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.

  • Cara Brook

Today we release the genome of the third and last of the three species of Old World Fruit Bat endemic to the island of Madagascar: Eidolon dupreanum.

Eidolon dupreanum. Photo by Cara Brook.

Bats (order: Chiroptera) make up more than one-fifth of mammalian diversity, and they can broadly be classed into two major sub-orders: the largely insectivorous and small-bodied Yangochiropterans—which typically echolocate to catch insect prey and are distributed widely across both the New and the Old Worlds—and the larger-bodied Yinpterochiropterans, including those in the family Pteropodidae (previously known as the ‘megabats’), which use sight and smell to track down fruit and nectar resources. Pteropodids are found only in Africa, Asia, and Australia.


The International Union for the Conservation of Nature classes some 35% of pteropodids under some category of threat, more than three times that of all other bat species combined [1]. These large fruit bats are particularly vulnerable to habitat destruction and land conversion and are also disproportionately hunted as a source of human food. As a result of higher human-bat contact rates resulting from human hunting and fruit bat consumption of domestic crops, Yinpterochiropterans bats have played important roles in the emergence of several recent viruses known to infect humans, including SARS-CoV-2, the cause of COVID-19, which is derived from Rhinolophous spp. horseshoe bats in China.

Eidolon dupreanum. Photo by Cara Brook.

On the Indian Ocean island nation of Madagascar, my team of young researchers, ‘Ekipa Fanihy’ (‘Team Fruit Bat’ in Malagasy), studies three species of pteropodid found nowhere else on Earth: Pteropus rufus, Rousettus madagascariensis, and Eidolon dupreanum. With this final release, we’ve now worked with DNA Zoo to construct genomes for all three endemic pteropodids on the island. (Read the blog posts for P. rufus and R. madagascariensis on dnazoo.org here and here!)


Eidolon dupreanum is noteworthy for being the only known sister species to the famous African Straw-Colored Fruit Bat, Eidolon helvum, which is distributed widely across the African continent and demonstrates the largest panmictic range ever described for any non-marine mammal [2]. (See the chromosome-length upgrade for Eidolon helvum from (Parker et al., 2013) on DNA Zoo website, here!) Sub-populations of E. helvum from Ghana to Kenya to Malawi demonstrate no genetic structure, a reflection of this species’ huge migratory capacity, with important implications for understanding zoonotic threats posed by the fruit bat virome to human communities.


While less is known about the sister species, Eidolon dupreanum, population genetic studies suggest that this bat is also largely panmictic across the Madagascar island but don’t be duped into thinking that these bats are the same! Eidolon dupreanum is highly genetically distinct from E. helvum, with estimates of species divergence times dating back to the mid- to late-Miocene—some ten to five million years ago [3]. Indeed, the two species show considerable dimorphism in size, color, and ecology—with E. dupreanum roosting in caves and crevasses, while E. helvum roosts in large congregations in trees [4]. Other recent work is beginning to shed light on the importance of E. dupreanum for dispersal of native fruit species in Madagascar [5], as well as highlight hunting threats to its population viability [6]. With DNA Zoo, we are excited to contribute one more piece of evidence to the growing knowledge base for this rare and important pteropodid species!

Assembly of this genome was financed by an NIH grant (R01-AI129822-01) administered Dr. Cara Brook of UC Berkeley and Dr. Jean-Michel Héraud of Institut Pasteur of Madagascar (link: http://grantome.com/grant/NIH/R01-AI129822-01).

Bibliography

[1] C.C. Voigt, T. Kingston, Bats in the Anthropocene: Conservation of bats in a changing world, 2016. doi:10.1007/978-3-319-25220-9.

[2] A.J. Peel, D.R. Sargan, K.S. Baker, D.T.S. Hayman, J. a Barr, G. Crameri, R. Suu-Ire, C.C. Broder, T. Lembo, L.-F. Wang, A.R. Fooks, S.J. Rossiter, J.L.N. Wood, A. a Cunningham, Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses, Nat. Commun. 4 (2013) 2770. doi:10.1038/ncomms3770.

[3] J.J. Shi, L.M. Chan, A.J. Peel, R. Lai, A.D. Yoder, S.M. Goodman, A deep divergence time between sister species of Eidolon (Pteropodidae) with evidence for widespread panmixia, Acta Chiropterologica. 16 (2014) 279–292. doi:10.3161/150811014X687242.

[4] A.O. Kamins, O. Restif, Y. Ntiamoa-Baidu, R. Suu-Ire, D.T.S. Hayman, a a Cunningham, J.L.N. Wood, J.M. Rowcliffe, Uncovering the fruit bat bushmeat commodity chain and the true extent of fruit bat hunting in Ghana, West Africa., Biol. Conserv. 144 (2011) 3000–3008. doi:10.1016/j.biocon.2011.09.003.

[5] M. Picot, R.K.B. Jenkins, O. Ramilijaona, P.A. Racey, S.M. Carrie, The feeding ecology of Eidolon dupreanum (Pteropodidae) in eastern Madagascar, Afr. J. Ecol. 45 (2007) 645–650. doi:10.1111/j.1365-2028.2007.00788.x.

[6] C.E. Brook, H.C. Ranaivoson, D. Andriafidison, M. Ralisata, J. Razafimanahaka, J. Héraud, A.P. Dobson, C.J. Metcalf, Population trends for two Malagasy fruit bats, Biol. Conserv. 234 (2019) 165–171. doi:10.1016/j.biocon.2019.03.032.

  • Ruqayya Khan

The Risso’s dolphin, Grampus griseus, sets some impressive #travelgoals. Some estimates say that the Risso’s dolphin may spend as much as 77% of their lives traveling [1]! Their geographical range is spread across the world, although they prefer deeper waters over the coast. From temperate to tropical waters, the Risso’s dolphin can be found in pods of 10-30 individuals [2].


Sometimes called the gray dolphin, the coloring of this species changes with age. Risso’s dolphins start their lives as black or dark gray in color and then lighten to a gray/white as they mature. The skin of this species is often marked by many scars, usually caused by teeth raking from other dolphins [3].


Unlike most cetaceans, the Risso’s dolphin lacks any upper teeth but instead can have several rows of peg-like teeth on their lower jaw. These teeth are useful in catching their preferred prey the cephalopods and also may play a role in mating behavior [4].

Risso's Dolphin, Grampus griseus by Robin Agarwal, [CC BY-NC 2.0], via flickr.com.

Today, we share the chromosome-length assembly for the Risso’s dolphin. This is a $1K de novo genome assembly with a contig N50 = 62 Kb and a scaffold N50 = 93 Mb. See Dudchenko et al., 2018 for details on the assembly procedure.


The sample for this genome assembly was provided to us by Barbie Halaska, Necropsy Manager at 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.


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.


Want to compare this genome against other members of the Delphinidae family? You’re in luck as this is the DNAZoo’s 8th genome assembly of a dolphin species! Check out the assembly pages for the bottlenose dolphin and the Commerson’s dolphin.


We thank Barbie Halaska, Laura Sherr, Giancarlo Rulli and Ben Neely for their help with this genome assembly!


Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the TMMC website at MarineMammalCenter.org.


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