A new 3D koala genome will aid efforts to defend the threatened species


Parwinder Kaur, University of Western Australia

Koalas are unique in the animal kingdom, living on a eucalyptus diet that would kill other creatures and drinking so little their name comes from the Dharug word gula, meaning “no water”. Today, many koala populations across Australia are in decline, due to habitat destruction caused by agriculture, urbanisation, droughts and bushfires intensified by climate change, and diseases such as chlamydia and koala retrovirus.

Genetic information can play a key role in the effort to conserve koalas and other species. A detailed map of the koala genome is vital to understanding their susceptibility to disease, their genetic diversity, and how they may respond to new environmental pressures.

We have created a new “chromosome-length” sequence of the koala genome, which will allow researchers to study its three-dimensional structure and understand its evolution.




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A unique creature under threat

The modern koala is the only living representative of the marsupial family Phascolarctidae, a family that once included several genera and species. During the Oligocene and Miocene epochs (from 34 to 5 million years ago), the ancestors of modern koalas lived in rainforests and didn’t eat only leaves.

During the Miocene, the Australian continent began drying out, leading to the decline of rainforests and the spread of open eucalyptus woodlands. Koalas evolved several adaptations that allowed them to live on a specialised eucalyptus diet. This specialisation makes them picky eaters, so they’re very prone to habitat loss.

Koalas are listed as a vulnerable species by the International Union for Conservation of Nature. It was hunted heavily in the early 20th century for its fur, and large-scale cullings in Queensland resulted in public outcry, initiating a movement to protect the species. Sanctuaries were established, and koalas whose habitat was disappearing were relocated.

Koalas are particularly vulnerable to bushfires; they are slow moving and eucalypt trees are very flammable. They instinctively seeks refuge in higher branches, exposing them to intense heat and flames. Bushfires also fragment the animal’s habitat, which restricts their movement and leads to population decline and loss of genetic diversity.

Piecing together the puzzle

The koala genome was first sequenced in 2013. This was only the first step in understanding koala genetics — akin to finding all the pieces of the puzzle, but being unsure how to put them all together into the meaningful patterns of genes and chromosomes.

Our new chromosome-length assembly follows the work of others, especially the Koala Genome Consortium and the Koala Genome Project led by Australian geneticist Rebecca Johnson. It is based on a draft by the Earlham Institute in the UK.

We used big-data sequencing methods such as Hi-C, 3D-DNA and Juicebox Assembly Tools courtesy of DNA Zoo labs to create our chromosome-length assembly.

We organised the genome into 8 chromosomes, a great improvement on the draft of 1,907 fragments we began with.

Vital for conservation

A high-quality genome sequence is essential if we want to bring genetic insights to conservation management initiatives. Some 200 Australian vertebrate species currently have species recovery plans, and 80% of those plans include genome-based actions. However, only 15% of those species have any genomic data available.

Our chromosome-length koala genome assembly enables a highly detailed 3D view of the genome architecture for koala. It is easier to use than earlier genomes, and means conservation management initiatives will have fast, cost-effective and reliable analysis options available.

This will give us insights into koalas’ genetic susceptibility to diseases like koala retrovirus (KoRV) and chlamydia. It may also form a basis for innovative vaccines. What’s more, it can be used in new conservation management strategies that aim to diversify the koala gene pool.




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The Conversation


Parwinder Kaur, Associate Professor | Director, DNA Zoo Australia, University of Western Australia

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

It’s not too late to save them: 5 ways to improve the government’s plan to protect threatened wildlife



Numbats are among 20 mammals on the federal government’s priority list.
Shutterstock

Euan Ritchie, Deakin University; Ayesha Tulloch, University of Sydney; Don Driscoll, Deakin University; Megan C Evans, UNSW, and Tim Doherty, University of Sydney

Australia’s Threatened Species Strategy — a five-year plan for protecting our imperilled species and ecosystems — fizzled to an end last year. A new 10-year plan is being developed to take its place, likely from March.

It comes as Australia’s list of threatened species continues to grow. Relatively recent extinctions, such as the Christmas Island forest skink, Bramble Cay melomys and smooth handfish, add to an already heavy toll.

Red handfish (Thymichthys politus), cousin of the recently extinct smooth handfish, are critically endangered. They’re small, bottom-dwelling fish that tend to ‘walk’ on their pectoral and pelvic fins rather than swim.
CSIRO Science Image, CC BY-SA

Now, more than ever, Australia’s remarkable species and environments need strong and effective policies to strengthen their protection and boost their recovery.

So as we settle into the new year, let’s reflect on what’s worked and what must urgently be improved upon, to turn around Australia’s extinction crisis.




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How effective was the first Threatened Species Strategy?

The Threatened Species Strategy is a key guiding document for biodiversity conservation at the national level. It identifies 70 priority species for conservation, made up of 20 birds, 20 mammals and 30 plants, such as the plains-wanderer, malleefowl, eastern quoll, greater bilby, black grevillea and Kakadu hibiscus.

These were considered among the most urgent in need of assistance of the more than 1,800 threatened species in Australia.

The strategy also identifies targets such as numbers of feral cats to be culled, and partnerships across industry, academia and government key to making the strategy successful.

The original strategy (2015-20) was eagerly welcomed for putting the national spotlight on threatened species conservation. It has certainly helped raise awareness of its priority species.

However, there’s little evidence the strategy has had a significant impact on threatened species conservation to date.

The midterm report in 2019 found only 35% of the priority species (14 in total) had improving trajectories compared to before the strategy (pre-2015). This number included six species — such as the brush-tailed rabbit-rat and western ringtail possum — that were still declining, but just at a slower rate.

Threatened Species Index trends for mammals (left) and birds (right) from 2000 to 2017. The index and y axes show the average change in populations (not actual population numbers) through time.
The Theatened Species Recovery Hub, Author provided

On average, the trends of threatened mammal and bird populations across Australia are not increasing.

Other targets, such as killing two million feral cats by 2020, were not explicitly linked to measurable conservation outcomes, such as an increase in populations of threatened native animals. Because of this, it’s difficult to judge their success.




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Feral cat cull: why the 2 million target is on scientifically shaky ground


What needs to change?

The previous strategy focused very heavily on feral cats as a threat and less so on other important and potentially compounding threats, particularly habitat destruction and degradation.

Targets from the first Threatened Species Strategy.
Department of Agriculture, Water and the Environment

For instance, land clearing has contributed to a similar number of extinctions in Australia (62 species) as introduced animals such as feral cats (64).

In fact, 2018 research found agricultural activities affect at least 73% of invertebrates, 82% of birds, 69% of amphibians and 73% of mammals listed as threatened in Australia. Urban development and climate change threaten up to 33% and 56% of threatened species, respectively.




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Other important threats to native Australian species include pollution, feral herbivores (such as horses and goats), very frequent or hot bushfires and weeds. Buffel grass was recently identified as a major emerging threat to Australia’s biodiversity, with the risk being as high as the threat posed by cats and foxes.

Five vital improvements

We made a submission to the Morrison government when the Threatened Species Strategy was under review. Below, we detail our key recommendations.

1. A holistic and evidence-based approach encompassing the full range of threats

This includes reducing rates of land clearing — a major and ongoing issue, but largely overlooked in the previous strategy.

A Leadbeater's possum peers out from behind a tree trunk.
Leadbeater’s possums are critically endangered. Their biggest threat is the destruction of hollow-bearing trees.
Shutterstock

2. Formal prioritisation of focal species, threats and actions

The previous strategy focused heavily on a small subset of the more than 1,800 threatened species and ecosystems in Australia. It mostly disregarded frog, reptile, fish and invertebrate species also threatened with extinction.

To reduce bias towards primarily “charismatic” species, the federal government should use an evidence-based prioritisation approach, known as “decision science”, like they do in New South Wales, New Zealand and Canada. This would ensure funds are spent on the most feasible and beneficial recovery efforts.

3. Targets linked to clear and measurable conservation outcomes

Some targets in the first Threatened Species Strategy were difficult to measure, not explicitly linked to conservation outcomes, or weak. Targets need to be more specific.

For example, a target to “improve the trajectory” of threatened species could be achieved if extinction is occurring at a slightly slower rate. Alternatively, a target to “improve the conservation status” of a species is achieved if new assessments rate it as “vulnerable” rather than “endangered”.

The ant plant (Myrmecodia beccarii) is one of the 30 plants on the federal government’s list of priority species. It is an ‘epiphyte’ (grows on other plants), and is threatened by habitat loss, invasive weeds, and removal by plant and butterfly collectors.
Dave Kimble/Wikimedia, CC BY-SA

4. Significant financial investment from government

Investing in conservation reduces biodiversity loss. A 2019 study found Australia’s listed threatened species could be recovered for about A$1.7 billion per year. This money could be raised by removing harmful subsidies that directly threaten biodiversity, such as those to industries emitting large volumes of greenhouse gases.

The first strategy featured a call for co-investment from industry. But this failed to attract much private sector interest, meaning many important projects aimed at conserving species did not proceed.

5. Government leadership, coordination and policy alignment

The Threatened Species Strategy should be aligned with Australia’s international obligations such as the United Nation’s Sustainable Development Goals and the federal Environment Protection and Biodiversity Conservation Act 1999 (which is also currently being reviewed). This will help foster a more coherent and efficient national approach to threatened species conservation.

The biggest threat to the critically endangered swift parrot is the clearing of their foraging and breeding habitat.
Shutterstock

There are also incredible opportunities to better align threatened species conservation with policies and investment in climate change mitigation and sustainable agriculture.

The benefits of investing heavily in wildlife reach beyond preventing extinctions. It would generate many jobs, including in regional and Indigenous communities.

Protecting our natural heritage is an investment, not a cost. Now is the time to seize this opportunity.




Read more:
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The Conversation


Euan Ritchie, Professor in Wildlife Ecology and Conservation, Centre for Integrative Ecology, School of Life & Environmental Sciences, Deakin University; Ayesha Tulloch, DECRA Research Fellow, University of Sydney; Don Driscoll, Professor in Terrestrial Ecology, Deakin University; Megan C Evans, Lecturer and ARC DECRA Fellow, UNSW, and Tim Doherty, ARC DECRA Fellow, University of Sydney

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

Australia-first research reveals staggering loss of threatened plants over 20 years


Ayesha Tulloch, University of Sydney; Elisa Bayraktarov, The University of Queensland; Hugh Possingham, The University of Queensland; Jaana Dielenberg, Charles Darwin University; Jennifer Silcock, The University of Queensland; Micha Victoria Jackson, The University of Queensland, and Nathalie Butt, The University of Queensland

When it comes to threatened species, charismatic animals usually get the most attention. But many of Australia’s plants are also in grave danger of extinction, and in many cases, the problem is getting worse.

New Australia-first research shows the population sizes of our threatened plants fell by almost three-quarters, on average, between 1995 and 2017. The findings were drawn from Australia’s 2020 Threatened Species Index, which combines data from almost 600 sites.

Plants are part of what makes us and our landscapes unique. They are important in their own right, but also act as habitat for other species and play critical roles in the broader ecosystem.

This massive data-crunching exercise shows that a lot more effort is needed if we want to prevent plant extinctions.

Plants, such as WA’s Endangered Foote’s grevillea, make our landscape unique.
Andrew Crawford / WA Department of Biodiversity Conservation and Attractions

Spotlight on plants

Australia’s plant species are special – 84% are found nowhere else in the world. The index shows that over about 20 years up to 2017, Australia’s threatened plant populations declined by 72%. This is faster than mammals (which declined by about a third), and birds (which declined by about half). Populations of trees, shrubs, herbs and orchids all suffered roughly similar average declines (65-75%) over the two decades.

Of the 112 species in the index, 68% are critically endangered or endangered and at risk of extinction if left unmanaged. Some 37 plant species have gone extinct since records began, though many others are likely to have been lost before scientists even knew they existed. Land clearing, changed fire regimes, grazing by livestock and feral animals, plant diseases, weeds and climate change are common causes of decline.




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Vulnerable plant populations reduced to small areas can also face unique threats. For example, by the early 2000s Foote’s grevillea (Grevillea calliantha) had dwindled to just 27 wild plants on road reserves. Road maintenance activities such as mowing and weed spraying became a major threat to its survival. For other species, like the button wrinklewort, small populations can lead to inbreeding and a lack of genetic diversity.

Fire, interrupted

Threatened plant conservation in fire-prone landscapes is challenging if a species’ relationship with fire is not known. Many Australian plant species require particular intensities or frequencies of burns for seed to be released or germinate. But since European settlement, fire patterns have been interrupted, causing many plant populations to decline.

Three threatened native pomaderris shrubs on the NSW South Coast are a case in point. Each of them – Pomaderris adnata, P. bodalla and P. walshii – have failed to reproduce for several years and are now found only in a few locations, each with a small number of plants.

Experimental trials recently revealed that to germinate, the seeds of these pomaderris species need exposure to hot-burning fires (or a hot oven). However they are now largely located in areas that seldom burn. This is important knowledge for conservation managers aiming to help wild populations persist.

Endangered sublime point pomaderris (Pomaderris adnata) requires high fire temperatures to germinate.
Jedda Lemmon /NSW DPIE, Saving our Species

Success is possible

A quarter of the species in the threatened plant index are orchids. Orchids make up 17% of plant species listed nationally as threatened, despite comprising just 6% of Australia’s total plant species.

The endangered coloured spider-orchid (Caladenia colorata) is pollinated only by a single thynnine wasp, and relies on a single species of mycorrhizal fungi to germinate in the wild.

Yet even for such a seemingly difficult species, conservation success is possible. In one project, scientists from the Royal Botanic Gardens Victoria, aided by volunteers, identified sites where the wasp was still naturally present. More than 800 spider orchid plants were then propagated in a lab using the correct symbiotic fungus, then planted at four sites. These populations are now considered to be self-sustaining.

In the case of Foote’s grevillea, a plant translocation program has established 500 plants at three new sites, dramatically improving the species’ long-term prospects.

Orchid flower
The coloured spider orchid, found in South Australia and Victoria, is endangered.
Noushka Reiter/Royal Botanic Gardens Victoria

But we aren’t doing enough

Both federal environment laws and the national threatened species strategy are under review. Submissions by research institutions and others have noted a lack of data, recovery actions and conservation funding for plants.

Our research found threatened plant populations at managed sites suffered declines of 60% on average, compared to 80% declines at unmanaged sites. This shows that while management is beneficial, it is not preventing overall declines.

New data on threatened species trends are added to the plant index each year, but many species are missing from the index because they aren’t being monitored.




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Australia’s threatened birds declined by 59% over the past 30 years


Monitoring of threatened species is undertaken by government and non-government groups, community groups, Indigenous organisations, citizen scientists, researchers and individuals. Without it, we have no idea if species are recovering or heading unnoticed towards extinction.

Woman measuring the height of a plant
Monitoring is essential to know if conservation actions are working.
Rebecca Dillon / WA Department of Biodiversity Conservation and Attractions

Australia has about 1,800 threatened species. Of these, 77% – or 1,342 species – are plants. However the index received monitoring data for only 10% of these plants, compared to 35% of threatened birds, which make up only 4% of threatened species.

If you’re keen to get involved in plant monitoring, it involves just a few simple steps:

  • find a local patch with a threatened plant species

  • revisit it once or twice a year to count the number of individuals in a consistent, well-defined area

  • use the same method and the same amount of effort each visit

  • take great care to not disturb the plant or its habitat when looking for it

  • contribute your data to the index.

Saving Australia’s flora

Australia must urgently change the way we prioritise conservation actions and enact environment laws, if we hope to prevent more plant extinctions.

Critical actions include stopping further habitat loss and more funding for recovery actions as well as extinction risk assessments. It is important that these assessments adhere to consistent criteria. This is something the common assessment method, agreed to by all states and territories, seeks to achieve.

Finally, more funding for research into the impacts of key threats (and how to manage them) will help ensure our unique flora are not lost forever.

Prof Hugh Possingham and Dr Ayesha Tulloch discuss the 2020 findings of the Threatened Plant Index.

CORRECTION: A previous version of this article incorrectly stated that reviews of federal environment laws and the threatened species strategy found a lack of data, recovery actions and conservation funding for plants. While those problems were identified in public submissions to the reviews, the reviews themselves are not yet finalised.The Conversation

Ayesha Tulloch, DECRA Research Fellow, University of Sydney; Elisa Bayraktarov, Postdoctoral Research Fellow in Conservation Biology, The University of Queensland; Hugh Possingham, Professor, The University of Queensland; Jaana Dielenberg, University Fellow, Charles Darwin University; Jennifer Silcock, Post-doctoral research fellow, The University of Queensland; Micha Victoria Jackson, Postdoctoral research fellow, The University of Queensland, and Nathalie Butt, Postdoctoral Fellow, The University of Queensland

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

‘Severely threatened and deteriorating’: global authority on nature lists the Great Barrier Reef as critical



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Jon C. Day, James Cook University and Scott F. Heron, James Cook University

The Great Barrier Reef is now in “critical” condition and the health of four other Australian World Heritage properties has worsened, according to a sobering report just released by the International Union for Conservation of Nature (IUCN).

The IUCN is the global authority on nature. Its third outlook report marks the first time the IUCN has declared an Australian property as critical, which means its values are severely threatened and deteriorating. The health of the Blue Mountains, Gondwana Rainforests, Shark Bay and the Ningaloo Coast has also been downgraded.




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The assessment, while chastening, is not surprising. The Great Barrier Reef has endured three mass coral bleaching events in five years, and last summer’s bushfires caused untold damage in the Blue Mountains and Gondwana Rainforests (not to mention the current fires at the reef’s Fraser Island).

Climate change remains the key issue for World Heritage places, not just in Australia but globally. In fact, the IUCN assessment found climate change threatens 11 of Australia’s 16 properties. This raises further questions over our national climate response.

World Heritage: the best of the best

The latest report builds on previous reports from 2014 and 2017, and shows the status and trends of World Heritage properties identified for their outstanding natural values. As the report states:

our ability to conserve these sites is thus a litmus test for the broader success of conservation worldwide.

To qualify for World Heritage listing for natural values, a place must meet one or more of four criteria: exceptional beauty, geology, ecological processes, and species and habitats.

Some properties are also recognised for cultural values and, if they have both, they’re referred to as “mixed”. Across the world there are 252 natural and mixed World Heritage properties, of which 16 are in Australia.

The IUCN is the official advisor on nature to UNESCO’s World Heritage Committee. The IUCN Outlook report involves assessments by hundreds of international experts, who examine the conservation prospects of all natural and mixed World Heritage properties. It focuses on their natural values, the threats to these values and the effectiveness of actions to protect them.

Threats to our iconic places

Climate change is now the most prevalent threat to natural World Heritage sites, and to many cultural sites.

Overall, the report assessed climate change as a high or a very high threat in 83 out of 252 global properties (33%). This rate is double in Australia, with climate change listed as a threat to 69% (11 of 16) of Australian properties.

And when considering the four natural criteria individually, climate change is the greatest threat to each. This is likely to get worse in future, as climate change is expected to affect more than three times the number of properties impacted by any other threat.

For many properties, the deteriorated conservation outlook is the result of accumulated threats. Impacts of climate change, like coral bleaching and bushfires, are often exacerbated by other threats. For example, the federal government’s 2019 Outlook Report for the Great Barrier Reef listed 45 threats including climate change. This included poor water quality from land-based runoff, coastal development and fishing.

Aerial view of seagrass meadows and headlands in Shark Bay
Seagrass meadows and headlands in the World Heritage-listed Shark Bay Conservation Area, now rated as ‘good with some concerns’.
Shutterstock

At the time of writing, the website which provides the full rationale behind the IUCN outlook was not yet publicly available. However the threats facing the five downgraded Australian sites are well documented.

These include marine heatwaves, which lead to coral bleaching in the Great Barrier Reef and Ningaloo. In Shark Bay, marine heatwaves also cause seagrass — critical habitat for a vast diversity of species — to die-off. Poor water quality, such as from urban and agricultural run-off, is another big threat to the Great Barrier Reef.




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More frequent and intense bushfires are a problem for the Blue Mountains, Shark Bay, and Gondwana Rainforests. These ancient rainforests, along with Ningaloo and Shark Bay, also face threats of invasive species, diseases and storms.

Punching below our weight

While there have been some successes globally, the threats facing our heritage places are escalating.

Since the 2017 assessment, of the 252 properties analysed globally, 16 (6%) have deteriorated and only eight (3%) showed improvement. Notably, Australia is punching below its weight, with 31% of properties having deteriorated (5 of 16) and zero with improvement.




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All of Australia’s World Heritage properties are recognised as having “highly effective” or “mostly effective” protection and management activities.

But the deterioration of the Great Barrier Reef, the Blue Mountains, Gondwana Rainforests, Shark Bay and Ningaloo Coast casts doubt on whether these actions are an effective response to threats, especially climate change.

A whale shark
Western Australia’s Ningaloo Coast, now downgraded to ‘good with some concerns’, is famous for its vast diversity of wildlife, including whale sharks.
Shutterstock

Australia’s climate response has been widely criticised, most recently by Christiana Figueres, the former chief of the UN Climate Framework. In a keynote to open the Australian Emissions Reductions Summit yesterday, Figueres said:

I have been pretty vocal about my frustration for so many years of the completely unstable, volatile, unpredictable stand and position on climate change in Australia.

“Meeting and beating” Australia’s 2030 emissions targets has been the Morrison government’s catch-cry. But the target lacks ambition and the government hasn’t ruled out using Kyoto carry-over credits to help meet it. The government has also refused to commit to a target of net-zero emissions by mid century, in contrast to the policies of many of our international peers.

Management of non-climate stressors is, and will remain, essential to halt the decline of the values of our properties. But Australia must adopt more ambitious climate goals to avoid losing those values that make our heritage places special, preserving them for future generations.




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The Conversation


Jon C. Day, PSM, Post-career PhD candidate, ARC Centre of Excellence for Coral Reef Studies, James Cook University and Scott F. Heron, Associate professor, James Cook University

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

Humans are changing fire patterns, and it’s threatening 4,403 species with extinction



The Leadbeater’s possum, one of thousands of species threatened by changing fire regimes.
Shutterstock

Luke Kelly, University of Melbourne; Annabel Smith, The University of Queensland; Katherine Giljohann, University of Melbourne, and Michael Clarke, La Trobe University

Last summer, many Australians were shocked to see fires sweep through the wet tropical rainforests of Queensland, where large and severe fires are almost unheard of. This is just one example of how human activities are changing fire patterns around the world, with huge consequences for wildlife.

In a major new paper published in Science, we reveal how changes in fire activity threaten more than 4,400 species across the globe with extinction. This includes 19% of birds, 16% of mammals, 17% of dragonflies and 19% of legumes that are classified as critically endangered, endangered or vulnerable.




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But, we also highlight the emerging ways we can help promote biodiversity and stop extinctions in this new era of fire. It starts with understanding what’s causing these changes and what we can do to promote the “right” kind of fire.

How is fire activity changing?

Recent fires have burned ecosystems where wildfire has historically been rare or absent, from the tropical forests of Queensland, Southeast Asia and South America to the tundra of the Arctic Circle.

Exceptionally large and severe fires have also been observed in areas with a long history of fire. For example, the 12.6 million hectares that burnt in eastern Australia during last summer’s devastating bushfires was unprecedented in scale.

The post-fire landscape in Flinders Chase National Park, Kangaroo Island, three months after an extremely large and severe bushfire last summer.
Luke Kelly

This extreme event came at a time when fire seasons are getting longer, with more extreme wildfires predicted in forests and shrublands in Australia, southern Europe and western United States.

But fire activity isn’t increasing everywhere. Grasslands in countries such as Brazil, Tanzania, and the United States have had fire activity reduced.

Extinction risk in a fiery world

Fire enables many plants to complete their life cycles, creates habitats for a wide range of animals and maintains a diversity of ecosystems. Many species are adapted to particular patterns of fire, such as banksias — plants that release seeds into the resource-rich ash covering the ground after fire.

But changing how often fires occur and in what seasons can harm populations of species like these, and transform the ecosystems they rely on.

We reviewed data from the International Union for Conservation of Nature (IUCN) and found that of the 29,304 land-based and freshwater species listed as threatened, modified fire regimes are a threat to more than 4,403.

Most are categorised as threatened by an increase in fire frequency or intensity.

For example, the endangered mallee emu-wren in semi-arid Australia is confined to isolated patches of habitat, which makes them vulnerable to large bushfires that can destroy entire local populations.

Likewise, the Kangaroo Island dunnart was listed as critically endangered before it lost 95% of its habitat in the devastating 2019-2020 bushfires.

Large bushfires threaten many birds, such as the mallee emu-wren.
Ron Knight/Wikimedia, CC BY

However, some species and ecosystems are threatened when fire doesn’t occur. Frequent fires are an important part of African savanna ecosystems and less fire activity can lead to shrub encroachment. This can displace wild herbivores such as wildebeest that prefer open areas.

How humans change fire regimes

There are three main ways humans are transforming fire activity: global climate change, land-use and the introduction of pest species.

Global climate change modifies fire regimes by changing fuels such as dry vegetation, ignitions such as lightning, and creating more extreme fire weather.

What’s more, climate-induced fires can occur before the dominant tree species are old enough to produce seed, and this is reshaping forests in Australia, Canada and the United States.

Humans also alter fire regimes through farming, forestry, urbanisation and by intentionally starting or suppressing fires.

Introduced species can also change fire activity and ecosystems. For example, in savanna landscapes of Northern Australia, invasive gamba grass increases flammability and fire frequency. And invasive animals, such as red foxes and feral cats, prey on native animals exposed in recently burnt areas.




Read more:
Fire-ravaged Kangaroo Island is teeming with feral cats. It’s bad news for this little marsupial


Importantly, cultural, social and economic changes underpin these drivers. In Australia, the displacement of Indigenous peoples and their nuanced and purposeful use of fire has been linked with extinctions of mammals and is transforming vegetation.

We need bolder conservation strategies

A suite of emerging actions — some established but receiving increasing attention, others new — could help us navigate this new fire era and save species from extinction. They include:

In Africa, reintroducing grazing animals such as rhinoceros create patchy fire regimes.
Sally Archibald, Author provided

Where to from here?

The input of scientists will be valuable in helping navigate big decisions about new and changing ecosystems.

Empirical data and models can monitor and forecast changes in biodiversity. For example, new modelling has allowed University of Melbourne researchers to identify alternative strategies for introducing planned or prescribed burning that reduces the risk of large bushfires to koalas.

New partnerships are also needed to meet the challenges ahead.

At the local and regional scale, Indigenous-led fire stewardship is an important approach for fostering relationships between Indigenous and non-Indigenous organisations and communities around the world.

Frank Lake, a co-author on our new paper, works with Yurok and Karuk fire practitioners, shown here burning under oaks.
Frank Lake, U.S Department of Agriculture Forest Service Pacific Southwest Research Station.

And international efforts to reduce greenhouse gas emissions and limit global warming are crucial to reduce the risk of extreme fire events. With more extreme fire events ahead of us, learning to understand and adapt to changes in fire regimes has never been more important.




Read more:
The world’s best fire management system is in northern Australia, and it’s led by Indigenous land managers


The Conversation


Luke Kelly, Senior Lecturer in Ecology and Centenary Research Fellow, University of Melbourne; Annabel Smith, Lecturer in Wildlife Management, The University of Queensland; Katherine Giljohann, Postdoctoral research fellow, University of Melbourne, and Michael Clarke, Professor of Zoology, La Trobe University

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.

Humans are encroaching on Antarctica’s last wild places, threatening its fragile biodiversity



SL Chown, CC BY-NC

Rachel Leihy, Monash University and Steven Chown, Monash University

Since Western explorers discovered Antarctica 200 years ago, human activity has been increasing. Now, more than 30 countries operate scientific stations in Antarctica, more than 50,000 tourists visit each year, and new infrastructure continues to be developed to meet this rising demand.

Determining if our activities have compromised Antarctica’s wilderness has, however, remained difficult.

Our study, published today in Nature, seeks to change that. Using a new “ecological informatics” approach, we’ve drawn together every available recorded visit by humans to the continent, over its 200 year history.

We found human activity across Antarctica has been extensive, especially in the ice-free and coastal areas, but that’s where most biodiversity is found. This means wilderness areas – parts of the continent largely untouched by human activity – do not capture many of the continent’s important biodiversity sites.

Historical and contemporary human activity on Deception Island.
SL Chown

One of the world’s largest intact wildernesses

So just how large is the Antarctic wilderness? For the first time, our study calculated this area and how much biodiversity it captures. And, like all good questions, the answer is “that depends”.

If we think of Antarctica in the same way as every other continent, then the whole of Antarctica is a wilderness. It has no farms, no cities, no suburbs, no malls, no factories. And for a continent so large, it has very few people.

Antarctica’s wilderness should be held to a higher standard.
SL Chown

But Antarctica is too different to compare to other continents – it should be held to a higher standard. And so we define “wilderness” as the areas that aren’t highly impacted by people. This would exclude, for example, tourist areas and scientific stations. And under this definition, the wilderness area is still large.

It’s about 13,598,148 square kilometres, or more than 99% of the continent. Only the wilderness in the vast forested areas of the far Northern Hemisphere is larger. Roughly, this area is nearly twice the size of Australia.




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On the other hand, the inviolate areas (places free from human interference) that the Antarctic Treaty Parties are obliged to identify and protect are dwindling rapidly.

Our analyses suggest less than 32% of the continent includes large, unvisited areas. And even that’s an overestimate. Not all visits have been recorded, and several new traverses – crossing large tracts of unvisited areas – are being planned.

Human activity has been extensive across Antarctica, but large areas with no visitation record might still exist across central parts of the continent.
Leihy et al. 2020 Nature

Wilderness areas have poor biodiversity value

If so much of the continent remains “wild”, how much of Antarctica’s biodiversity lives within these areas?

Surprisingly few sites considered really important for Antarctic biodiversity are represented in the “un-impacted” wilderness area.

For example, only 16% of the continent’s Important Bird Areas (areas identified internationally as critical for bird conservation) are located in wilderness areas. And only 25% of protected areas established for their species or ecosystem value, and less than 7% of sites with recorded species, are in wilderness areas.

This outcome is surprising because wilderness areas elsewhere, like the Amazon rainforest, are typically valued as crucial habitat for biodiversity.

Ice-free areas are critical habitat for Antarctic biodiversity, like Adélie penguins, and frequently visited by people as well.
SL Chown

Inviolate areas have seemingly even less biodiversity value. This is because people have mostly had to visit Antarctic sites to collect species data.

In the future, remote sensing technologies might allow us to investigate and monitor pristine areas without setting foot in them. But for now, most of our knowledge of Antarctic species comes from places that have been impacted to some extent by people.

How does human activity threaten Antarctic biodiversity?

Antarctica’s remaining wilderness areas need urgent protection from increasing human activity.

Even passing human disturbance can impact the biodiversity and wilderness value of sites. For example, sensitive vegetation and soil communities can take years to recover from trampling.

Increasing movement around the continent also increases the risk people will transfer species between isolated regions, or introduce new alien species to Antarctica.

Expanding the existing network of Antarctic protected areas can secure remaining wilderness areas into the future.
SL Chown

So how can we protect it?

Protecting the Antarctic wilderness could be achieved by expanding the existing Antarctic Specially Protected Areas network to include more wilderness and inviolate areas where policymakers would limit human activity.

When planning how we’ll use Antarctica in the future, we could also consider the trade off between the benefits of science and tourism activities, and the value of retaining pristine wilderness and inviolate areas.




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This could be done explicitly through the environmental impact assessments required for activities in the region. Currently, impacts on the wilderness value of sites are rarely considered.

We have an opportunity in Antarctica to protect some of the world’s most intact and undisturbed environments, and prevent further erosion of Antarctica’s remarkable wilderness value.The Conversation

Ross Sea Region, Antarctica. Few sites considered really important for Antarctic biodiversity are represented in the wilderness area.
SL Chown

Rachel Leihy, PhD candidate, Monash University and Steven Chown, Professor of Biological Sciences, Monash University

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

Back from extinction: a world first effort to return threatened pangolins to the wild



Alex Braczkowski, Author provided

Alexander Richard Braczkowski, Griffith University; Christopher O’Bryan, The University of Queensland; Duan Biggs, Griffith University, and Raymond Jansen, Tshwane University of Technology

Pangolins are one of the most illegally trafficked animals on the planet and are suspected to be linked to the current coronavirus pandemic.

Pangolins are also one of the world’s most threatened species but new efforts are underway to reintroduce pangolins to parts of Africa where the animal has been extinct for decades.




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The reintroduction of pangolins has not been easy. But it’s vital to prevent this shy, mysterious creature from being lost forever.

A cute but threatened species

Pangolins are the only mammals wholly-covered in scales, which they use to protect themselves from predators. They can also curl up into a tight ball.

They eat mainly ants, termites and larvae which they pick up with their sticky tongue. They can grow up to 1m in length from nose to tail and are sometimes referred to as scaly anteaters.

But all eight pangolin species are classified as “threatened” under International Union for Conservation of Nature criteria.

There is an unprecedented demand for their scales, primarily from countries in Asia and Africa where they are used in food, cultural remedies and medicine.

Between 2017 and 2019, seizures of pangolin scales tripled in volume. In 2019 alone, 97 tons of pangolin scales, equivalent to about 150,000 animals, were reportedly intercepted leaving Africa.

There is further evidence of the illegal trade in pangolin species openly on social media platforms such as Facebook.

The intense global trafficking of the species means the entire order (Pholidota) is threatened with extinction. For example, the Temminck’s pangolins (Smutsia temminckii) went extinct in South Africa’s KwaZulu Natal Province three decades ago.

Reintroduction of an extinct species

Each year in South Africa the African Pangolin Working Group (APWG) retrieves between 20 and 40 pangolins through intelligence operations with security forces.

These pangolins are often-traumatised and injured and are admitted to the Johannesburg Wildlife Veterinary Hospital for extensive medical treatment and rehabilitation before they can be considered for release.

In 2019, seven rescued Temminck’s pangolins were reintroduced into South Africa’s Phinda Private Game Reservein the KwaZulu Natal Province.

Nine months on, five have survived. This reintroduction is a world first for a region that last saw a viable population of this species in the 1980s.

During the release, every individual pangolin followed a strict regime. They needed to become familiar with their new surroundings and be able to forage efficiently.

Pangolins curl up into a tight ball of scales.
Alex Braczkowski

Previous releases, including early on in South Africa and in other countries such as the Philippines, the Democratic Republic of the Congo and Thailand had minimal post-release monitoring.

Pangolins released immediately following medical treatment had a low level of survival for various reasons, including inability to adapt to their release sites.

A ‘soft release’ in to the wild

The process on Phinda game reserve involved a more gentle ease into re-wilding a population in a region that had not seen pangolins for many decades.

The soft release had two phases:

  1. a pre-release observational period
  2. an intensive monitoring period post release employing GPS satellite as well as VHF tracking tags.
A satellite tag is fitted to each pangolin before release and transmits its location on an hourly basis.
Alex Braczkowski

The pre-release period lasted between two to three weeks and were characterised by daily walks (three to five hours) of individuals on the reserves. These walks were critical for acclimatising individuals to the local habitat, its sounds, smells and possible threats. It also helped them source suitable and sufficient ant and termite species for food.

Following that, the post release period of two to three months involved locating released pangolins daily at first, and then twice per week where they were weighed, a rapid health assessment was made and habitat features such as burrows and refuges monitored.

Phinda reserve manager Simon Naylor said:

A key component of the post release period was whether individuals gained or maintained their weight.

The way the animals move after release also reveals important clues to whether they will stay in an area; if they feed, roll in dung, enter burrows. Much of this behaviour indicates site fidelity and habitat acceptance.




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Following nine months of monitoring and tracking, five of the seven survived in the region. One died of illness while the other was killed by a Nile crocodile.

Released pangolins are located at burrows like this one.
Alex Braczkowski

Why pangolin reintroduction is important

We know so little about this group of mammals that are vastly understudied and hold many secrets yet to be discovered by science but are on the verge of collapse.

The South African and Phinda story is one of hope for the Temminck’s pangolin where they once again roam the savanna hills and plains of Zululand.

The process of relocating these trade animals back into the wild has taken many turns, failures and tribulations but, the recipe of the “soft release” is working.The Conversation

Alexander Richard Braczkowski, Research Associate, Griffith University; Christopher O’Bryan, Postdoctoral Research Fellow, School of Earth and Environmental Sciences, The University of Queensland; Duan Biggs, Senior Research Fellow Social-Ecological Systems & Resilience, Griffith University, and Raymond Jansen, Professor: Zoology & Ecology, Tshwane University of Technology

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

We’ve just discovered two new shark species – but they may already be threatened by fishing



One of the newly discovered sixgilled sawshark species (Pliotrema kajae).
Simon Weigmann, Author provided

Per Berggren, Newcastle University and Andrew Temple, Newcastle University

Finding a species that’s entirely new to science is always exciting, and so we were delighted to be a part of the discovery of two new sixgill sawsharks (called Pliotrema kajae and Pliotrema annae) off the coast of East Africa.

We know very little about sawsharks. Until now, only one sixgill species (Pliotrema warreni) was recognised. But we know sawsharks are carnivores, living on a diet of fish, crustaceans and squid. They use their serrated snouts to kill their prey and, with quick side-to-side slashes, break them up into bite-sized chunks.

The serrated snout of a sixgill sawshark (Pliotrema annae).
Ellen Barrowclift-Mahon/Marine MEGAfauna Lab/Newcastle University., Author provided

Sawsharks look similar to sawfish (which are actually rays), but they are much smaller. Sawsharks grow to around 1.5 metres in length, compared to 7 metres for a sawfish and they also have barbels (fish “whiskers”), which sawfish lack. Sawsharks have gills on the side of their heads, whereas sawfish have them on the underside of their bodies.

A sixgill sawshark (Pliotrema annae) turned on its side, showing gills and barbels.
Ellen Barrowclift-Mahon, Author provided

Together with our colleagues, we discovered these two new sawsharks while researching small-scale fisheries that were operating off the coasts of Madagascar and Zanzibar. While the discovery of these extraordinary and interesting sharks is a wonder in itself, it also highlights how much is still unknown about biodiversity in coastal waters around the world, and how vulnerable it may be to poorly monitored and managed fisheries.

The three known species of sixgill sawshark. The two new species flank the original known species. From left to right: Pliotrema kajae, Pliotrema warreni (juvenile female) and Pliotrema annae (presumed adult female).
Simon Weigmann, Author provided

Fishing in the dark

Despite what their name might suggest, small-scale fisheries employ around 95% of the world’s fishers and are an incredibly important source of food and money, particularly in tropical developing countries. These fisheries usually operate close to the coast in some of the world’s most important biodiversity hotspots, such as coral reefs, mangrove forests and seagrass beds.

For most small-scale fisheries, there is very little information available about their fishing effort – that is, how many fishers there are, and where, when and how they fish, as well as exactly what they catch. Without this, it’s very difficult for governments to develop management programmes that can ensure sustainable fishing and protect the ecosystems and livelihoods of the fishers and the communities that depend on them.

Small-scale fishers of Zanzibar attending their driftnets.
Per Berggren/Marine MEGAfauna Lab/Newcastle University, Author provided

While the small-scale fisheries of East Africa and the nearby islands are not well documented, we do know that there are at least half a million small-scale fishers using upwards of 150,000 boats. That’s a lot of fishing. While each fisher and boat may not catch that many fish each day, with so many operating, it really starts to add up. Many use nets – either driftnets floating at the surface or gillnets, which are anchored close to the sea floor. Both are cheap but not very selective with what they catch. Some use longlines, which are effective at catching big fish, including sharks and rays.




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In 2019, our team reported that catch records were massively underreporting the number of sharks and rays caught in East Africa and the nearby islands. With the discovery of two new species here – a global hotspot for shark and ray biodiversity – the need to properly assess the impact of small-scale fisheries on marine life is even more urgent.

Pliotrema kajae, as it might look swimming in the subtropical waters of the western Indian Ocean.
Simon Weigmann, Author provided

How many other unidentified sharks and other species are commonly caught in these fisheries? There is a real risk of species going extinct before they’re even discovered.

Efforts to monitor and manage fisheries in this region, and globally, must be expanded to prevent biodiversity loss and to develop sustainable fisheries. There are simple methods available that can work on small boats where monitoring is currently absent, including using cameras to document what’s caught.

A selection of landed fish – including sharks, tuna and swordfish.
Per Berggren, Author provided

The discovery of two new sixgill sawsharks also demonstrates the value of scientists working with local communities. Without the participation of fishers we may never have found these animals. From simple assessments all the way through to developing methods to alter catches and manage fisheries, it’s our goal to make fisheries sustainable and preserve the long-term future of species like these sawsharks, the ecosystems they live in and the communities that rely on them for generations to come.The Conversation

Per Berggren, Marine MEGAfauna Lab, Newcastle University and Andrew Temple, Postdoctoral Research Associate in Marine Biology, Newcastle University

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