Skates and salmon farms: science is part of the equation

Can the threatened Maugean skate coexist with Tasmania’s salmon industry? Lauren Fuge talks to the experts on the ground – and on the water.

In the tannin-stained waters of a remote Tasmanian harbour, a prehistoric creature prowls the darkness. This ray-like predator has hunted the shallow harbour for tens of thousands of years, yet it was unknown to science until 1988. Now, there’s a risk that it could soon become the first marine fish in modern times to go extinct due to human activity.

The only place the endangered Maugean skate (Zearaja maugeana) calls home is Macquarie Harbour, which has been shaped and scarred by human hands since European colonisation. In recent decades, the vast circular pens of salmon farms have begun to dot the harbour, producing Atlantic salmon as well as producing controversy about how the salmon industry affects the unique and delicate ecosystem of Macquarie Harbour.

Some wonder if this means the end for the skate. The Tasmanian government says that the salmon farming industry and the skate can co-exist. But does this claim stack up with the science?

A unique harbour

Macquarie Harbour is an enormous estuary in western Tasmania, covering 315 square kilometres.

“It’s about six times the size of Sydney Harbour,” says David Moreno, a researcher at the Institute for Marine and Antarctic Studies (IMAS) at the University of Tasmania. “It’s a beautiful area. The bottom half of the harbour is a World Heritage Area, and it’s surrounded by some pretty ancient forests. It’s on the west coast of Tasmania, so it’s exposed to the Roaring 40s – really big weather, lots of rain.”

Moreno explains that both the King and Gordon rivers flow into the harbour, creating stratified water columns: “You basically will always, year-round, have a freshwater layer on top, and then a brackish layer in the middle, and then a full marine layer down on the bottom.” And there’s very little mixing between layers.

The freshwater is dark because it’s full of tannins, making it difficult for light to get through. Even though the harbour is relatively shallow (up to 50 metres in depth), its bottom layers are more like a deep-sea environment with little light or plant life.

The mouth of the harbour is also narrow and shallow, so that the amount of freshwater pouring out of the rivers determines how much ocean water can get in through the mouth. This exchange of oceanic water is one of the few ways oxygen can get to the depths of the harbour.

“Because of those oxygen conditions and the light and the low productivity, it’s naturally low in life,” Moreno says. “Quite a simplistic food chain lives there. The animals there are pretty unique.”

One of the most remarkable species in the harbour is the Maugean skate.

Skates are part of the ancient lineage of cartilaginous fishes, along with sharks and rays. Skates resemble stingrays, but have short, thick and fleshy tails without stingers. They are also egg-laying creatures, while rays give birth to live young. Maugean skates spend their time hunting crustaceans on the sea floor.

The Maugean skate was first discovered in 1988, in the brackish waters of Bathurst Harbour further south. In 1994, CSIRO technician Mark Lewis collected five specimens in Macquarie Harbour. Since 1992 the skate has not been spotted outside Macquarie Harbour, and scientists believe it holds the species’ sole remaining viable population.

Given their apparently small population and geographic range, Maugean skates have been listed as endangered since 2000. And human activity in the harbour isn’t helping their survival.

Landscape shapers

Macquarie Harbour has a long history of human industrial impact, dating back to the start of European colonisation.

A stone wall was built in the 19^th century to keep the channel open, which affected the transfer of water – and oxygen – in and out. Mining wastewater used to flow down the rivers and contaminate the sediment with heavy metals. Hydroelectric dam projects upriver changed the natural patterns of freshwater flows.

Then salmon aquaculture kicked off in the 1980s, producing Atlantic salmon in netted pens on the surface. The industry began a massive expansion in 2009 after an environmental impact study that suggested the harbour could support 29,500 tonnes of salmon production per year, more than double what they had previously been producing.

Huon Aquaculture, Tassal and Petuna – the three aquaculture companies that operate in the harbour – signed an agreement in 2012 to “avoid significant impacts” on the World Heritage Area and the Maugean skate.

But a 2014 monitoring report led by CSIRO and IMAS found that the dissolved oxygen levels in the harbour’s depths had steeply declined since 2009. Timewise, this corresponds to the expansion of the salmon industry.

However, experts say that this isn’t the whole picture.

Salmon vs skate

IMAS senior researcher Jeff Ross says the oxygen levels in the harbour are dynamic, and this decline in oxygen was linked to several different factors.

“We’ve seen temperatures go up by a couple of degrees, and warm water holds less oxygen,” he says. “We also know that in Macquarie harbor, the rivers play a really important role in determining how much oxygen can come in from the ocean.”

And then there’s salmon farming.

“There are a number of ways that salmon aquaculture can affect the environment,” says Ross. “One is their dissolved waste. So when the fish eat, they excrete urea and it becomes ammonia … The other major source is solid waste, so that’s any feed that the salmon don’t eat, and also their faeces.”

This waste will float down to the sediments of the seafloor to be processed by worms and bacteria, which consume oxygen. More waste means more seafloor life, to a point. If the oxygen runs out, it can be catastrophic.

“One of the most important things to acknowledge with Macquarie Harbour is that it is a naturally low-oxygen environment,” says Ross. “We’ve seen before farming that the oxygen levels were low, and that’s what we’d expect in a system like that, but what we saw in about 2009 is the oxygen levels declining even further, and 2014, ‘15 and ‘16 … there were periods of time in the bottom waters where there was very little oxygen at all.”

These levels are linked to the health of the environment on the sea floor. In 2016, sediment samples showed that the microfauna living on the sea floor had dramatically decreased in abundance.

These oxygen levels also affect species like the Maugean skate.

“This animal has evolved in this very unique ecosystem for a very long time, and therefore it has a very close relationship to the conditions,” Moreno says.

Over time, it has developed mechanisms to cope with the challenge of a low-oxygen ecosystem.

“But it also means that if you push them beyond that, there is a pretty steep tipping point.”

Population mystery

A recent estimate from Moreno’s team at IMAS indicates that the skate population may be bouncing back after a steep decline. But it’s extremely difficult to know how many of these elusive skates are in the dark, deep harbour.

Moreno says they know with certainty there aren’t tens of thousands of animals, and there also aren’t just a few hundred. “Beyond that, we’re still working on it,” he says.

The team made the first population estimate of the skate in 2014, which was around 3,000 animals – plus or minus 1,500.

They continued to monitor the animals, both via catching them and via electronic tags. The year 2019 saw two widespread mortality events, resulting in a 2021 report estimating a 47% population drop since 2014. Both of these die-offs were attributed to a drop in oxygen levels in the water, as shown by environmental sensors mounted in tracking tags. But this was not necessarily linked to salmon aquaculture.

Moreno says the first event was caused by a layer of freshwater preventing new, oxygen-rich oceanic water coming in. The other was likely the result of a huge westerly storm that pushed low-oxygen water from the deep ocean up to skate habitat.

After these mortality events, IMAS’s most recent monitoring report in 2024 suggested an upward tick in the population trend. It found “a significant increase in relative abundance from 2022, with current estimates now not significantly different to 2014”. This means that the number of animals caught in comparable amounts of fishing effort was the same.

“That’s not to say that there was a proportional increase in the population,” Moreno clarifies. “Several things can affect an animals’ catchability, so we are not yet fully in a position where we can understand how that translates to the actual population …

“It’s important to know that we don’t know that the population has bounced back.”

The other challenge is that the skate – although ancient – is new to science.

“Unfortunately, there isn’t very good historical data to compare to, so the estimates that we have for historical trends begin after the environmental impacts had already begun,” Moreno says.

“Long story short, we don’t fully know how many animals are in the population at the moment.”

Counting cleverly

IMAS and CSIRO teams have been developing experimental techniques to more accurately estimate the total population, because conventional approaches haven’t worked.

At first, they looked at the skates’ genetic data. For many animals, this can give a good estimate of population size. But the naturally low genetic diversity of the skates poses a problem.

“There are just too many untested assumptions to use that technique effectively,” Moreno says. “That was one of the first things that we attempted and realised that it was not going to yield very useful results.”

Instead, skate researchers at IMAS are trying genomic approaches, looking at bigger chunks of the skate’s genes to have a better chance of finding variability.

Meanwhile, a CSIRO team led by Toby Patterson is also working on applying a genetic analysis technique called close-kin mark recapture (CKMR) to the skate. The technique involves taking a small sample from each animal caught, building its genetic profile, and comparing it to every other animal caught to see if and how they are related.

The goal is to count the close relationships (like parent-offsprings, or half-sibling pairs). If the population is low, then it’s more likely to find close relationships between the survivors.

Moreno and colleagues are also developing acoustic imaging technology to spot skates in the water. This is akin to ultrasounds, which use ultra-high-frequency sound (around 3 Megahertz) to generate an image.

“You don’t need light,” Moreno says. “In very … turbid, mixed water environments like Macquarie Harbour, you can generate a very nice result.”

But because the technology uses such a high frequency of sound, it can’t travel far. The imaging device – which looks like a handheld video camera – must be underwater and close to the subject.

The team is working on cost-effective ways to survey larger parts of the harbour, to provide the statistical power to estimate the skate population with more certainty.

Breeding for the future

The federal government has committed $5.7 million to help protect the skate, with the Tasmanian government contributing $4 million. This included $2.1 million to initiate a captive breeding program in Hobart – one of only three captive breeding programs for skates and rays in the world.

Led by IMAS Professor Jayson Seemens, the program began in the summer of 2023, when a large marine heatwave was predicted to hit Tasmania – creating similar conditions to 2019, which saw multiple die-offs.

“Deep water temperatures in Macquarie Harbour have warmed in the last 30 years at the same rate as the surface temperatures in the outside, so by 1.5 to 2.5 degrees Celsius,” Moreno says.

This heat affects the water’s capacity to hold oxygen. “There was a genuine fear that if we got unlucky, [the heatwave] could spell out natural extinction for this species,” explains Moreno, who works on the program with Seemens.

So they moved fast to set up a captive population.

In December 2023, they collected four carefully selected adult animals, as well as 50 eggs, 26 of which soon hatched. One of the adults was pregnant, and has since laid more than 100 eggs in captivity. In December 2024, the first captive-hatched skate celebrated its first birthday – a huge milestone.

“This species had never been kept in captivity for more than two weeks, so there were a lot of uncertainties about whether it was even possible,” Moreno says.

The program has enabled field biologists to study the captive animals in depth, building on their understanding of the species.

The next step is to supplement the recovery of the wild population.

“The best captive breeding program is the one you don’t need anymore,” Moreno says.

However, the captive animals have been held in tanks in pristine conditions, with water high in oxygen, so it is unclear how they will fare in the wild. That is, unless oxygen levels improve.

Re-oxygenating Macquarie Harbour

In 2024, researchers began a pilot study that used a modified barge to pump reoxygenated water into the harbour.

“We essentially were bringing water up from 30 metres [below the surface], where it’s low in oxygen but it’s saline, and then we had a system that pumped that water full of oxygen, and then we took that saturated water and we put it back down at depth,” says Ross, who heads the project.

“Then we monitored all around that point. So we’ve got real time sensors of oxygen, currents, heavy metals, fauna…”

When tests showed that the oxygen was staying down at depth and spreading out as required, the team started scaling the operation. They are now injecting four tonnes of dissolved oxygen per day into the harbour, with further increases to come.

Ross believes this is a promising tool to promote oxygen levels in the harbour. Data shows that levels are improving, but only partly due to the reoxygenation project. The recovery also comes from a reduction in salmon farming (down to 9,500 tonnes in 2024) and a few years of low river flows, meaning ocean water can more readily enter the harbour.

However, the system requires ongoing monitoring to know whether it is rebalancing.

“In the next few years, we can become more confident as to whether that’s a genuine recovery, because we know that oxygen can come up and down,” Ross says.

Looking to the future

So, can the skates and the salmon industry co-exist?

“We’ve got good signs in terms of oxygen levels, and some encouraging signs seen with skate numbers,” Ross says. “That would tend to suggest it’s possible.”

But, he adds, we need to see if these conditions are sustained, and whether the system can be in balance with the salmon biomass.

“It’s not an opportunity to take our hands off the wheel,” he says.

Moreno agrees that the conditions of the harbour are vital to skate survival.

“What needs to happen for the remediation of the species is the remediation of the habitat,” he says. “One doesn’t exist without the other.

“One thing that the science definitely shows with certainty is that if conditions are improved, every characteristic – genetic, physiological, biological, reproductive – of the species suggests that they have the capacity for recovery. So if you give them an inch, they’ll take it and go a mile.”

However, Moreno also notes that the skate will likely remain endangered – “it’s reliant on this one place, so it’s always going to be vulnerable,” he says.

“Micro-endemics are rare. Large, vertebrate, carnivorous micro-endemics are incredibly rare all around the world. In Tasmania, we are very lucky to have had three: the Tasmanian devil, the Maugean skate and the thylacine.

“One of them, of course, is a textbook example of what can happen when a conservation intervention doesn’t happen on time.”

But the research is going full steam ahead, and there are reasons to be optimistic.

“We’re monitoring in the field,” Moreno says. “We’re trying new technologies. We’re working hard on novel molecular and genetic analysis to try to understand the history of the population.

“We’re looking into assisted reproduction technologies for artificial insemination – anything that can help with the captive breeding.

“We’re trying everything.”

But the scientists are only one part of the equation that determines the skate’s fate, which also includes federal and state politicians, the salmon industry, conservation organisations, grassroots movements, local businesses and more.

“Our job is to produce the best possible quality science to inform everything that’s happening – all the management actions and population recovery and action plan,” Moreno says. “And that’s what we try to do, regardless of what’s happening outside of that.”

What happens with the skate will be a litmus test for the future of other species, too.

“The reality is that changing environmental conditions are going to affect the vast majority of marine species in coastal habitats in the next 30 years, and what we’re seeing here is sort of a microcosm of what’s coming for a lot of species,” Moreno says.

The skate will serve as a model for understanding how other species will react – and a model for what the research and management processes might look like to successfully help a species recover.

It’ll be a challenge, Moreno adds: “This is a remote, not very abundant, cryptic, endangered animal, so it’s a hard problem. But that’s our job – to find solutions to hard problems.”

Lauren Fuge is a former editor of Cosmos. She is a winner of the UNSW Bragg Prize for Science Writing and an AAAS Kavli Award for her work in Cosmos.