish Australia). The Hi-C work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA), DNA Zoo and Monash University, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, David Weisz, Ashling Charles & Parwinder Kaur.

Blog by: Parwinder Kaur, Alexandra Pavlova and Paul Sunnucks

Citations

1. Faulks, L.K., Gilligan, D.M. & Beheregaray L.B. (2010). Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica. Conservation Genetics. DOI 10.1007/s10592-009-9936-7.

2. Pavlova, A., H. M. Gan, Y. P. Lee, C. M. Austin, D. Gilligan, M. Lintermans, and P. Sunnucks. 2017. Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish. Heredity 118:466–476.

3. Cadwallader, P.L. & Eden, A.K. 1979. Observations on the food of Macquarie Perch, Macquaria australasica (Pisces: Percicthyidae) in Victoria, Australian Journal of Marine and Freshwater Research 30: 401–409.

4. Lake, J.S. (1971). Freshwater Fishes and Rivers of Australia. Page(s) 61. Melbourne: Thomas Nelson.

5. Cadwallader, P. and P. Rogan. 1977. The Macquarie perch, Macquria australasica (Pisces: Percichthyidae), of Lake Eildon, Victoria. Australian Journal of Ecology 2:409-418

6. Trueman, W. T. 2011. True Tales of the Trout Cod: River Histories of the Murray-Darling Basin. MDBA Publication No. 215/11.

7. Lintermans, M. (2007). Fishes of the Murray–Darling Basin: An introductory guide. Canberra, ACT: Murray–Darling Basin Commission.

8. Pavlova, A., Beheregaray, L.B., Coleman, R., Gilligan, D., Harrisson, K.A., Ingram, B.A., Kearns, J., Lamb, A.M., Lintermans, M., Lyon, J., Nguyen, T.T.T., Sasaki, M., Tonkin, Z., Yen, J.D.L., Sunnucks, P., 2017. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evolutionary Applications 10, 531-550.

9. Commonwealth of Australia. 2018. National Recovery Plan for the Macquarie Perch (Macquaria australasica).

10. Lutz, M,, Tonkin, Z., Yen, J.D.L., Johnson, G., Ingram, B.A., Sharley, J., Lyon, J., Chapple, D.G., Sunnucks, P., Pavlova, A. Using multiple sources during reintroduction of a locally extinct population benefits survival and reproduction of an endangered freshwater fish. Evolutionary Applications, EVA-2020-125-OA, resubmitted 22/08/2020.

11. Ralls, K., Sunnucks, P., Lacy, R.C., Frankham, R., 2020. Genetic rescue: A critique of the evidence supports maximizing genetic diversity rather than minimizing the introduction of putatively harmful genetic variation. Biological Conservation 251, 108784.