We’ve cracked the cane toad genome, and that could help put the brakes on its invasion



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Cane toads are on the march, but new genetic research could slow them down.
Michael Linnenbach

Peter White, UNSW; Alice Russo, UNSW, and Rick Shine, University of Sydney

We and our international colleagues have deciphered the genetic code of the cane toad. The complete sequence, published today in the journal GigaScience, will help us understand how the toad can quickly evolve to adapt to new environments, how its infamous toxin works, and hopefully give us new options for halting this invader’s march across Australia.

Since its introduction into Queensland in 1935, the cane toad has spread widely and now occupies more than 1.2 million square kilometres of Australia. It is fatally poisonous to predators such as the northern quoll, freshwater crocodiles, and several species of native lizards and snakes.

Previous attempts to sequence the cane toad, by WA researchers more than 10 years ago, were not successful, largely because the existing technology could not assemble the genetic pieces to create a genome. But thanks to new methods, we have succeeded in piecing together the entire genetic sequence.




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Our team, which also featured researchers from Portugal and Brazil, worked at the Ramaciotti Centre for Genomics at UNSW. This centre played a key role in decoding the genomes of other iconic Australian species, including the koala.

Sequencing, assembling and annotating a genome (working out which genes go where) is a complicated process. The cane toad genome is similar in size to that of humans, at roughly 3 billion DNA “letters”. By using cutting-edge technology, our team sequenced more than 360 billion letters of cane toad DNA code, and then assembled these overlapping pieces to produce one of the best-quality amphibian genomes to date.

We deduced more than 90% of the cane toad’s genes using technology that can sequence very long pieces of DNA. This made the task of putting together the genome jigsaw much easier.

Toxic toads

The cane toad has iconic status in Australia, with many Aussies loving to hate the poisonous invasive amphibian. This is a little unfair. It’s not the cane toad’s fault – it was humans who chose to bring it to Australia.

Our obsession with sugar in the 1800s led to the toad’s introduction to many countries around the world. Wherever sugar cane was planted, the cane toad followed, taken from plantation to plantation by landowners as the warty interlopers travelled from South America to the Caribbean and then on to Hawaii and Australia.

But unlike most other places to which the cane toad was introduced, Australia lacks any native toads of its own. The cane toad’s powerful poisons are deadly to native species that have never before encountered this amphibian’s arsenal.

The cane toad has therefore been subject to detailed evolutionary and ecological research in Australia, revealing not only its impact but also its amazing capacity for rapid evolution. Within 83 years of its introduction, cane toads in Australia have evolved a wide range of modifications that affect their body shape, physiology and behaviour.

For example, cane toads at the invasion front are longer-legged and bolder than those in long-colonised areas and invest less into their immune defences (for a summary, see Cane Toad Wars by Rick Shine).

The new genome will give us insights into how evolution transformed a sedentary amphibian into a formidable invasion machine. And it could give us new weapons to help stop, or at least slow, this invasion.

Cracking the cane toad genome.

Viral control

Current measures such as physical removal have not been successful in preventing cane toads from spreading, so fresh approaches are needed. One option may be to use a virus to help control the toad population.

Viruses such as myxomatosis have been successfully used to control rabbits. But the cane toad viruses studied so far are also infectious to native frogs. The new genome could potentially help scientists hunt for viruses that attack only toads.

In a study published this month, we and other colleagues describe how we sampled genetic sequences from cane toads from different Australian locations, and found three viruses that are genetically similar to viruses that infect frogs, reptiles and fish. These viruses could potentially be used as biocontrol agents, although only after comprehensive testing to check that they pose no danger to any other native species.




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Come hither… how imitating mating males could cut cane toad numbers


The full cane toad genome will help to accelerate this kind of research, as well as research on the toads’ evolution and its interactions with the wider ecosystem. The published sequence is freely available for anyone to use in their studies. It is one of very few amphibian genomes sequenced so far, so this is also great news for amphibian biologists in general.

As the cane toads continue their march across the Australian landscape, this milestone piece of research should help us put a few more roadblocks in their path.The Conversation

Peter White, Professor in Microbiology and Molecular Biology, UNSW; Alice Russo, PhD candidate, UNSW, and Rick Shine, Professor in Evolutionary Biology, University of Sydney

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

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Desal plants might do less damage to marine environments than we thought



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Some sea creatures are displaced by the desalination plant, but others actually grow.
Supplied

Graeme Clark, UNSW and Emma Johnston, UNSW

Millions of people all over the world rely on desalinated water. Closer to home, Australia has desalination plants in Melbourne, Adelaide, Perth, the Gold Coast, and many remote and regional locations.

But despite the growing size and number of desalination plants, the environmental impacts are little understood. Our six-year study, published recently in the journal Water Research, looked at the health the marine environment before, during and after the Sydney Desalination Plant was operating.




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Our research tested the effect of pumping and “diffusing” highly concentrated salt water (a byproduct of desalination) back into the ocean.

Contrary to our expectation that high salt levels would impact sea creatures, we found that ecological changes were largely confined to an area within 100m of the discharge point, and reduced shortly after the plant was turned off. We also found the changes were likely a result of strong currents created by the outfall jets, rather than high salinity.

Desalination is growing

We examined six underwater locations at about 25m depth over a six-year period during which the plant was under construction, then operating, and then idle. This let us rigorously monitor impacts to and recovery of marine life from the effects of pumping large volumes of hypersaline water back into the ocean. We tested for impacts and recovery at two distances (30m and 100m) from the outfall.

This study provides the first before-and-after test of ecological impacts of desalination brine on marine communities, and a rare insight into mechanisms behind the potential impacts of a growing form of human disturbance.

About 1% of the world’s population now depends on desalinated water for daily use, supplied by almost 20,000 desalination plants that produce more than 90 million cubic meters of water per day.

Increasingly frequent and severe water shortages are projected to accelerate the growth in desalination around the world. By 2025, more than 2.8 billion people in 48 countries are likely to experience water scarcity, with desalination expected to become an increasingly crucial water source for many coastal populations.

Effect of the diffusers

The diffusers that pump concentrated salt water into the ocean at a high velocity (to increase dilution) are so effective that salinity was almost at background levels within 100m of the outfall. However, the diffusion process increased the speed of currents close to the outfall.

This strong current affects species differently, depending on how they settle and feed. Marine species with strong swimming larvae, such as barnacles, can easily settle in high flow and then benefit from faster delivery of food particles. These animals increased in number and size near the outfall. In contrast, species with slow swimming larvae, such as tubeworms, lace corals and sponges, prefer settling and feeding in low current and became less abundant near the outfall.

Therefore, the high-pressure diffusers designed to reduce hypersalinity may have inadvertently caused impacts due to flow. However, these ecological changes may be less concerning than those caused by hypersalinity, as the currents were still within the range that marine communities experience naturally.

Our findings are important, because as drought conditions around the nation worsen and domestic water supplies are coming under strain, desalination is starting to ramp up in eastern and southern Australia.

For instance, water levels at Sydney’s primary dam at Warragamba have dropped to around 65% and the desalination plant is contracted to start supplying drinking water back into the system when dam levels fall below 60%. This plant can potentially double in capacity if needed.




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Melbourne’s desalination plant is just one part of drought-proofing water supply


There is a rapid expansion of the use of desalination, with global capacity increasing by 57% between 2008 and 2013. Our results will help designers and researchers in this area ensure desalination plants minimise their effect on local coastal systems.The Conversation

Graeme Clark, Senior Research Associate in Ecology, UNSW and Emma Johnston, Professor and Dean of Science, UNSW

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

The backflip over Sydney’s marine park is a defiance of science



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Sydney’s iconic beaches are not yet part of a marine park.
John Turnbull

David Booth, University of Technology Sydney and John Turnbull, UNSW

The New South Wales government’s decision to back away from establishing no-fishing zones in waters around Sydney leaves significant question marks over the plan, which is open for public consultation until September 27.

Fisheries Minister Niall Blair explained the apparent backflip by saying he was “confident that fishing is not the key threat to the sustainability of our marine environment”, after receiving what he described as “robust” feedback from local communities and anglers.

The original plans for Sydney’s marine park. Click image to enlarge.
NSW government

The originally proposed Sydney Marine Park comprised 17 “sanctuary zones” (totalling 2.4% of the area, including estuaries), 3 “conservation zones” totalling 2.6%, and 21 “special purpose zones”, which would allow (and in some cases protect) fishing.

Sanctuary zones allow no fishing; conservation zones allow taking of lobster and abalone (see below); and special purpose zones have a range of restrictions or allowances, not necessarily of any conservation benefit. For instance, four offshore artificial reefs are classed as special purpose zones.

The plans cover the waters around Sydney, stretching from Newcastle in the north to Wollongong in the south. Formally known as the Hawkesbury Shelf marine bioregion, it is the only bioregion wholly in NSW that does not have a marine park. This is despite Sydney’s magnificent array of underwater and coastal habitats, which are home to more fish species than the entire British Isles.




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Recreational fishing in marine parks: you can’t be serious!


New zones and ranked threats

The original marine park proposal was far from ideal. A good marine park should have a string of closely connected sanctuary zones, but there was a large gap from southern Sydney to Wollongong where no sanctuary zones were proposed.

Instead, there was a new “conservation zone” to allow fishing for lobster and abalone. Yet lobster in particular are important to this ecosystem, because they protect kelp by preying on sea urchins.

Threats to the marine region around Sydney, as ranked in a NSW government report. Click image to enlarge.
NSW government

The NSW government based its earlier proposal on a principle called TARA, short for “threat and risk assessment”, in which all perceived factors are ranked according to their environmental, social and economic outcomes.

While other major threats such as climate change and pollution are ranked highly, fishing doesn’t appear until number 18 on the government’s list (see page 8 here. One reason for this is that fishing is split into eight categories (such as “recreational fishing by boat – line and trap”), masking its overall impact. Even 4WDs on beaches are ranked as a greater threat to the environment than many types of fishing.

Premier Gladys Berejiklian’s press release about the marine park public consultation didn’t mention the environmental threat posed by fishing at all. Yet there is clear evidence that fishing directly harms fish stocks.

One recent study shows that stocks of inshore fish species have declined in Australia by 30% in a decade, except in sanctuary zones. Worldwide, sanctuary zones (also called no-take zones) have been shown to help fish grow larger and more abundant. And recent studies in NSW coastal waters have reiterated the benefits of no-take zones for species such as morwong, bream, and snapper.

Partial protection doesn’t work

The latest proposals, which would allow recreational but not commercial fishing, would be much less effective than full protection. One recent study suggested that partial protection is no better than no protection at all.

According to a NSW government estimate, recreational fishing removes more than 3 million fish, crustaceans and molluscs from NSW coastal waters every year. But marine parks are primarily about conservation, and this requires us to face some stark realities. With more than 8 million people likely to call Sydney home in the next 40 years, pressures on our coasts will only increase.

Sanctuary zones are one of the best available conservation tools to guard against these impacts. These zones have also been shown to make wildlife more resilient to climate change.

Even before the government’s decision to rescind the proposed sanctuary zones, the original plan for no-take zones to cover just 2.4% of the region was a severe compromise. By comparison, the Great Barrier Reef Marine Park has 30% sanctuary zone coverage, and the rest of NSW has 7-8%. International best practice recommends at least 20%, and even the Commonwealth Marine Reserves Management Plan offers 6% no-take coverage.

But now, with no sanctuary zones, Sydney’s proposed “marine park” is not worthy of the name.

Wrong priorities

A peculiar contradiction is that despite one-quarter of the listed threats being fishing-related, the NSW government’s marine estate management strategy includes an initiative to encourage fishing. Pollution is also a high-priority threat, and fishing is the largest source of subtidal debris.

Kelp and a tangle of discarded fishing line.
John Turnbull

If local-level threats such as fishing and litter are not dealt with, resilience to climate change suffers as a result. We must tackle all threats – overfishing, pollution, climate change – and not shy away from one because it’s politically unpalatable.




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Marine parks for fish and people: here’s how to do it


It is frustrating that the NSW government has opted to abolish these marine sanctuaries before the public consultation was complete. The wider public understands the value of sanctuary zones, as indicated in recent opinion polls showing clear support for the original plans among Sydneysiders – even many of those who fish.

Some fishers are now calling for sanctuary zones to be scrapped or wound back in other iconic NSW marine parks, such as Lord Howe Island and Solitary Islands. This move would be a defiance of the science. The evidence shows that sanctuary zones are essential for restoring and preserving our marine estate for future generations.The Conversation

David Booth, Professor of Marine Ecology, University of Technology Sydney and John Turnbull, , UNSW

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