This adorable mouse was considered extinct for over 100 years — until we found it hiding in plain sight


Wayne Lawler/Australian Wildlife Conservancy, Author provided

Emily Roycroft, Australian National UniversityAustralia has the world’s worst track record for wiping out mammals, with 34 species declared extinct since European colonisation. Many of these are humble native rodents, who’ve suffered the highest extinction rate of any mammal group.

But today, we bring some good news: one rodent species, Gould’s mouse (Pseudomys gouldii), is set to be crossed off Australia’s extinct species list. This means the number of Australia’s extinct mammals will drop from 34 to 33.

Our new research compared genome sequences across Australia’s rodents, including eight extinct species and their 42 living relatives. In a case of historical mistaken identity, we found the Gould’s mouse was genetically indistinguishable from another living species, the Shark Bay mouse (Pseudomys fieldi), also known by the Indigenous name “Djoongari” from the Pintupi and Luritja languages.

But it’s not all good news. A lack of genetic diversity in remaining populations means Djoongari are less resilient to changing environments, including from climate change. We can’t let this species die out — this time, there’d be no coming back.

Back from the dead

When Europeans colonised Australia, they rapidly and catastrophically changed the environments in which native species thrived. The introduction of feral cats, foxes and other invasive species, agricultural land clearing, inappropriate fire management, and new diseases decimated native rodent populations.

Along with many other native mammals, some rodent species were also intensely hunted for bounty in the late 19th and early 20th centuries.

DNA from this specimen of Gould’s mouse, collected in 1837 from the Hunter Valley of NSW, reveals the species should no longer be considered extinct.
Trustees of the Natural History Museum, London Photographer: C. Ching, Author provided

In 1837, a Gould’s mouse specimen was collected for the Natural History Museum, London, from the Hunter Valley of New South Wales. The last verified time it was seen alive was in 1857, near the border of Victoria and NSW.

After genomic analysis of these specimens, we found the species has been hiding in plain sight for more than 100 years, under a different name, thousands of kilometres away in Western Australia. Djoongari will now be reclassified under the scientific name Pseudomys gouldii.

Djoongari is a shaggy-coated mouse weighing 45 grams on average, making it twice the size of the invasive house mouse. It’s omnivorous, and feeds on a variety of flowers, leaves, fungi, insects and spiders. It also build tunnels and runways to travel at night, and uses above-ground nests as refuges during the day.

Not safe yet

The resurrection of the Gould’s mouse is positive news given Australia’s alarming rate of recent extinctions, but the species remains at risk.

Once occurring across mainland Australia, it now survives only on predator-free islands in Shark Bay, WA. Islands have been an important refuge for the species, protecting them from cats, foxes, diseases and other threats on the mainland.

Feral and pet cats are huge threats to small native animals. If you own a cat, make sure you keep it indoors to protect Australia’s wildlife.
Shutterstock

Conservation efforts are underway to protect the mouse in Shark Bay, with insurance populations established on other nearby islands.

Now we know Djoongari once roamed as far east as the Hunter Valley in NSW, there’s greater scope to reintroduce the species to predator-proof protected areas on the mainland. This would mean more insurance populations, but also contribute towards restoring natural ecosystems on mainland Australia — also known as “rewilding”.

However, remnant populations of this once widespread species contain only a fraction of its original genetic diversity.




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Genetic diversity is often used as a proxy for estimating the resilience of a species to threats and its potential to adapt to changes in its environment. When species have low genetic diversity, or are inbred, they are more susceptible to disease, and more likely to accumulate harmful genetic mutations.

Other eye-opening revelations

Our study also examined the genomes of seven other rodent species lost to extinction: the white-footed rabbit rat, lesser stick-nest rat, Bramble Cay melomys, short-tailed hopping mouse, long-tailed hopping mouse, big-eared hopping mouse and long-eared mouse.

Brown rodent
Bramble cay melomys were declared extinct in 2016.
Ian Bell, EHP, State of Queensland, CC BY-SA

In most cases, we found these now-extinct native rodents had relatively high genetic diversity immediately before they became extinct. High genetic diversity usually means large population sizes, suggesting native rodent populations were stable before European invasion.

This puts an end to any suggestion that these species were already on their way out prior to the arrival of Europeans.

Reports from early naturalists back up our findings. In 1846, John Cotton referred to the now-extinct white-footed rabbit rat as “the common rat of the country”. And in 1866, Gerard Krefft described the now-extinct lesser stick-nest rat as occurring in “great numbers”.




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These species went from common to extinct in less than 150 years. That’s alarmingly fast by any standard.

It shows even though genetic diversity in now-extinct rodents was high prior to colonisation, it wasn’t enough. The environment and threats changed so dramatically and rapidly, these species didn’t have the chance to adapt.

There’s a clear lesson in all this

The threats to native wildlife brought by Europeans — including feral cat predation and land clearing — are ongoing. And under climate change, the environment as we know it is set to change further, dramatically.

It’s not enough to only establish insurance populations to save species. We need to control feral predators, protect and restore habitats, and curb emissions, so more species don’t endure a rapid wipe out.

In total, we’ve lost almost 100 species to extinction since 1788, and that’s just those we know about. In native rodents alone, in less than 150 years, the equivalent of more than 10 million years of unique evolutionary history has been lost forever.

Extinction doesn’t usually offer second chances, but we’ve now got another shot to protect Gould’s mouse. We need to act now, before it’s too late.




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Scientists re-counted Australia’s extinct species, and the result is devastating


The Conversation


Emily Roycroft, Postdoctoral Research Fellow, Australian National University

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

Beautiful, rare ‘purple cauliflower’ coral off NSW coast may be extinct within 10 years


Author supplied

Meryl Larkin, Southern Cross University; David Harasti, Southern Cross University; Steve Smith, Southern Cross University, and Tom R DavisWhen we think of Australia’s threatened corals, the Great Barrier Reef probably springs to mind. But elsewhere, coral species are also struggling – including a rare type known as “cauliflower soft coral” which is, sadly, on the brink of extinction.

This species, Dendronephthya australis, looks like a purple cauliflower due to its pink-lilac stems and branches, crowned with white polyps.

The coral primarily occurs at only a few sites in Port Stephens, New South Wales, and is a magnet for divers and underwater photographers. But sand movements, boating and fishing have reduced the species’ population dramatically.

Recent flooding in NSW compounded the problem – in fact, it may have reduced the remaining coral population by 90%. Our recent research found cauliflower soft coral may become extinct in the next decade unless we urgently protect and restore it.

An ovulid on a cauliflower coral colony. Such coral may be extinct within a decade.
Author supplied

Lilac underwater gardens

Cauliflower soft corals are predominantly found in estuarine environments on sandy seabeds with high current flow. They rely on tidal currents to transport plankton on which they feed.

The species is most commonly found in the Port Stephens estuary, about 200 kilometres north of Sydney. It’s also found in the Brisbane Water estuary in NSW, and has been found sporadically in other locations south to Jervis Bay.

The coral colonies form aggregations or “gardens”. At Port Stephens, these gardens are the preferred habitat for the endangered White’s seahorse and protected species of pipefish. They also support juvenile Australasian snapper, an important species for commercial and recreational fishers.

In recent months, the cauliflower soft coral has been listed as endangered in NSW and nationally.




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An alarming decline

Scientists first mapped the distribution of the cauliflower soft coral in 2011. They found none of the biggest colonies in the Port Stephens estuary were protected by “no take” zones – areas where fishing and other extractive activities are banned.

In research in 2016, we found a sharp decline in the extent and distribution of cauliflower soft coral.

Our recent study examined the problem in more detail. It involved mapping the southern shoreline of Port Stephens, using an underwater camera towed by a vessel.

We found the cauliflower soft coral in the Port Stephens estuary has declined by almost 70% over just eight years. It now occurs over 9,300 square metres – down from 28,600 square metres in 2011.

Our subsequent modelling sought to identify what was driving the corals’ decline. We found a correlation between coral loss and sand movements over the last decade.

Human changes to shorelines, such as marina developments, have changed the dynamic of currents across the estuary. For example, previous research found a large influx of sand from the western end of Shoal Bay smothered cauliflower soft coral colonies at two nearby locations. As of 2018, those colonies had disappeared completely.

While diving as part of the project, we identified other causes of damage to the coral. Dropped boat anchors and the installation of moorings had damaged some colonies. Others were injured after becoming entangled in fishing line.

It is possible that disease, and pollution or other water quality issues, may also be contributing to the species’ decline.

Fishing line damaging a colony of cauliflower soft coral in Port Stephens.
Author supplied

Then the floods hit

Some 18 months after our most recent mapping, cauliflower soft corals suffered yet another blow. Major flooding in NSW in March this year caused a massive amount of fresh water to discharge from the Karuah River into the Port Stephens estuary, where sea water is dominant. Fresh water can kill cauliflower soft corals.

Following the floods, we conducted exploratory dives at locations where the cauliflower soft corals had been thriving at Port Stephens. We found much of the coral had disintegrated and disappeared. In fact, we estimated as much as 90% of the remaining cauliflower soft coral population was gone.

We plan to remap the estuary in the coming weeks, and feel confident our initial estimates will be close to the mark. If so, this means less than 5% of the species area mapped in 2011 now remains.

The floods also devastated kelp forests and other canopy-forming habitats in the estuary. Further work by scientists at the NSW Department of Primary Industries is underway to quantify these losses and monitor the recovery.




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Monitoring of existing cauliflower coral aggregations is ongoing.
Author supplied

Urgent work required

The cauliflower soft coral urgently needs protecting. This will require ongoing, coordinated research and management.

Clearly, action must be taken to reduce threats such as anchoring, fishing, and development that may magnify sand movement.

Best-practice rehabilitation is also needed. This may involve rearing the coral off-site and transplanting it into suitable habitat. Such trials at Port Stephens have shown promising signs.

Human activities are causing species loss at an alarming rate. We must do everything in our power to prevent the extinction of the cauliflower soft coral, and other threatened species, to preserve the balance of nature and its ecosystems.




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The Conversation


Meryl Larkin, PhD Candidate, Southern Cross University; David Harasti, Adjunct assistant professor, Southern Cross University; Steve Smith, Professor of Marine Science, National Marine Science Centre, Southern Cross University, and Tom R Davis, Research Scientist – Marine Climate Change

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

New research reveals these 20 Australian reptiles are set to disappear by 2040



Cape Melville leaf-tailed gecko
Conrad Hoskin, Author provided

Hayley Geyle, Charles Darwin University and David Chapple, Monash University

Action came too late for the Christmas Island forest skink, despite early warnings of significant declines. It was lost from the wild before it was officially listed as “threatened”, and the few individuals brought into captivity died soon after.

Australia is home to about 10% of all known reptile species — the largest number of any country in the world. But many of our reptiles are at risk of the same fate as the Christmas Island forest skink: extinction.

In new research published today, we identified the 20 terrestrial snakes and lizards (collectively known as “squamates”) at greatest risk of extinction in the next two decades, assuming no changes to current conservation management.

Preventing extinctions of Australian lizards and snakes.

While all 20 species meet international criteria to be officially listed as “threatened”, only half are protected under Australian environmental legislation— the Environment Protection and Biodiversity Conservation (EPBC) Act. This needs urgent review.

Many of these reptiles receive little conservation action, but most of their threats can be ameliorated. By identifying the species at greatest risk of extinction, we can better prioritise our recovery efforts — we know now what will be lost if we don’t act.

Six species more likely than not to go extinct

Our research team — including 27 reptile experts from universities, zoos, museums and government organisations across the country — identified six species with greater than 50% likelihood of extinction by 2040.

This includes two dragons, one blind snake and three skinks. Experts rated many others as having a 30-50% likelihood of extinction over the next 20 years.

More than half (55%) of the 20 species at greatest risk occur in Queensland. Three live on islands: two on Christmas Island and one on Lancelin Island off the Western Australian coast.

Two more species are found in Western Australia, while the Northern Territory, the Australian Capital Territory, Victoria and New South Wales each have one species.




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Each of the 20 species at greatest risk occur in a relatively small area, which partly explains the Queensland cluster — many species in that state naturally have very small distributions.

Most of the top 20 occupy a total range of fewer than 20 square kilometres, so could be lost to a single catastrophic event, such as a large bushfire.

A map of Australia showing where the 20 snakes and lizards are located
The approximate locations of the 20 terrestrial snakes and lizards at greatest risk of extinction.
Author provided

So why are they dying out?

Reptile species are declining on a global scale, and this is likely exacerbated by climate change. In Australia, where more than 90% of our species occur nowhere else in the world, the most threatened reptiles are at risk for two main reasons: they have very small distributions, and ongoing, unmitigated threats.

The Cape Melville leaf-tailed gecko meets this brief perfectly. This large and spectacular species was only discovered in 2013, on a remote mountain range on Cape York. It’s threatened by virtue of its very small distribution and population size, and by climate change warming and drying its upland habitat.

Arnhem Land gorges skink
The Arnhem Land gorges skink is considered more likely than not to become extinct by 2040. Threats include changes to food resources and habitat quality, feral cats, and possibly poisoning by cane toads.
Chris Jolly

Habitat loss is also a major threat for the top 20 species. Australia’s most imperilled reptile, the Victoria grassland earless dragon, used to be relatively common in grasslands in and around Melbourne. But the grasslands this little dragon once called home have been extensively cleared for agriculture and urban development, and now cover less than 1% of their original extent.




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Little conservation attention

For most reptile species, there has been less conservation work to address the declines, partly because reptiles have historically received less scientific attention than birds or mammals.

We also still don’t fully understand just how many species there are in Australia. New reptile species are being scientifically described at an average rate of 15 per year (a higher rate than for other vertebrate groups) and many new reptiles are already vulnerable to extinction at the time of discovery.

The Mount Surprise slider, a light-brown snake
The Mount Surprise slider is threatened by invasive plant species and cattle compacting sandy soils.
Stephen Zozaya, Author provided

To make matters worse, few reptiles in Australia are well-monitored. Without adequate monitoring, we have a poor understanding of population trends and the impacts of threats. This means species could slip into extinction unnoticed.

Reptiles also lack the public and political profile that helps generate recovery support for other, (arguably) more charismatic Australian threatened animals — such as koalas and swift parrots — leading to little resourcing for conservation.

Lessons from the past

Only one Australian reptile, the Christmas Island forest skink, is officially listed as extinct, but we have most probably lost others before knowing they exist. Without increased resourcing and management intervention, many more Australian reptiles could follow the same trajectory.

The Roma earless dragon sitting up on hind legs.
Habitat loss and degradation due to agriculture is a major threat to the Roma earless dragon. It has not been listed under Australian legislation.
A. O’Grady Museums Victoria, Author provided

But it’s not all bad news. The pygmy bluetongue skink was once thought to be extinct until a chance discovery kick-started a long conservation and research program.

Animals are now being taken from the wild and relocated to new areas to establish more populations, signifying that positive outcomes are possible when informed by good science.

And the very restricted distributions of most of the species identified here should allow for targeted and effective recovery efforts.

By identifying the species at greatest risk, we hope to give governments, conservation groups and the community time to act to prevent further extinctions before it’s too late. Neglect should no longer be the default response for our fabulous reptile fauna.




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The Conversation


Hayley Geyle, Research Assistant, Charles Darwin University and David Chapple, Associate Professor in Evolutionary and Conservation Ecology, Monash University

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

Scientists re-counted Australia’s extinct species, and the result is devastating



The Tasmanian tiger is among the best known of our extinct species, but researchers have now revealed the extent of the crisis.
TASMANIAN MUSEUM AND ART GALLERY

John Woinarski, Charles Darwin University; Brett Murphy, Charles Darwin University; Dale Nimmo, Charles Sturt University; Michael F. Braby, Australian National University; Sarah Legge, Australian National University, and Stephen Garnett, Charles Darwin University

It’s well established that unsustainable human activity is damaging the health of the planet. The way we use Earth threatens our future and that of many animals and plants. Species extinction is an inevitable end point.

It’s important that the loss of Australian nature be quantified accurately. To date, putting an exact figure on the number of extinct species has been challenging. But in the most comprehensive assessment of its kind, our research has confirmed that 100 endemic Australian species living in 1788 are now validly listed as extinct.

Alarmingly, this tally confirms that the number of extinct Australian species is much higher than previously thought.

A southern black-throated finch, which conservationists say is threatened by the Adani coal mine.
ERIC VANDERDUYS/BirdLife Australia

The most precise tally yet

Counts of extinct Australian species vary. The federal government’s list of extinct plants and animals totals 92. However 20 of these are subspecies, five are now known to still exist in Australia and seven survive overseas – reducing the figure to 60.

An RMIT/ABC fact check puts the figure at 46.

The states and territories also hold their own extinction lists, and the International Union for Conservation of Nature keeps a global database, the Red List.

An endangered Manning River turtle.
AUSTRALIAN REPTILE PARK

Our research collated these separate listings. We excluded species that still exist overseas, such as the water tassel-fern. We also excluded some species that, happily, have been rediscovered since being listed as extinct, or which are no longer recognised as valid species (such as the obscure snail Fluvidona dulvertonensis).

We concluded that exactly 100 plant and animal species are validly listed as having become extinct in the 230 years since Europeans colonised Australia:

  • 38 plants, such as the magnificent spider-orchid
  • 1 seaweed species
  • 34 mammals including the thylacine and pig-footed bandicoot
  • 10 invertebrates including a funnel-web spider, beetles and snails
  • 9 birds, such as the paradise parrot
  • 4 frogs, including two species of the bizarre gastric-brooding frog which used its stomach as a womb
  • 3 reptiles including the Christmas Island forest skink
  • 1 fish, the Pedder galaxias.
A 19th century illustration of the Pig-footed bandicoot.
Wikimedia

Our tally includes three species listed as extinct in the wild, with two of these still existing in captivity.

The mammal toll represents 10% of the species present in 1788. This loss rate is far higher than for any other continent over this period.

The 100 extinctions are drawn from formal lists. But many extinctions have not been officially registered. Other species disappeared before their existence was recorded. More have not been seen for decades, and are suspected lost by scientists or Indigenous groups who knew them best. We speculate that the actual tally of extinct Australian species since 1788 is likely to be about ten times greater than we derived from official lists.

And biodiversity loss is more than extinctions alone. Many more Australian species have disappeared from all but a vestige of their former ranges, or persist in populations far smaller than in the past.

The geographical spread of extinctions across Australia. Darker shading represents a higher extinction tally.

Dating the losses

Dating of extinctions is not straightforward. For a few Australian species, such as the Christmas Island forest skink, we know the day the last known individual died. But many species disappeared without us realising at the time.

Our estimation of extinction dates reveals a largely continuous rate of loss – averaging about four species per decade.

Continuing this trend, in the past decade, three Australian species have become extinct – the Christmas Island forest skink, Christmas Island pipistrelle and Bramble Cay melomys – and two others became extinct in the wild.

Cumulative tally of Australian extinctions since 1788.

The extinctions occurred over most of the continent. However 21 occurred only on islands smaller than Tasmania, which comprise less than 0.5% of Australia’s land mass.

This trend, repeated around the world, is largely due to small population sizes and vulnerability to newly introduced predators.

We must learn from the past

The 100 recognised extinctions followed the loss of Indigenous land management, its replacement with entirely new land uses and new settlers introducing species with little regard to detrimental impacts.

Introduced cats and foxes are implicated in most mammal extinctions; vegetation clearing and habitat degradation caused most plant extinctions. Disease caused the loss of frogs and the accidental introduction of an Asian snake caused the recent loss of three reptile species on Christmas Island.

The causes have changed over time. Hunting contributed to several early extinctions, but not recent ones. In the last decade, climate change contributed to the extinction of the Bramble Cay melomys, which lived only on one Queensland island.

The prospects for some species are helped by legal protection, Australia’s fine national reserve system and threat management. But these gains are subverted by the legacy of previous habitat loss and fragmentation, and the ongoing damage caused by introduced species.

Our own population increase is causing further habitat loss, and new threats such as climate change bring more frequent and intense droughts and bushfires.

Environment laws have demonstrably failed to stem the extinction crisis. The national laws are now under review, and the federal government has indicated protections may be wound back.

But now is not the time to weaken environment laws further. The creation of modern Australia has come at a great cost to nature – we are not living well in this land.


The study on which this article is based was also co-authored by Andrew Burbidge, David Coates, Rod Fensham and Norm McKenzie.The Conversation

John Woinarski, Professor (conservation biology), Charles Darwin University; Brett Murphy, Associate Professor / ARC Future Fellow, Charles Darwin University; Dale Nimmo, Associate professor/ARC DECRA fellow, Charles Sturt University; Michael F. Braby, Associate Professor, Australian National University; Sarah Legge, Professor, Australian National 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.

Why we’re not giving up the search for mainland Australia’s ‘first extinct lizard’



A grassland earless dragon at Jerrabomberra, NSW, November 1991. The search is now on for this species’ Victorian cousin.
CSIRO/Wikimedia Commons, CC BY

Jane Melville, Museums Victoria

You may have seen news in recent days of the suspected demise of the Victorian grassland earless dragon – now thought to be the first lizard species to be driven to extinction by humans in mainland Australia.

That suspicion arose on the basis of a newly published study in Royal Society Open Science by our research team, in which we discovered that the grassland earless dragons of southeastern Australia are not a single species, but four distinct ones: one that lives around Canberra, two in New South Wales, and one restricted to the Melbourne region.

The most recent confident sighting of the Melbourne species was 50 years ago, in 1969 – hence the fears that the Victorian species has already succumbed.

But despite this worrying news, we’re not leaving this lizard for dead just yet. Conservationists are now combing remaining grassland around Melbourne in a search for survivors.




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Although no lizard species have previously been declared extinct on the Australian mainland, the grassland earless dragons (Tympanocryptis) of southeastern Australia have long been the subject of conservation concern. Even before being split into four separate species, they were already officially listed as endangered.

The Victorian grassland earless dragon (Tympanocryptis pinguicolla) is known only to occur in the native grasslands around Melbourne. A review of historical collections at Museums Victoria show that it was found at several locations including Sunbury, Maribyrnong River (then called “Saltwater River”), and as far west as the Geelong area until the late 1960s.

Although there is little information available about the ecology of this species, it was described by Lucas and Frost in 1894 as:

Inhabiting stony plains and retreating into small holes, like those of the ‘Trap-door Spider,’ in the ground when alarmed […] Often met with under loose basalt boulders.

The last confirmed sighting was near Geelong in July 1969.

First mainland extinction?

Globally, 31 reptiles have been listed as extinct or extinct in the wild, according to the IUCN Red List, the global authority on the status of species. Two skinks and one gecko species have been declared extinct in the wild on Christmas Island, a remote Australian territory in the Indian Ocean. But until now there have been no recorded reptile extinctions on the Australian mainland.

Yet it is too early to give up on the Australian grassland earless dragon. Zoos Victoria researchers have completed a mapping analysis of potential grassland habitats. But this doesn’t give us enough information to say whether or not any grassland earless dragons remain.

There are several factors that leave open the possibility that the Victorian grassland earless dragon is still clinging to survival. There are some remaining habitat areas that have not yet been surveyed, and this species is small, secretive and hard to find. We urgently need more surveys to try and find any remaining populations.




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If these lizards are not yet extinct, their protection will clearly become an urgent conservation priority. But it is hard to develop a conservation program without knowing where the target species actually lives, or indeed whether it is still alive at all.

Zoos Victoria is now leading a campaign, alongside expert ecologists and local communities, to try and confirm the presence or absence of the Victorian grassland earless dragon. This involves various methods, including habitat mapping, camera trapping, and active searching. The team is also working to identify unsurveyed areas that might potentially be home to these elusive lizards.

Last year the team deployed a series of small pitfall traps at two locations in Little River. Unfortunately, no earless dragons were detected during the survey and few lizards of any species were caught, despite the fact that these locations seemed to offer appropriate food and habitat.

The team is not giving up yet and is committed to continuing the search, with Zoos Victoria researchers having identified sites with suitable habitat both within and outside of the historical distribution, which they aim to survey intensively over the coming years. Meanwhile, reptile keepers at Zoos Victoria are developing husbandry techniques to help look after the grassland earless dragon species from Canberra and NSW.

The conservation challenge has got harder, because where previously we were tasked with looking after one species, we now have to safeguard at least three – and hopefully four!


This article is based on a blog post that originally appeared here. It was coauthored by Adam Lee and Deon Gilbert of Zoos Victoria.The Conversation

Jane Melville, Senior Curator, Terrestrial Vertebrates, Museums Victoria

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

A report claims koalas are ‘functionally extinct’ – but what does that mean?



Koalas are facing serious threats in the wild.
Mathias Appel/Flickr

Christine Adams-Hosking, The University of Queensland

Today the Australian Koala Foundation announced they believe “there are no more than 80,000 koalas in Australia”, making the species “functionally extinct”.

While this number is dramatically lower than the most recent academic estimates, there’s no doubt koala numbers in many places are in steep decline.

It’s hard to say exactly how many koalas are still remaining in Queensland, New South Wales, Victoria, South Australia and the Australian Capital Territory, but they are highly vulnerable to threats including deforestation, disease and the effects of climate change.

Once a koala population falls below a critical point it can no longer produce the next generation, leading to extinction.




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What does ‘functionally extinct’ mean?

The term “functionally extinct” can describe a few perilous situations. In one case, it can refer to a species whose population has declined to the point where it can no longer play a significant role in their ecosystem. For example, it has been used to describe dingoes in places where they have become so reduced they have a negligible influence on the species they prey on.

Dingoes are top predators, and therefore can play a significant role in some ecosystems. Our innocuous, leaf-eating koala cannot be considered a top predator.

For millions of years koalas have been a key part of the health of our eucalyptus forests by eating upper leaves, and on the forest floor, their droppings contribute to important nutrient recycling. Their known fossil records date back approximately 30 million years so they may have once been a food source for megafauna carnivores.

Functionally extinct can also describe a population that is no longer viable. For example in Southport, Queensland, native oyster reef beds are functionally extinct because more than 99% of the habitat has been lost and there are no individuals left to reproduce.

Finally, functionally extinct can refer to a small population that, although still breeding, is suffering from inbreeding that can threaten its future viability. We know that at least some koala populations in urban areas are suffering in this way, and genetic studies on the Koala Coast, located 20kms south-east of Brisbane, show that the population is suffering from reduced genetic variation. In South East Queensland, koalas in some areas have experienced catastrophic declines




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We also know that koala populations in some inland regions of Queensland and New South Wales are affected by climate extremes such as severe droughts and heatwaves and have declined by as much as 80%.

Exhaustive multi-disciplinary koala research continues apace in an effort to find ways of protecting wild koala populations and ensuring that they remain viable now and into the future. Habitat loss, population dynamics, genetics, disease, diet and climate change are some key areas being studied.

How many koalas are there?

Koala researchers are often asked “how many koalas are in the wild?” It’s a hard question to answer. Koalas are not stationary, are patchily distributed throughout an extremely wide range encompassing urban and rural areas in four states and one territory, and are usually difficult to see.

To determine whether each population of koalas scattered across eastern Australia is functionally extinct would require a gargantuan effort.

Koalas are a key part of eucalyptus forests’ health.
Dave Hunt/Flickr, CC BY-NC-SA

In 2016, in an attempt to determine population trends for the koala within the four states, a panel of 15 koala experts used a structured, four-step question format to estimate bioregional population sizes of koalas, and changes in those sizes.

The estimated percentage of koala population loss in Queensland, New South Wales, Victoria and South Australia was 53%, 26%, 14% and 3%, respectively. The estimated total number of koalas for Australia was 329,000 (within a range of 144,000–605,000), with an estimated average decline of 24% over the past three generations and the next three generations.

Since May 2012, koalas have been listed as vulnerable in Queensland, New South Wales and the Australian Capital Territory because populations in these regions have declined significantly or are at risk of doing so.

In the southern states of Victoria and South Australia, koala populations vary widely from abundant to low or locally extinct. Although not currently listed as vulnerable, these koalas are also experiencing a range of serious threats, including low genetic diversity.

To date, the present “vulnerable” listing has not achieved any known positive results for koala populations in Queensland and New South Wales. In fact, recent research invariably shows the opposite.




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This is because the key threats to koalas remain, and are mostly increasing. The primary threat is habitat loss. Koala habitat (primarily eucalyptus woodlands and forests) continues to rapidly diminish, and unless it is protected, restored, and expanded, we will indeed see wild koala populations become “functionally extinct”. We know what comes after that.The Conversation

Christine Adams-Hosking, Honorary Research Fellow, The University of Queensland

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

Deadly frog fungus has wiped out 90 species and threatens hundreds more



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The Mossy Red-eyed Frog is among hundreds of species threatened with extinction at the hands of chytrid fungus.
Jonathan Kolby/Honduras Amphibian Rescue and Conservation Center

Benjamin Scheele, Australian National University and Claire Foster, Australian National University

It started off as an enigma. Biologists at field sites around the world reported that frogs had simply disappeared. Costa Rica, 1987: the golden toad, missing. Australia, 1979: the gastric brooding frog, gone. In Ecuador, Arthur’s stubfoot toad was last seen in 1988.

By 1990, cases of unexplained frog declines were piling up. These were not isolated incidents; it was a global pattern – one that we now know was due to chytridiomycosis, a fungal disease that was infecting and killing a huge range of frogs, toads and salamanders.

Our research, published today in Science, reveals the global number of amphibian species affected. At least 501 species have declined due to chytrid, and 90 of them are confirmed or believed extinct.




Read more:
Where did the frog pandemic come from?


When biologists first began to investigate the mysterious species disappearances, they were at a loss to explain them. In many cases, species declined rapidly in seemingly pristine habitat.

Species declines typically have obvious causes, such as habitat loss or introduced species like rats. But this was different.

The first big breakthrough came in 1998, when a team of Australian and international scientists led by Lee Berger discovered amphibian chytrid fungus. Their research showed that this unusual fungal pathogen was the cause of frog declines in the rainforests of Australia and Central America.

However, there were still many unknowns. Where did this pathogen come from? How does it kill frogs? And why were so many different species affected?

After years of painstaking research, biologists have filled in many pieces of the puzzle. In 2009, researchers discovered how chytrid fungus kills frogs. In 2018, the Korean peninsula was pinpointed as the likely origin of the most deadly lineage of chytrid fungus, and human dispersal of amphibians suggested as a likely source of the global spread of the pathogen.

Yet as the mystery was slowly but surely unravelled, a key question remained: how many amphibian species have been affected by chytrid fungus?

Early estimates suggested that about 200 species were affected. Our new study reveals the total is unfortunately much larger: 501 species have declined, and 90 confirmed or suspected to have been killed off altogether.

The toll taken by chytrid fungus on amphibians around the world. Each bar represents one species; colours reveal the extent of population declines.
Scheele et al. Science 2019

Devastating killer

These numbers put chytrid fungus in the worst league of invasive species worldwide, threatening similar numbers of species as rats and cats. The worst-hit areas have been in Australia and Central and South America, which have many different frog species, as well as ideal conditions for the growth of chytrid fungus.

Large species and those with small distributions and elevational ranges have been the mostly likely to experience severe declines or extinctions.

Together with 41 amphibian experts from around the world, we pieced together information on the timing of species declines using published records, survey data, and museum collections. We found that declines peaked globally in the 1980s, about 15 years before the disease was even discovered. This peak coincides with biologists’ anecdotal reports of unusual amphibian declines that occurred with increasing frequency in the late 1980s.

Encouragingly, some species have shown signs of natural recovery. Twelve per cent of the 501 species have begun to recover in some locations. But for the vast majority of species, population numbers are still far below what they once were.

Most of the afflicted species have not yet begun to bounce back, and many continue to decline. Rapid and substantial action from governments and conservation organisations is needed if we are to keep these species off the extinct list.




Read more:
Saving amphibians from a deadly fungus means acting without knowing all the answers


In Australia, chytrid fungus has caused the decline of 43 frog species. Of these, seven are now extinct and six are at high risk of extinction due to severe and ongoing declines. The conservation of these species is dependent on targeted management, such as the recovery program for the iconic corroboree frogs.

The southern corroboree frog: hopefully not a disappearing icon.
Corey Doughty

Importantly, there are still some areas of the world that chytrid has not yet reached, such as New Guinea. Stopping chytrid fungus spreading to these areas will require a dramatic reduction in the global trade of amphibians, as well as increased biosecurity measures.

The unprecedented deadliness of a single disease affecting an entire class of animals highlights the need for governments and international organisations to take the threat of wildlife disease seriously. Losing more amazing species like the golden toad and gastric brooding frog is a tragedy that we can avoid.The Conversation

Benjamin Scheele, Research Fellow in Ecology, Australian National University and Claire Foster, Research Fellow in Ecology and Conservation, Australian National University

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

Why extinct species seem to be returning from the dead



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The first Fernandina giant tortoise seen in over 112 years.
Galapagos National Park Directorate

David Roberts, University of Kent

Like something out of a zombie movie, species that were once thought extinct seem to be rising from the dead. Between February 21 and March 4 2019, three notable rediscoveries were announced – the Fernandina Island Galápagos tortoise (Chelonoidis phantasticus), which was last seen in 1906; Wallace’s giant bee (Megachile pluto), which had supposedly disappeared in 1980; and the Formosan clouded leopard (Neofelis nebulosa brachyura), which disappeared after the last sighting in 1983 and was officially declared extinct in 2013.

These rediscoveries suggest we may know very little about some of the world’s rarest species, but they also raise the question of how species are declared extinct in the first place. The IUCN Red List collates a global register of threatened species and measures their relative risks of extinction. The Red List has a set of criteria to determine the threat status of a species, which are only listed as “Extinct” when…

… there is no reasonable doubt that the last individual has died.

According to the Red List, this requires…

… exhaustive surveys in known and/or expected habitat, at appropriate times… throughout its historic range [which] have failed to record an individual. Surveys should be over a time frame appropriate to the taxon’s life cycle and life form.

Given all the evidence – or rather, lack of evidence – that’s needed, it’s surprising that any species is ever declared extinct. The criteria show that to understand whether a species is extinct, we need to know what it was doing in the past.

The world’s largest bee was presumed extinct before rediscovery in Indonesia in February 2019.
Stavenn/Wikipedia, CC BY-SA

Sightings at a certain time and in a certain place make up our knowledge of a species’ survival, but when a species becomes rare, sightings are increasingly infrequent so that people start to wonder whether the species still exists.

People often use the time since the last sighting as a measure of likelihood when deciding if a species has died out, but the last sighting is rarely the last individual of the species or the actual date of extinction.

Instead, the species may persist for years without being seen, but the length of time since the last sighting strongly influences assumptions as to whether a species has gone extinct or not.

But what is a sighting? It can come in a variety of forms, from direct observation of a live individual in the flesh or in photographs, indirect evidence such as foot prints, scratches and faeces, and oral accounts from interviews with eyewitnesses.

The Formosan clouded leopard is endemic to Taiwan and considered extinct, but eyewitness accounts keep speculation alive.
Joseph Wolf/Wikipedia

But these different lines of evidence aren’t all worth the same – a bird in the hand is worth more than a roomful of recollections from people who saw it in the past. Trying to determine what are true sightings and what are false complicates the declaration of extinction.

The idea of a species being “rediscovered” can confuse things further. Rediscovery implies that something was lost or forgotten but the term often gives the impression that a species has returned from the dead – hence the term “lazarus species”. This misinterpretation of lost or forgotten species means the default assumption is extinction for any species that hasn’t been seen for a number of years.

So, what does this mean for the three recently “rediscovered” species?

While a living specimen of the Fernandina Island Galápagos tortoise had not been seen since 1906, indirect observations of tortoise faeces, footprints and tortoise-like bite marks out of prickly pear cacti had been made as recently as 2013.

The uncertainty around the quality of these later observations and the long time since the last living sighting probably contributed to it being declared “Critically Endangered (Possibly Extinct)” in 2015. In the natural world, a species is presumed extinct until proven living.

Thought to be the last of its kind, this Fernandina Island Galápagos tortoise specimen was collected in 1906.
John Van Denburgh/Wikipedia

Wallace’s giant bee may not have been recorded in the last 38 years but it was never actually declared extinct according to the IUCN Red List. In fact, for many years it languished under the criteria of Data Deficient and was only recently assessed as Vulnerable.

So, while this is an exciting find for something that hadn’t been seen for so long, its rediscovery shows how little is known about many rare species in the wild, rather than how scarce they are.

The Formosan clouded leopard, meanwhile, was actually listed as Extinct. The last sighting of the species was in 1983, based on interviews with 70 hunters, and extensive camera trapping during the 2000s failed to detect its presence. It was officially declared extinct in 2013.

While the giant tortoise and bee were proclaimed alive after living specimens were found, the clouded leopard’s rediscovery is more uncertain. Based on sightings on two separate occasions by two sets of wildlife rangers, the evidence is compelling. But whether the Formosan Clouded Leopard has really risen from the dead will require considerably more effort to prove.The Conversation

David Roberts, Reader in Biodiversity Conservation, University of Kent

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

An end to endings: how to stop more Australian species going extinct



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John Gerrard Keulemans. Published by Muséum national d’histoire naturelle (France)

John Woinarski, Charles Darwin University; Sarah Legge, Australian National University, and Stephen Garnett, Charles Darwin University

This is part of a major series called Advancing Australia, in which leading academics examine the key issues facing Australia in the lead-up to the 2019 federal election and beyond. Read the other pieces in the series here.


We need nature. It gives us inspiration, health, resources, life. But we are losing it. Extinction is the most acute and irreversible manifestation of this loss.

Australian species have suffered at a disproportionate rate. Far more mammal species have become extinct in Australia than in any other country over the past 200 years.

The thylacine is the most recognised and mourned of our lost species, but the lesser bilby has gone, so too the pig-footed bandicoot, the Toolache wallaby, the white-footed rabbit-rat, along with many other mammals that lived only in Australia. The paradise parrot has joined them, the robust white-eye, the King Island emu, the Christmas Island forest skink, the southern gastric-brooding frog, the Phillip Island glory pea, and at least another 100 species that were part of the fabric of this land, part of what made Australia distinctive.

And that’s just the tally for known extinctions. Many more have been lost without ever being named. Still others hover in the graveyard – we’re not sure whether they linger or are gone.




Read more:
What makes some species more likely to go extinct?


The losses continue: three Australian vertebrate species became extinct in the past decade. Most of the factors that caused the losses remain unchecked, and new threats are appearing, intensifying, expanding. Many species persist only in slivers of their former range and in a fraction of their previous abundance, and the long-established momentum of their decline will soon take them over the brink.

The toolache wallaby is just one of Australia’s many extinct species.
John Gould, F.R.S., Mammals of Australia, Vol. II Plate 19, London, 1863

Unnecessarily extinct

These losses need not have happened. Almost all were predictable and preventable. They represent failures in our duty of care, legislation, policy and management. They give witness to, and warn us about, the malaise of our land and waters.

How do we staunch the wound and maintain Australia’s wildlife? It’s a problem with many facets and no single solution. Here we provide ten recommendations, based on an underlying recognition that more extinctions will be inevitable unless we treat nature as part of the essence of this country, rather than as a dispensable tangent, an economic externality.

  1. We should commit to preventing any more extinctions. As a society, we need to treat our nature with more respect – our plants and animals have lived in this place for hundreds of thousands, often millions, of years. They are integral to this country. We should not deny them their existence.

  2. We should craft an intergenerational social contract. We have been gifted an extraordinary nature. We have an obligation to pass to following generations a world as full of wonder, beauty and diversity as our generation has inherited.

  3. We should highlight our respect for, and obligation to, nature in our constitution, just as that fusty document could be refreshed and some of its deficiencies redressed through the Uluru Statement from the Heart. Those drafting the blueprint for the way our country is governed gave little or no heed to its nature. A constitution is more than a simple administrative rule book. Countries such as Ecuador, Palau and Bhutan have constitutions that commit to caring for their natural legacy and recognise that society and nature are interdependent.

  4. We should build a generation-scale funding commitment and long-term vision to escape the fickle, futile, three-year cycle of contested government funding. Environmental challenges in Australia are deeply ingrained and longstanding, and the conservation response and its resourcing need to be implemented on a scale of decades.

  5. As Paul Keating stated in his landmark Redfern speech, we should all see Australia through Aboriginal eyes – more deeply feel the way the country’s heart beats; become part of the land; fit into the landscape. This can happen through teaching curricula, through reverting to Indigenous names for landmarks, through reinvigorating Indigenous land management, and through pervasive cultural respect.

  6. We need to live within our environmental limits – constraining the use of water, soil and other natural resources to levels that are sustainable, restraining population growth and setting a positive example to the world in our efforts to minimise climate change.

  7. We need to celebrate and learn from our successes. There are now many examples of how good management and investments can help threatened species recover. We are capable of reversing our mismanagement.

  8. Funding to prevent extinctions is woefully inadequate, of course, and needs to be increased. The budgeting is opaque, but the Australian government spends about A$200 million a year on the conservation of threatened species, about 10% of what the US government outlays for its own threatened species. Understandably, our American counterparts are more successful. For context, Australians spend about A$4 billion a year caring for pet cats.

  9. Environmental law needs strengthening. Too much is discretionary and enforcement is patchy. We suggest tightening the accountability for environmental failures, including extinction. Should species die out, formal inquests should be mandatory to learn the necessary lessons and make systemic improvements.

  10. We need to enhance our environmental research, management and monitoring capability. Many threatened species remain poorly known and most are not adequately monitored. This makes it is hard to measure progress in response to management, or the speed of their collapse towards extinction.




Read more:
Eulogy for a seastar, Australia’s first recorded marine extinction


Extinction is not inevitable. It is a failure, potentially even a crime – a theft from the future that is entirely preventable. We can and should prevent extinctions, and safeguard and celebrate the diversity of Australian life.The Conversation

John Woinarski, Professor (conservation biology), Charles Darwin University; Sarah Legge, Professor, Australian National 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.