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Swingers' hookup program can find the right match for endangered species
A quick look at the popularity of online dating services like OkCupid and eHarmony shows us that people are pretty comfortable with letting an algorithm choose them a mate. Now we at the Flinders Molecular Ecology Lab want to do a similar thing for other animals.
With human-driven extinctions on the rise, many species are likely to be left relying on captive breeding for their survival. We hope that our algorithm will help ensure these breeding programs are successful, by pairing up matches who will have healthy, thriving offspring.
Unlike human dating services, we cannot ask a snake, fish or possum to answer questions. But we can look at their DNA. This allows us to breed individuals who are not closely related, avoiding the genetic problems that arise from inbreeding, and thus producing healthy populations with a diverse gene pool.
We have created Swinger, a computer program that uses DNA profiling to matchmake endangered animals for captive breeding - especially those that have multiple mates - and which we describe in a paper published in the journal Molecular Ecology Resources. We envision it helping to conserve many endangered animals, with the first animals being native freshwater fishes in Australia.
It’s all in the DNAGenetic diversity is crucial, because it helps populations to adapt and evolve in response to environmental changes that they may encounter in the future. So maintaining a large gene pool is an important consideration for captive breeding programs, particularly in populations that have already dwindled to small numbers. This makes avoiding inbreeding vitally important.
Many species kept in zoos – such as pandas – have clear family relationships or are bred in pairs and so their parentage is certain. Armed with pedigree information, it is relatively easy for zoos to select unrelated breeding pairs, often by working in collaboration with other zoos.
But most animals in the world are polygamous, with each individual naturally having multiple partners, even around the same time. This is where it becomes harder to track family relationships, unless you can examine their DNA.
It’s easier with pandas - well, the choosing part at least. Ritesh251123/Wikimedia Commons, CC BY-SAThe matchmaking algorithm is also ideal for starting a captive breeding program from individuals newly brought into captivity. This is because we often have no idea about their relationships to each other, except through DNA, and they may be highly related individuals.
The very circumstances that brought about the need for captive breeding also often results in inbreeding in wild populations. This is because the population has reduced in size to the point that individuals may unavoidably breed with their close relatives. This makes it especially important to ensure breeding in captivity occurs between unrelated individuals.
Captive breeding of swingersEven when dealing with such serious issues as extinction, we like to keep a sense of humour – hence the name Swinger, which we feel is pretty appropriate given that individuals of most species in the world are naturally polygamous. Indeed, our algorithm is just as suitable for setting up polygamous breeding groups as monogamous ones.
The algorithm is inspired by our efforts to save freshwater fishes in Australia. Native freshwater fish lineages recently became at risk of extinction due to human activities during the Millennium Drought in the Murray-Darling Basin, in southeastern Australia. The fish needed to be saved by their removal from the wild before their habitat completely dried out.
We created breeding groups of these rescued polygamous fish. This was done by using DNA information to create, by hand, “swinger” groups of unrelated individuals. The breeding was successful, with offspring reintroduced to the wild. However, the breeding groups were unavoidably sub-optimal because at that time we had no algorithm to work out the best possible mates for individuals.
Swinger is now being used to save native rainbowfish in northern Queensland. Although it is still early days, the rainbowfish breeding has been very successful, producing thousands of fingerlings that our collaborators are releasing to the wild.
We are also using Swinger to inform the design of a breeding program of endangered species of Galápagos giant tortoises previously considered extinct. These tortoises were rediscovered in a remote volcano and moved to the captive breeding facility of the Galápagos National Park. The aim is to reintroduce the captive-born offspring to the island where they evolved.
The brilliance of DNA is that it is in all living things. This means that Swinger could potentially be used to help breed all endangered species with sexual reproduction - especially, of course, the many polygamous species.
To borrow another concept from the world of human dating, there will hopefully soon be “Plenty of Fish” as a result of our efforts.
Catherine R. M. Attard has received funding from the Australian Government and other organisations.
Luciano Beheregaray receives funding from the Australian Research Council.
Jonathan Sandoval Castillo ne travaille pas, ne conseille pas, ne possède pas de parts, ne reçoit pas de fonds d'une organisation qui pourrait tirer profit de cet article, et n'a déclaré aucune autre affiliation que son poste universitaire.
Firestorms: the bushfire/thunderstorm hybrids we urgently need to understand
The journal Climatic Change has published a special edition of review papers discussing major natural hazards in Australia. This article is one of a series looking at those threats in detail.
Fire has been a driving force across Australia for millennia. Indeed, the health of many of our ecosystems is intrinsically dependent on fire. But bushfires are also one of our most frequent natural hazards, with a total cost estimated at A$8.5 billion per year.
In the past decade or so, extreme bushfires in southeastern Australia have burned more than a million hectares, claiming more than 200 lives and over 4,000 homes. Similar losses in other major urban areas have prompted questions about whether we are seeing a shift towards a significantly more hazardous fire regime, characterised by increasing fire frequency and intensity, and the development of catastrophic “firestorms”.
While these extreme bushfires account for only a very small percentage of fire events, they are responsible for the lion’s share of bushfire-related losses.
In contrast to typical bushfires, which spread across the landscape as well-defined burning fronts with smoke plumes perhaps a few kilometres high, extreme bushfires exhibit deep and widespread flaming and produce smoke plumes that can extend 10-15km into the atmosphere.
At these altitudes, bushfire plumes can actually develop into thunderstorms (hence the term “firestorm”). As such, extreme bushfires become much more difficult for emergency services to handle, making them all but impossible to suppress and their spread difficult to predict.
Beyond hot, dry and windyLike other dangerous bushfires, firestorms are driven by hot, dry and windy weather. But to spawn a firestorm, a range of other conditions must also be met; these can include a rugged landscape, particularly nasty weather events that produce “spikes” in fire danger, and conditions in the upper atmosphere that allow fire plumes to grow to considerable heights.
While previous studies have considered past and projected changes in the hot, dry and windy aspect of fire danger, less research has been done on the future projections for these other types of conditions. This means that we have quite a poor understanding of how extreme bushfires might affect us in the future.
As part of a series of reviews produced by the Australian Energy and Water Exchange initiative, my colleagues and I have taken a closer look at the most catastrophic bushfire cases and the factors that drive them, beyond the usual hot, dry and gusty weather.
There has been an overall increase in the frequency of major bushfire events in southeastern Australia since the mid-19th century. In particular, in the past 15 years a major fire event has occurred every 5 years or less. While some of this increase is due to changes in land use since European colonisation, there is also strong evidence of climate-driven changes.
We found that besides increases in dangerous surface fire danger conditions, upper atmospheric conditions have also become more conducive to explosive fire growth. High levels of the c-Haines index, which signals greater potential for a fire’s plume to rise high into the atmosphere, have become considerably more prevalent since the 1980s. The effects of droughts and widespread heatwaves have also contributed to the occurrence of extreme bushfires.
Looking into the future, high c-Haines values are projected to grow more prevalent still, albeit more gradually than over recent decades. Frontal weather patterns associated with particularly bad fire days are also projected to become more frequent during this century, and rainfall is projected to decrease over southwest and southeastern Australia.
All of this suggests that extreme bushfires will become a more common occurrence into the future.
What we still don’t knowOur methods for assessing fire danger do not explicitly account for the effects of extended drought and heatwaves on larger fuel elements such as branches and logs, and so may not properly account for their effects on fire spread and heat release into the atmosphere.
There is also considerable uncertainty about how fuel loads will change into the future. It is possible that the higher fire intensities expected to result from the direct effects of a warmer, drier climate may be offset by lower fuel loads.
Our understanding of extreme fire occurrence is also hampered by the lack of long-term and prehistoric climate data, which makes it hard to work out what the “normal” level of extreme bushfires has been in the past. While charcoal records show promise in this regard, we still don’t know enough about how charcoal is generated, deposited and subsequently preserved during extreme fires.
To predict the future occurrence of extreme bushfires, we also have more work to do in understanding how the trends forecast by global climate models will play out in terms of creating regional-scale fire weather conditions. And we still need to figure out the likely effects of other large-scale patterns such as El Niño.
Given the relatively recent advances that have been made in understanding the key drivers of extreme bushfires, the field is now ready for targeted studies that will help us estimate the future risk of extreme bushfires – and how best we can confront the threat.
Jason Sharples receives funding from the Australian Research Council and the Bushfire and Natural Hazards Cooperative Research Centre.
Air pollution is driving us all down a road to ruin | Letters
That the government is now at last being forced to do more to reduce the dangerous levels of nitrogen dioxide air pollution is welcome news (Court defeat for government on air pollution, 3 November). More than a year on from the “dieselgate” revelations, ministers should have been in no doubt about the dishonest and illegal methods used by some manufacturers to cheat emissions tests. Not only has the government failed to update its pollution modelling based on realistic emissions figures, it has also done nothing to support the 1.2 million UK diesel vehicle owners caught up in this scandal.
If anything, the government seems to be going out of its way to protect manufacturers. Cars fitted with the defeat device software are still able to pass MOT emissions tests, so the Driver and Vehicle Standards Agency seems to have turned a blind eye to this.
Continue reading...Leprosy revealed in red squirrels across British Isles
Scientists believe the animals have been infected with the disfiguring disease for centuries and pose little risk to humans today
Leprosy has been found in red squirrels across the British Isles and scientists believe they have been infected with the disfiguring disease for centuries.
The endangered animals carry the same bacteria that cause the human disease, research has revealed. This results in lesions on their muzzles, ears and paws, adding to the sharp decline in their numbers caused by invading grey squirrels, which appear immune to the disease.
Continue reading...From snorting smallpox scabs to...
What Trump win means for US science
Dartmoor livestock 'at risk from fun seekers'
Farming in Devon national park, and sheep and cattle welfare, jeopardised by climbers, cyclists and campers, says livestock society
Adventure seekers who visit one of Britain’s great wild places are making life more difficult for farmers and putting cattle and sheep in danger, a livestock welfare charity claims.
The chair of the Dartmoor Livestock Protection Society, which was formed in 1963, says the “idle amusement” of millions of visitors is threatening to squeeze out hill farmers.
Continue reading...The dinosaur almost blown to oblivion
Unknown dinosaur almost blown to oblivion
The water crisis facing California – in pictures
Mustafah Abdulaziz has spent years documenting humanity’s relationship to a precious natural resource – water. His latest work focuses on the challenges facing California, a highly populated state and a major agricultural center. Water: California was the first prize winner in the Syngenta photography award professional commission category for 2014–15, and will be on display at the National Geographic Museum in Washington DC from 12 November to 30 January 2017
Continue reading...Otters, geese and grebes: your photos as the Wetland Trust turns 70
To celebrate the Wildfowl and Wetland Trust’s 70th anniversary, we asked you to share pictures of wetlands around the UK. From incoming flocks to frolicking otters, here are some of our favourites
Satellite Eye on Earth: October 2016 - in pictures
Changing autumn colours in the US, New Delhi’s architecture and Hurricane Matthew were among the images captured by European Space Agency and Nasa satellites last month
The snowy landscape of the Putoransky state nature reserve, a Unesco world heritage site in the central area of the Putorana Plateau in northern central Siberia. The site, about 100km north of the Arctic Circle, serves as a major reindeer migration route – an increasingly rare natural phenomenon – and is one of the very few centres of plant species richness in the Arctic. Virtually untouched by human influence, this isolated mountain range includes pristine forests and cold-water lake and river systems. The lakes are characterised by elongated, fjord-like shapes, such as lake Ayan in the upper-central part of the image. Zooming in on the lake we can see that it is mostly ice-covered, with small patches of water peeking through around its lower reaches. Another feature of this area are the flat-topped mountains, formed by a geological process called ‘plume volcanism’: a large body of magma seeped through Earth’s surface and formed a blanket of basalt kilometres thick. Over time, cracks in the rock filled with water and eroded into the rivers and lakes we see today.
Continue reading...They elected Trump; now conservatives own climate change
Anyone who voted for Trump shares the responsibility for the climate damages resulting from his presidency
Many of us in the United States are in deep shock and despair. The election of Donald Trump speaks of a country and a world that represents so many things that go against our deepest grains. However, as I told my children this morning, the Earth will still turn, the sun will still rise. In fact, a Trump presidency will not have the dire consequences that many of us fear – especially for people like me who will be insulated from his policies. Surely it will change the economics and courts in the US, among other things. But really, all of these are transient.
The one thing that isn’t transient is the impact this will have on climate change. It is now virtually certain the world will not meet any of its climate targets. If Trump (and the Republican-controlled Congress) stand by their pledges, we will see a major rollback of the tremendous progress that has been made on reducing emissions. A Trump presidency will likely set us back at least a decade, perhaps longer. And that is a decade we can’t afford.
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Underworld: an exploration of London's sewers – video trailer
Underworld is an immersive exploration of London’s Victorian sewers and is the Guardian’s latest virtual reality offering. Step into the shoes of an urban explorer and experience the labyrinth of subterranean tunnels and hidden waterways that run beneath the city
Action to combat UK air pollution crisis delayed again
Ministers reject court proposal to deliver an effective plan within eight months following their legal defeat against NGO ClientEarth last week
Action to combat the UK’s air pollution crisis has been delayed again after the government rejected a proposal to deliver an effective action plan within eight months.
Environmental lawyers ClientEarth inflicted a humiliating legal defeat on ministers last week – its second in 18 months – when the high court ruled that ministers’ plans to tackle illegal levels of air pollution in many UK cities and towns were unlawfully poor.
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