Breakthrough allows scientists to determine the age of endangered native fish using DNA


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Benjamin Mayne, CSIROIdentifying the age of animals is fundamental to wildlife management. It helps scientists know if a species is at risk of extinction and the rate at which it reproduces, as well as determining what level of fishing is sustainable.

Determining the age of fish has been difficult in the past — primarily involving extracting the inner ear bone, also known as the “otolith”. Layers of growth in the otolith are counted like rings on a tree to reveal an individual’s age. Unless a dead specimen is available, this method requires killing a fish, making it unsuitable for use on endangered populations.

However a non-lethal DNA test developed by the CSIRO enables researchers to determine fish age for three iconic and threatened Australian freshwater species: the Australian lungfish, the Murray cod and the Mary River cod. We outline the technological breakthrough in our research just published.

Our fast, accurate and cost-effective test can be adapted for other fish species. We now hope to share this method to improve the protection of wild fish populations and help promote sustainable fisheries around the world.

gloved hands cut open fish with sciessors
Traditionally, age could only be determined on a dead fish. The new method is non-lethal.
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Iconic species at risk

Human activity has led to the population declines of the three Australian fish species at the centre of our research.

The threatened Australian lungfish is found in rivers and lakes in southeast Queensland. It’s often referred to as a “living fossil” because its extraordinary evolutionary history stretches back more than 100 million years, before all land animals including dinosaurs.

Man-made barriers in rivers reduce the movement of water, which lowers lungfish breeding rates.

Older lungfish do not have hard otolith structures, which makes determining their age difficult. Bomb radiocarbon, which analyses carbon levels in organic matter, has been used to age Australian lungfish, but this method is too expensive to be widely used.

Australian lungfish
In the past, determining the age of Australian lungfish has been challenging.

The threatened Murray cod is Australia’s largest freshwater fish. The Mary River cod is one of Australia’s most endangered fish, found in less than 30% of its former range in Queensland’s Mary River.

Habitat destruction and overfishing are major threats to Murray cod and Mary River cod populations.

Otoliths can be used to determine age for both these cod species, however this has only been done on a population-wide scale for the more prevalent Murray cod.




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Mary River cod
CSIRO estimated the age of Mary River cod.

Our DNA breakthrough

When cells divide to make new cells, DNA is replicated. This can lead to DNA methylation, which involves the addition or the loss of a “methyl group” molecule at places along the DNA strand.

Research has found the level of DNA methylation is a reliable predictor of age, particularly in mammals, including humans.

To develop our test, we first worked with zebrafish. This species is useful when studying fish biology because it has a short lifespan and high reproductive rates. We took zebrafish whose ages were known, then removed a tiny clip of their fin. We then examined DNA methylation levels in the fin sample to identify the fish’s age.

Following this successful step, we transferred the method to Australian lungfish, Murray cod and Mary River cod. Again, we used fish of known ages, as well as bomb radiocarbon dating of scales and ages determined from otoliths.

We found despite the zebrafish and the study fish species being separated by millions of years of evolution, our method worked in all four species. This suggests the test can be used to predict age in many other fish species.




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Good news from the River Murray: these 2 fish species have bounced back from the Millennium Drought in record numbers


DNA strand
The test uses co-called DNA methylation to estimate age.
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A conservation management boom?

In the same way human population demographers use census data to understand and model human populations, we now have the tools to do this with animals.

We are looking to expand this DNA-based method to determine the age of the endangered eastern freshwater cod and trout cod. We will also continue to test the method across other species including reptiles and crustaceans.

This work is part of CSIRO’s ongoing efforts to use DNA to measure and monitor the environment. This includes estimating the lifespan of vertebrate species such as long-lived fish and surveying biodiversity in seawater using DNA extracted from the environment.

We envisage that in the not too distant future, these methods may be used by other researchers to better understand and manage wild animal populations.




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The Conversation


Benjamin Mayne, Molecular biologist and bioinformatician, CSIRO

This article is republished from The Conversation under a Creative Commons license. Read the original article.

About 500,000 Australian species are undiscovered – and scientists are on a 25-year mission to finish the job


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Kevin Thiele, The University of Western Australia and Jane Melville, Museums VictoriaHere are two quiz questions for you. How many species of animals, plants, fungi, fish, insects and other organisms live in Australia? And how many of these have been discovered and named?

To the first, the answer is we don’t really know. But the best guess of taxonomists – the scientists who discover, name, classify and document species – is that Australia’s lands, rivers, coasts and oceans probably house more than 700,000 distinct species.

On the second, taxonomists estimate almost 200,000 species have been scientifically named since Europeans first began exploring, collecting and classifying Australia’s remarkable fauna and flora.

Together, these estimates are disturbing. After more than 300 years of effort, scientists have documented fewer than one-third of Australia’s species. The remaining 70% are unknown, and essentially invisible, to science.

Taxonomists in Australia name an average 1,000 new species each year. At that rate, it will take at least 400 years to complete even a first-pass stocktake of Australia’s biodiversity.

This poor knowledge is a serious threat to Australia’s environment. And a first-of-its kind report released today shows it’s also a huge missed economic opportunity. That’s why today, Australia’s taxonomists are calling on governments, industry and the community to support an important mission: discovering and documenting all Australian species within 25 years.

Australia: a biodiversity hotspot

Biologically, Australia is one of the richest and most diverse nations on Earth – between 7% and 10% of all species on Earth occur here. It also has among the world’s highest rates of species discovery. But our understanding of biodiversity is still very, very incomplete.

Of course, First Nations peoples discovered, named and classified many species within their knowledge systems long before Europeans arrived. But we have no ready way yet to compare their knowledge with Western taxonomy.

Finding new species in Australia is not hard – there are almost certainly unnamed species of insects, spiders, mites and fungi in your backyard. Any time you take a bush holiday you’ll drive past hundreds of undiscovered species. The problem is recognising the species as new and finding the time and resources to deal with them all.

Taxonomists describe and name new species only after very careful due diligence. Every specimen must be compared with all known named species and with close relatives to ensure it is truly a new species. This often involves detailed microscopic studies and gene sequencing.

More fieldwork is often needed to collect specimens and study other species. Specimens in museums and herbaria all over the world sometimes need to be checked. After a great deal of work, new species are described in scientific papers for others to assess and review.

So why do so many species remain undiscovered? One reason is a shortage of taxonomists trained to the level needed. Another is that technologies to substantially speed up the task have only been developed in the past decade or so. And both these, of course, need appropriate levels of funding.

Of course, some groups of organisms are better known than others. In general, noticeable species – mammals, birds, plants, butterflies and the like – are fairly well documented. Most less noticeable groups – many insects, fungi, mites, spiders and marine invertebrates – remain poorly known. But even inconspicuous species are important.

Fungi, for example, are essential for maintaining our natural ecosystems and agriculture. They fertilise soils, control pests, break down litter and recycle nutrients. Without fungi, the world would literally grind to a halt. Yet, more than 90% of Australian fungi are believed to be unknown.




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fungi on log
Fungi plays an essential ecosystem role.
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Mind the knowledge gap

So why does all this matter?

First, Australia’s biodiversity is under severe and increasing threat. To manage and conserve our living organisms, we must first discover and name them.

At present, it’s likely many undocumented species are becoming extinct, invisibly, before we know they exist. Or, perhaps worse, they will be discovered and named from dead specimens in our museums long after they have gone extinct in nature.

Second, many undiscovered species are crucial in maintaining a sustainable environment for us all. Others may emerge as pests and threats in future; most species are rarely noticed until something goes wrong. Knowing so little about them is a huge risk.

Third, enormous benefits are to be gained from these invisible species, once they are known and documented. A report released today
by Deloitte Access Economics, commissioned by Taxonomy Australia, estimates a benefit to the national economy of between A$3.7 billion and A$28.9 billion if all remaining Australian species are documented.

Benefits will be greatest in biosecurity, medicine, conservation and agriculture. The report found every $1 invested in discovering all remaining Australian species will bring up to $35 of economic benefits. Such a cost-benefit analysis has never before been conducted in Australia.

The investment would cover, among other things, research infrastructure, an expanded grants program, a national effort to collect specimens of all species and new facilities for gene sequencing.




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Two scientists walk through wetlands holding boxes
Discovering new species often involves lots of field work.
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Mission possible

Australian taxonomists – in museums, herbaria, universities, at the CSIRO and in
government departments – have spent the last few years planning an ambitious mission to discover and document all remaining Australian species within a generation.

So, is this ambitious goal achievable, or even imaginable? Fortunately, yes.

It will involve deploying new and emerging technologies, including high-throughput robotic DNA sequencing, artificial intelligence and supercomputing. This will vastly speed up the process from collecting specimens to naming new species, while ensuring rigour and care in the science.

A national meeting of Australian taxonomists, including the young early career researchers needed to carry the mission through, was held last year. The meeting confirmed that with the right technologies and more keen and bright minds trained for the task, the rate of species discovery in Australia could be sped up by the necessary 16-fold – reducing 400 years of effort to 25 years.

With the right people, technologies and investment, we could discover all Australian species. By 2050 Australia could be the world’s first biologically mega-rich nation to have documented all our species, for the direct benefit of this and future generations.




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The Conversation


Kevin Thiele, Adjunct Assoc. Professor, The University of Western Australia and Jane Melville, Senior Curator, Terrestrial Vertebrates, Museums Victoria

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Under the moonlight: a little light and shade helps larval fish to grow at night



Jeffrey Shima, Author provided

Jeffrey Shima, Te Herenga Waka — Victoria University of Wellington; Craig W. Osenberg, University of Georgia; Stephen Swearer, The University of Melbourne, and Suzanne Alonzo, University of California, Santa Cruz

At night on any one of hundreds of coral reefs across the tropical Pacific, larval fish just below the sea surface are gambling on their chances of survival.

Our latest research shows the brightness of the Moon could play a major role in that struggle for survival by affecting the availability of prey and keeping predators away.

Understanding how that works could help in fisheries management, specifically the prediction of changes to harvested fish stocks that allow us to anticipate how many adult fish can be taken without destabilising the fishery.

Many fish populations experience boom-and-bust cycles largely because parents routinely produce millions of offspring that have very low, but fluctuating, survival rates.

The large number of larval fish that are produced means any environmental conditions — for example, increased nutrients — that improve survival odds even only marginally can lead to a big influx in the number of surviving offspring.

Several sixbar wrasse swim above a reef.
Adult sixbar wrasse in courtship.
Author?, Author provided

When the Sun goes down

In the past we failed to take into account the influences the night may have on fish development.

In our research we found the daily growth rates of the larvae of sixbar wrasse (Thalassoma hardwicke) around the island of Mo’orea, in French Polynesia, are strongly linked to phases of the Moon.




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Their growth appears to be maximised when the first half of the night is dark and the second half of the night is bright.

Cloudy nights obscure the Moon, and thus allowed us to check our models by contrasting growth on cloudy versus clear nights, which confirmed the effect of moonlight on growth of these fish.

Phases of the Moon

We found that on the best nights of the lunar month for sixbars, around the last Quarter Moon when the Moon rises around midnight, larval fish grew about 0.012mm a day more than average.

But on the worst nights, around the first Quarter Moon when the Moon is overhead at sunset and sets around midnight, they grew about 0.014mm a day less than average.

From First Quarter to Full Moon then Last Quarter.
Phases of the Moon from the Southern Hemisphere.
Wikimedia, CC BY-SA

For a typical larval sixbar of 37.5 days old, that means its growth is 24% more on the best night than on the worst one. This is important, as growth is inextricably linked to survival and ultimately fisheries productivity.

We think the Moon affects larval growth in this way because of how it changes the movements of deeper-dwelling animals, those that migrate into shallow water each night to hunt for food under the cover of darkness.

Zooplankton — potential prey for larval sixbars — respond quickly to the arrival of darkness, and move into the surface water to supplement the diets of sixbars.

Micronekton, such as lanternfishes, which hunt larval fishes, may take much longer to reach surface waters and seek out their prey, due to their migration from much deeper depths.

Four graphs showing different phases of the Moon and the amount of predator/prey during each phase.
Four graphs showing the larval fish (in yellow) and the amount of predator (red shading area) and prey (brown shading area) rising to the surface during each phase of he Moon.
Proceedings of the Royal Society B, Author provided

As a consequence, prey availability for sixbars in surface waters may be hindered by early nocturnal brightness while the arrival of predators may be impeded by late nocturnal brightness.

Thus, larval fish grow best when their predators are absent but their prey are abundant — around the last Quarter Moon.

In contrast, around the first Quarter Moon, prey are suppressed but predators are not, leading to the slowest growth.

During the New Moon, when the surface waters remain dark throughout the night, influxes of both prey and predators may be high, with the latter preventing the larval fish from enjoying the increased numbers of prey.

On the other hand, during the Full Moon, when surface waters are well-lit, the movement of prey and predators may be suppressed, reducing the risk to the fish but also eliminating their food.

Impact on fishing

More research is needed to quantify these lunar effects on other marine populations. But our findings to date are good news for those working to strengthen fisheries management, given that phases of the Moon are predictable and cloud cover that can modify moonlight is being measured by satellites.

A diver underwater keeping watch on one of the sixbar wrasse fish.
Observing the sixbar wrasse spawning.
Author?, Author provided

This makes the incorporation of moonlight into existing fisheries management models relatively simple.

We think this will have implications around the world, not just in the tropics. This is because the nightly upward movements of deep-water animals is ubiquitous — it is the largest mass migration of biomass on the planet, and it happens everywhere.

The suppressive effect of moonlight on this movement of potential predators and prey is also a global phenomenon.

We evaluated effects of the Moon on growth of larval temperate fish in an earlier study and found a similar effect (moonlight enhanced growth).




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The effect is stronger and more nuanced in our latest study, most likely because the waters in the tropics are comparatively clear.

Our findings also hint that other factors which affect night-time illumination of the sea may disrupt marine ecosystems. This includes the reflection of artificial lights from coastal cities, suspended sediments in the water column, and changes in cloud cover due to climate change.

In the future, we may be able to harness this extra information to help forecast fish population change to better guide the management and conservation of fisheries around the world.The Conversation

Jeffrey Shima, Professor of Ecology, Te Herenga Waka — Victoria University of Wellington; Craig W. Osenberg, Professor of Ecology, University of Georgia; Stephen Swearer, Professor of Marine biology, The University of Melbourne, and Suzanne Alonzo, Professor of Ecology & Evolutionary Biology, University of California, Santa Cruz

This article is republished from The Conversation under a Creative Commons license. Read the original article.

We found algae-farming fish that domesticate tiny shrimp to help run their farms



Longfin damselfish (left) have domesticated mysid shrimps (right).
Rohan Brooker, Author provided

William Feeney, Griffith University and Rohan Brooker, Deakin University

Humans are experts at domesticating other species and our world would be unrecognisable without it. There would be no cities, no supermarkets, and no pets. Domestication is a special kind of cooperative relationship, where one species provides prolonged support in exchange for a predictable resource.

While humans have domesticated various plants and animals, these relationships are surprisingly rare in other species. It’s true some insects (ants, beetles, and termites among them) domesticate fungi, but few other examples exist outside the insect world.

In our new study, we describe what appears to be first example of a non-human vertebrate domesticating another animal.

Reef in Belize
On the coral reefs off the coast of Belize, in Central America, longfin damselfish create, manage and feed from algae farms.
By Andy Blackledge – P4120130, CC BY 2.0, CC BY



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Farming fish domesticate shrimps

On the coral reefs off the coast of Belize, in Central America, longfin damselfish create, manage and feed from algae farms. We noticed they regularly have “swarms” of tiny crustaceans called mysid shrimps floating above their farms.

We found this unusual, as most farming damselfishes chase away anything that ventures near their farm. We were unsure why these species associated with one another, so we decided to try to find out what was going on.

First, to see whether mysid shrimps and farming damselfish are regularly found together, we ran a series of what’s known as “transects”. In other words, we conducted a series of 30 metre swims along the reef, and during each one we recorded each time we saw mysid shrimps, as well as whether they were near farming damselfish or other fish species.

We found these mysids were far more likely to be found near farming species, like the longfin damselfish, than other species.

The Smithsonian’s Carrie Bow Cay Marine Research Station off the coast of Belize.
Rohan Brooker

Next, we wanted to know if the mysids specifically seek out their damselfish partners.

So, we collected mysid shrimps from the field, brought them into the lab and exposed the mysids to water soaked with different things. For example, do they avoid the smell of a predator? Are they attracted to the smell of a farming damselfish?

We found the mysids shrimps were attracted to the longfin damselfish, repulsed by a predator and indifferent towards a non-farming fish — and to the farm itself.

I help you, you help me

Many fish eat mysid shrimps, so we ran an experiment to see if longfin damselfish provided protection to the mysids when they are in the fish’s farm.

To do this, we placed mysid shrimps in a clear plastic bag and placed the bag either inside or outside a farm.

We found that when placed outside a farm, other fish tried to eat the mysid shrimps. When inside the farms, any fish that tried to come close to the bag was chased off by the longfin damselfish. This suggested the mysids seek out longfin damselfish, as they provide mysids with protection from predators.

Slippery Dick Wrasse is a common predator of shrimps.
Slippery Dick Wrasse is a common predator of mysid shrimps.
Brian Gratwicke/Flickr, CC BY

One question remained: do the mysid shrimps provide a benefit to the longfin damselfish?

Given the damselfish eat the algae they farm, we thought maybe by hovering above the farm, the mysid shrimps waste might act as fertiliser.

To test this, we examined the quality of the algae within farms that did, or did not have mysid shrimps. We also examined the body condition of fish that did, or did not, have mysid shrimps within their farms.

We found farms with shrimps had higher quality algae, and fish from farms with mysid shrimps were in better condition.

Insight into how domestication happens

These different analyses together suggest longfin damselfish have domesticated mysid shrimps. The longfin damselfish provide a safe refuge, and in exchange the mysid shrimps provide the damselfish with fertiliser for its farm.

This relationship is important, because while fantastic research has provided insight into the history of domestication in our ancestors, these things happened in the distant past.

In the longfin damselfish, we can watch the early stages of domestication occur as it’s happening.

This is fascinating because it’s very similar to the proposed series of events that led to our domestication of species such as chickens, cats, dogs and pigs.




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The Conversation


William Feeney, Postdoctoral Research Fellow in Evolutionary Ecology, Griffith University and Rohan Brooker, Casual Research Fellow, Deakin University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Good news from the River Murray: these 2 fish species have bounced back from the Millennium Drought in record numbers



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Brenton Zampatti, CSIRO and Chris Bice

This year marks a decade since the end of the Millennium Drought, when flood waters reached the mouth of the River Murray in 2010. For 1,200 days prior, Australia’s most iconic river had ceased flowing to the sea, causing populations of fish and other aquatic animals to plummet.

In particular, native migratory fish, including congolli (Pseudaphritis urvilli) and pouched lamprey (Geotria australis), were severely impacted by barriers to migration — such as barrages and weirs — and a lack of river flow.

However, our research has shown some clever engineering and increasing volumes of water for the environment are helping congolli and pouched lamprey to bounce back in record numbers.

With native fish in the Murray-Darling Basin just a fraction of what they were before European colonisation, rebuilding populations will be a long process. But learning from successes like this along the way will aid in the journey toward a healthier river.

An adult female congolli
An adult female congolli. These fish will spend 3-4 years in the River Murray before returning to the ocean to spawn.
Brenton Zampatti, Author provided

What happened to fish in the Millennium Drought?

From 2001 to 2009, south-eastern Australia experienced the most severe drought in recorded history.

Unprecedented low rainfall and water extraction for irrigation and human consumption reduced water flows in the lower Murray by around 70%. Water levels in the Lower Lakes at the terminus of the river system fell to more than one metre below sea level.

To prevent saltwater from the ocean mixing with critical storages of freshwater, tidal barrages (dam-like structures) were closed, and the River Murray was disconnected from the sea.




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This was a big problem for a number of migratory species, including pouched lamprey and congolli, which need to migrate between freshwater and saltwater to complete their lifecycles.

During the Millennium Drought, no lamprey were seen in the Lower Lakes and Coorong, while numbers of juvenile congolli declined. After more than three years of barrage closure, local populations were threatened with extinction.

But in late 2010, both species were saved by major flooding, when the Murray once again flowed to the sea, and abundances have continued to steadily improve over the past decade.

Several management initiatives were also critical in supporting recovery, even through the most recent drought. Notably, the installation of fish ladders and better water management. Fish ladders are water-filled channels with a series of steps that enable fish to swim around or over dams and weirs.

A fish ladder on the Murray Barrages. Fish swim through this structure to move from the estuary.
into the freshwater lakes and River Murray. Without fish ladders, fish are seldom able to move past the barrages.

Brenton Zampatti, Author provided

Supporting fish migrations

Native fish populations in the Murray-Darling Basin are estimated to be approximately 10% of those pre-European settlement. Barriers to fish movement and altered river flows are two principal causes of decline.

The Murray Barrages were constructed in the 1930s, without consideration of fish passage, and it was 70 years before the first fish ladder was constructed in 2003.




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In 2020, there are now 11 fish ladders spread across the Murray Barrages, and our research has shown they effectively support vital migrations.

More fish ladders have been built on upstream weirs, together opening more than 2,000 kilometres of the River Murray to fish migration.

However, water must be available to operate the fish ladders, and this is where environmental water plays a role.

In 2009-10, approximately 120 gigalitres of environmental water were delivered across the Basin. By 2017-18, this volume was greater than 1,200 gigalitres and included substantial volumes across the Murray Barrages.




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This increase has enabled the River Murray to continuously flow to the sea, restoring its natural characteristics, albeit at a significantly reduced volume.

What’s more, water for the environment has supported constant operation of the barrage fish ladders since 2010 — a huge win for lamprey and congolli.

The bounce back

From the lows of the Millennium Drought we have so far this year caught a record 101 individual pouched lamprey moving through the barrage fish ladders and proceeding upstream. This is up from last year’s catch of 61 fish.

Pouched lamprey
Pouched lamprey has been found in record numbers.
Brenton Zampatti, Author provided

Congolli populuations are also booming. From 2007 to 2010, we sampled a combined total of just over 1,000 congolli. Compare this to the summer of 2014-15, when we sampled more than 200,000 passing through the fishways.

Congolli is now one of the most abundant fish in the Coorong and upstream of the barrages in the Lower Lakes.

What the rest of the basin can learn from this

Fish ladders and environmental water have been successful in supporting fish migration at the Murray Barrages, yet across the Murray-Darling Basin, thousands of barriers remain and more are being considered, particularly in the northern Basin.

These barriers can impede the movements of fish that migrate wholly within freshwater, such as golden perch (Macquaria ambigua) and the threatened silver perch (Bidyanus bidyanus). This includes the spawning migrations of adults and downstream dispersal of juveniles.

Mitigating the impacts of existing and new structures on the movement of fish is crucial to restoring native fish populations in the Murray-Darling Basin.

To help restore migratory fish throughout the basin, there must be greater understanding of the movement requirements of all fish life stages, the construction of effective fish ladders, and river flows must be sufficient to facilitate downstream movement, including of eggs and larval fish. The removal of barriers may also be a feasible option.

In any case, after 15 years of experience in the lower River Murray we’ve learnt protecting migratory fish is best achieved when researchers, the community, water managers and river operators collaborate closely. Such partnerships are the bedrock to establishing a healthier river.




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The Conversation


Brenton Zampatti, Principal Research Scientist, CSIRO and Chris Bice, Research scientist at SARDI

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Australia’s smallest fish among 22 at risk of extinction within two decades



Red-finned blue-eye
Bush Heritage Australia / Adam Kerezsy

Mark Lintermans, University of Canberra; Hayley Geyle, Charles Darwin University; Jaana Dielenberg, The University of Queensland; John Woinarski, Charles Darwin University; Stephen Beatty, Murdoch University, and Stephen Garnett, Charles Darwin University

The tragic fish kills in the lower Darling River drew attention to the plight of Australia’s freshwater fish, but they’ve been in trouble for a long time.

Many species have declined sharply in recent decades, and as many as 90 of Australia’s 315 freshwater fish species may now meet international criteria as threatened.




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No Australian fish species is yet listed officially as extinct, but some have almost certainly been lost before scientists even knew they existed. With so many species at risk, understanding which are in greatest peril is a vital first step in preventing extinctions.

This is what our new research has done. We’ve identified 20 freshwater fish species with a 50% or greater probability of extinction within the next two decades, and a further two with a 40-50% chance – unless there’s new targeted conservation action.

The Australian freshwater fishes at greatest risk of extinction.

Slipping through the conservation cracks

Many small-bodied species, including Australia’s smallest fish the red-finned blue-eye, look likely to be lost within a single human generation. These fish have evolved over millions of years.

Twelve of the species identified have only been formally described in the past decade, and seven are still awaiting description.

This highlights the urgent need to act before species are listed under the national legislation that gives fishes their conservation status, and even before they’re formally described.

These processes can take many years, at which point it may be too late for some species.

More than half the species on our list are galaxiids – small, scaleless fish, that live in cooler, upland streams and lakes. Trout, an introduced, predatory species, also favour these habitats, and the trout have taken a heavy toll on galaxiids and many other small species in southern Australia.

Shaw galaxias, a long light-brown fish.
Victoria’s Shaw galaxias – one of 14 galaxias species identified at high risk of extinction.
Tarmo Raadik

For example, the Victorian Shaw galaxias has been eaten out of much of its former range. Now just 80 individuals survive, protected by a waterfall from the trout below. We estimate the Shaw galaxias has an 80% chance or more of extinction within the next 20 years.




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Many galaxiids do not thrive or readily breed in captivity, so suitable trout-free streams are essential for their survival.

Improving trout management requires an urgent, sustained conservation effort, including collaborations with recreational fishers, increased awareness and changing values among government and key sectors of society.

Without this, trout will almost certainly cause many native galaxiids to go extinct.

Two researchers face a waterfall surounded by bushland.
This waterfall in NSW is all that protects the last population of stocky galaxias from the predatory trout below.
Mark Lintermans

Native fish out of their natural place can also be a problem. For example, sooty and khaki grunters – native fishing species people in northern Australia have widely moved – threatening the ancient Bloomfield River cod.

One disaster can lead to extinction

All of the most imperilled species are now highly localised, which means they’re restricted to very small areas. Their distributions range from only four to 44 square kilometres.

A single catastrophic event could completely wipe out these species, such as a large bushfire that fills their streams with ash and robs them of oxygen.

The SW Victoria River blackfish persists as three very small, isolated populations. The main threat to this species is recreational angling.
Tarmo Raadik

For example, until 2019 the Yalmy galaxias had survived in the cool creeks of the Snowy River National Park. But after the devastating Black Summer fires, just two individuals survived, one male and one female, in separate areas.

Millions of years of evolution could be lost if a planned reunion is too late.

One of the key steps to reduce this risk is moving fish to new safe locations so there are more populations. Researchers choose these new locations carefully to make sure they’re suitable for different species.

Climate change is another threat to all identified species, as it’s likely to reduce flows and water quality, or increase fires, storms and flooding. Many species have been forced to the edge of their range and a prolonged drought could dry their remaining habitat.

The short-tail galaxias existed in two small separated populations in creeks of the upper Tuross River Catchment, in the south coast of NSW. One stream dried in the recent drought, and the other was burnt in the subsequent fires.

Luckily the species is still hanging on in the burnt catchment, but only a single individual has been found in the drought-affected creek.

Rainbowfish swim among reeds
The main threat to the Daintree rainbowfish is loss of stream flow due to drought, climate change and water extraction.
Michael Hammer / Museum and Art Gallery of the Northern Territory, Author provided

Unlisted, unprotected

Our study is part of a larger project to identify plants and animals at high risk of extinction.

We found the extinction risks of the 22 freshwater fish species are much higher than those of the top 20 birds or mammals, yet receive far less conservation effort.

Only three of the highly imperilled fish species are currently listed as threatened under national environmental legislation: the red-finned blue-eye, Swan galaxias and little pygmy perch.

Listing species is vital to provide protection to survivors and can prompt recovery action. Given our research, 19 fish species should urgently be added to the national threatened species list, but conservation action should start now.

The little pygmy perch in the far south-west corner of WA is one of only three of the 22 imperilled species identified that’s formally protected under Australian laws.
Stephen Beatty/Harry Butler Institute, Murdoch University

Small native freshwater fishes are worth saving. They play a vital role in our aquatic ecosystems, such as predating on pest insect larvae, and are part of our natural heritage.

By identifying and drawing attention to their plight, we are aiming to change their fates. We cannot continue with business as usual if we want to prevent their extinctions.The Conversation

Mark Lintermans, Associate professor, University of Canberra; Hayley Geyle, Research Assistant, Charles Darwin University; Jaana Dielenberg, Science Communication Manager, The University of Queensland; John Woinarski, Professor (conservation biology), Charles Darwin University; Stephen Beatty, Research Leader (Catchments to Coast), Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, and Stephen Garnett, Professor of Conservation and Sustainable Livelihoods, Charles Darwin University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Double trouble: this plucky little fish survived Black Summer, but there’s worse to come



Tarmo A. Raadik

Mark Lintermans, University of Canberra

This article is part of Flora, Fauna, Fire, a special project by The Conversation that tracks the recovery of Australia’s native plants and animals after last summer’s bushfire tragedy. Explore the project here and read more articles here.


On a coastal holiday last summer, I was preoccupied. Bushfires were tearing through southeast Australia, and one in particular had me worried. Online maps showed it moving towards the last remaining population of a plucky little fish, the stocky galaxias.

I’ve worked in threatened fish conservation and management for more than 35 years, but this species is special to me.

The stocky galaxias was formally described as a new species in 2014. Its only known population lives in a short stretch of stream in Kosciuszko National Park in New South Wales. A single event could wipe them out.

On January 2 the bushfires forced my family and I to evacuate our holiday home. As we returned to Canberra, I was still worried. Fire maps showed the stocky’s stream virtually surrounded by fire.

A few days later, I prepared for an emergency rescue.

Fire tore through south east Australia in January, threatening the stocky galaxias.
Victorian government

In critical danger

The stocky galaxias is the monarch of its small stream; the only fish species present. I’ve been trying to protect the stocky galaxias before it was even formally recognised.

Over the last century or more, the species has seen off threats from predatory trout, storms, droughts and bushfires. Snowy 2.0 is the latest danger.

It’s listed as critically endangered in NSW and is being assessed for a federal threatened listing. Before the fires, there were probably no more than 1,000-2,000 adults left in the wild.




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After the bushfires, we helped choose the animals and plants in most need. Here’s how we did it


As the fires burned, I knew we had to move quickly. I wanted to collect up to 200 stocky galaxias and take them away for safekeeping.

Rainfall after bushfires is major threat to fish, because it washes ash and sediment into streams. Storms were forecast for the afternoon of January 15. So early that morning, myself and two colleagues, escorted by two staff from the NSW National Parks and Wildlife Service, drove to the stocky galaxias stream.

A colleague and I waded in and began electrofishing. This involved passing an electrical current through water, stunning fish momentarily so we could catch them.

The author and his colleagues used electrofishing to catch the fish.
Mark Lintermans

After 45 minutes we’d collected 68 healthy stocky galaxias. Woohoo! Further downstream we collected 74 more. By now, fire burned along the stream edge. We packed the fish into drums in the back of my car and drove out.

We headed to the NSW Department of Primary Industries’ trout hatchery at Jindabyne, where we measured each fish and took a genetic sample. I felt immensely relieved and satisfied that we’d potentially saved a species from extinction.

The fish have been thriving in the hatchery building. Stocky galaxias have never been kept in captivity before, but our years of field work told us the temperatures they encountered in the wild, so holding tanks could be set up appropriately.




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Conservation scientists are grieving after the bushfires — but we must not give up


Back to the stream

The captive fish can be used for breeding, but the species has never been captive-bred before and this is not a trivial task.

When they’re reintroduced to the wild, the sites must be free of trout, and other invasive fish like climbing galaxias. Natural or artificial barriers should be in place to prevent invasive fish invasion.

In late March I finally got back to the stocky galaxias’ stream to see whether they’d survived. At the lower stretch of its habitat, the fire was not severe and the stream habitat looked good, with only a small amount of ash and sediment.

Upstream, the fire had been more severe. At the edge of the stream, heath was razed and patches of sphagnum moss were burnt. Again, sediment in the stream was not too abundant. But fish numbers were lower than normal, suggesting some there had not survived.

Stocky Galaxias live in a short stretch of a single stream.
Credit to come

The fight’s not over

The stocky galaxias species might have survived yet another peril, but the battle isn’t over.

Feral horse numbers in Kosciuszko National Park have increased dramatically in the last decade. They’ve degraded the banks of the stocky galaxias’ stream, making it wider and shallower and filling sections with fine sediment. This smothers the fish’s food resources, spawning sites and eggs.

Before the fires, plans were already afoot to fence off much of the stocky galaxias habitat to keep horses out. Fire damage to the park has delayed construction until early 2021.




Read more:
Snowy 2.0 threatens to pollute our rivers and wipe out native fish


The biggest long-term threat to the species is the Snowy 2.0 pumped hydro development. It threatens to transfer an invasive native fish, the climbing galaxias, to within reach of stocky galaxias habitat. There, it would compete for food with, and prey on, stocky galaxias – probably pushing it into extinction.

Despite this risk, in May this year the NSW government approved the Snowy 2.0 expansion, with approval conditions that I believe fail to adequately protect the stocky galaxias population. The project has also received federal approval.

Future in the balance

The stocky galaxias is unique and irreplaceable. I want my grandchildren to be able to show their grandchildren this little Aussie battler thriving in the wild.

The damage wrought by Snowy 2.0 may not be apparent for several decades. By then many politicians and bureaucrats now deciding the future of the stocky galaxias will be gone, as will I.

But 2020 will go down in history as the year the species was saved from fire, then condemned to possible extinction.

The Conversation

Mark Lintermans, Associate professor, University of Canberra

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Don’t count your fish before they hatch: experts react to plans to release 2 million fish into the Murray Darling



Dean Lewins/AAP

Lee Baumgartner, Charles Sturt University; Jamin Forbes, Charles Sturt University, and Katie Doyle, Charles Sturt University

The New South Wales government plans to release two million native fish into rivers of the Murray-Darling Basin, in the largest breeding program of its kind in the state. But as the river system recovers from a string of mass fish deaths, caution is needed.

Having suitable breeding fish does not always guarantee millions of healthy offspring for restocking. And even if millions of young fish are released into the wild, increased fish populations in the long term are not assured.

For stocking to be successful, fish must be released into good quality water, with suitable habitat and lots of food. But these conditions have been quite rare in Murray Darling rivers over the past three years.

We research the impact of human activity on fish and aquatic systems and have studied many Australian fish restocking programs. So let’s take a closer look at the NSW government’s plans.

A mass fish kill at Menindee in northern NSW in January 2019 depleted Fisk stocks.
AAP

Success stories

According to the Sydney Morning Herald, the NSW restocking program involves releasing juvenile Murray cod, golden perch and silver perch into the Darling River downstream of Brewarrina, in northwestern NSW.

Other areas including the Lachlan, Murrumbidgee, Macquarie and Murray Rivers will reportedly also be restocked. These species and regions were among the hardest hit by recent fish kills.

Fish restocking is used worldwide to boost species after events such as fish kills, help threatened species recover, and increase populations of recreational fishing species.

Since the 1970s in the Murray-Darling river system, millions of fish have been bred in government and private hatcheries in spring each year. Young fish, called fingerlings, are usually released in the following summer and autumn.




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There have been success stories. For example, the endangered trout cod was restocked into the Ovens and Murrumbidgee Rivers between 1997 and 2006. Prior to the restocking program, the species was locally extinct. It’s now re-established in the Murrumbidgee River and no longer requires stocking to maintain the population.

In response to fish kills in 2010, the Edward-Wakool river system was restocked to help fish recover when natural spawning was expected to be low. And the threatened Murray hardyhead is now increasing in numbers thanks to a successful stocking program in the Lower Darling.

After recent fish kills in the Murray Darling, breeding fish known as “broodstock” were rescued from the river and taken to government and private hatcheries. Eventually, it was expected the rescued fish and their offspring would restock the rivers.

A Murray hardyhead after environment agencies transplanted a population of the endangered native fish.
North Central Catchment Management Authority

Words of caution

Fish hatchery managers rarely count their fish before they hatch. It’s quite a challenge to ensure adult fish develop viable eggs that are then fertilised at high rates.

Once hatched, larvae must be transported to ponds containing the right amount of plankton for food. The larvae must then avoid predatory birds, be kept free from disease, and grow at the right temperatures.




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When it comes to releasing the fish into the wild, careful decisions must be made about how many fish to release, where and when. Factors such as water temperature, pH and dissolved oxygen levels must be carefully assessed.

Introducing hatchery-reared fish into the wild does not always deliver dramatic improvements in fish numbers. Poor water quality, lack of food and slow adaptation to the wild can reduce survival rates.

In some parts of the Murray-Darling, restocking is likely to have slowed the decline in native fish numbers, although it has not stopped it altogether.

Address the root cause

Fish stocking decisions are sometimes motivated by economic reasons, such as boosting species sought by anglers who pay licence fees and support tourist industries. But stocking programs must also consider the underlying reasons for declining fish populations.

Swan Hill, home to a larger-than-life replica of the Murray cod, is just one river community that relies on anglers for tourism.
Flickr

Aside from poor water quality, fish in the Murray Darling are threatened by being sucked into irrigation systems, cold water pollution from dams, dams and weirs blocking migration paths and invasive fish species. These factors must be addressed alongside restocking.

Fish should not be released into areas with unsuitable habitat or water quality. The Darling River fish kills were caused by low oxygen levels, associated with drought and water extraction. These conditions could rapidly return if we have another hot, dry summer.

Stocking rivers with young fish is only one step. They must then grow to adults and successfully breed. So the restocking program must consider the entire fish life cycle, and be coupled with good river management.

The Murray Darling Basin Authority’s Native Fish Recovery Strategy includes management actions such as improving fish passage, delivering environmental flows, improving habitat, controlling invasive species and fish harvest restrictions. Funding the strategy’s implementation is a key next step.

Looking ahead

After recent rains, parts of the Murray Darling river system are now flowing for the first time in years. But some locals say the flows are only a trickle and more rain is urgently needed.

Higher than average rainfall is predicted between July and September. This will be needed for restocked fish to thrive. If the rain does not arrive, and other measures are not taken to improve the system’s health, then the restocking plans may be futile.




Read more:
We wrote the report for the minister on fish deaths in the lower Darling – here’s why it could happen again


The Conversation


Lee Baumgartner, Professor of Fisheries and River Management, Institute for Land, Water, and Society, Charles Sturt University; Jamin Forbes, Freshwater Ecologist, Charles Sturt University, and Katie Doyle, Freshwater Ecologist, Charles Sturt University

This article is republished from The Conversation under a Creative Commons license. Read the original article.