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“Since then, however, technologies have improved and we’ve come to understand what we can use genomes for and the huge power they have,” explains Dr Carolyn Hogg, senior research manager of the Australasian Wildlife Genomics Group at the University of Sydney. “We’ve come to realise during the past 10 years that genomes are such powerful tools for not only answering complex biological questions but also for helping to make smarter conservation planning and management decisions.
“So we’re now on a mission to sequence the genomes of 50 of Australia’s most threatened species during the next three years.” By doing that, Carolyn and her colleagues hope the fates of species already well on the path to extinction, including the critically endangered woylie and orange-bellied parrot, can be turned around, and fast.
The grand vision Carolyn is talking about is being coordinated through a new national project called the Threatened Species Initiative (TSI), for which she is the science leader.
The TSI was officially launched in May 2020 and is undertaking a pilot phase that’s running genetics-based conservation projects for the endangered eastern bristlebird, Hastings River mouse, two species of barred bandicoot, the ghost bat, and the critically endangered Swan galaxias (a freshwater Tasmanian fish), orange-bellied parrot and native guava (an eastern Australian bush tucker plant).
Initially, the TSI will oversee the creation of a library of genetic information for 50 of the most threatened species of Australian flora and fauna and support its use in biodiversity conservation. But there is already hopeful talk about extending the scope of the project to cover all 480 animals and 1294 plants currently listed nationally as threatened in Australia. It’s also being seen as a significant start to cataloguing the genetic make-up of all of Australia’s largely unique biodiversity. The TSI is being supported by funding from the non-profit Bioplatforms Australia, which – through the National Collaborative Research Infrastructure Strategy – manages federal government funding in the cutting-edge fields of genomics, proteomics, metabolomics and bioinformatics.
After last summer’s bushfire crisis pushed dozens of Australian species close to the brink of extinction (see Unbearable loss, AG 155), it seems the new conservation promise of genomes being made available through the TSI couldn’t have come at a better time.
SO WHAT EXACTLY is a genome? Put simply it’s an organism’s complete set of genetic material…every gene involved in how it looks and behaves, responds to disease, copes with climate stress, and more. Sequencing a genome means identifying each of those genes and its chemical structure. It might sound obvious that knowing the full genetic make-up of an animal in this way should be very useful. But the massive amount of data in a genome can make it an overwhelming and unwieldy piece of information to work with.
“A marsupial genome, for example, is 3.5 gigabases, which is 3.5 billion base pairs of information,” Carolyn explains. “And a problem has been how do you compute all of this information?” She likes to use a jigsaw puzzle as a metaphor to explain: “Look
To tease out useful insights and understand what you can do with all this information in terms of preserving biodiversity usually takes a very high level of genetic understanding. And there are just a handful of people with that sort of knowledge – conservation geneticists – in Australia, of which Carolyn is one.
And so, much of the information contained in the small number of native Australian animal and plant genomes that have so far been sequenced sits tucked away, remote and inaccessible, like good china that only comes out for dinner parties.
That was until now. As well as the University of Sydney, TSI partners include: the federal Department of Agriculture, Water and the Environment; the WA Department of Biodiversity, Conservation and Attractions; the NSW Saving our Species program; Amazon Web Services (AWS); the Australian Wildlife
“RONIN is literally high-performance computing – cloud computing – for dummies,” Carolyn explains. “What it does is support biologists or conservation managers who understand what they’re looking for in a massive set of biological data like a genome, but don’t have the computing
working on sequencing
the bilby genome, which is
due to be published soon.
_______
number of native Australian species to
have had their genomes sequenced.
“That means the genomes for initially up to 50 threatened Australian species can be made publicly available through the TSI project and usable by anyone in science,” Carolyn elaborates. “In particular, the conservation community will be able to use the information held in those genomes to tackle critical biological and conservation issues.”
It’s not that this type of information hasn’t been available before. But accessing and using it has previously required the sort of computing grunt that’s only available in massive memory supercomputers at universities. Using that sort of technology doesn’t only take a high level of computer know-how but is also costly.
“Using cloud computing as we have now started to do allows you to manage not only a very tight research budget, but also how quickly you want the information,” Carolyn explains. In practical terms, what this means is that a research task that would have taken 10 days to complete can now be performed in as little as five hours for a cost of $25.
For whatever reason – perhaps because the TSI was launched during the height of the COVID-19 crisis, or because this work relies heavily on highly complex areas of computing and genetics – the significance of the project seems to have largely slipped under the public’s radar. But for conservation management in Australia, it’s potentially transformative.
“So we went to a massive computer company that has no idea about genomes or wildlife and they have really stepped up to help us,” Carolyn says. “They know technology and they know how they can process big data in a way that we could only have ever dreamt of.”
WHAT SORT OF practical ways can the information available in sequenced genomes be used to help threatened species? Already Carolyn has had success
The bilby is another target. Carolyn’s team has been working on sequencing the bilby genome, which is due to be published soon. The information contained in that has been put to good use already on projects to breed bilbies in captivity for release into fenced reserves in NSW, such as those at Pilliga and Mallee Cliffs, operated by the Australian Wildlife Conservancy, and Sturt National Park, overseen by the NSW government.
In other work, information in the koala genome, which was sequenced in 2018, is being used to understand why some koalas respond better than others to a vaccine against the chlamydia disease that’s been contributing to widespread declines in koala populations.
There’s also talk of genomic information being used to support the recovery of populations of the critically endangered Kangaroo Island dunnart, which was decimated during the 2019–20 bush-fires (see AG 156) and the plains-wanderer, a bird that’s become critically endangered due the clearing of its habitat (see AG 158).
“I think we are really now at a point in time in biology where we have all this amazing technology around to create a conservation legacy for Australia’s threatened species,” Carolyn says. “And I truly believe that’s what we have just embarked on.”
Beauty on the brink
IT’S JUST AFTER lunchtime, the morning rains have finally cleared and the sun begins breaking through the clouds. Max Breckenridge, a captive release project officer with BirdLife Australia (BLA) is slowly walking along a dirt road that cuts through a patch of untouched spotted gum–ironbark forest in the Lower Hunter Valley in New South Wales.
Lifeblood of the nation
Below the modern Brewarrina Weir in north-western New South Wales, a 2km bend holds the remains of this ancient structure, a complex of dry-stone walls and a site of engineering brilliance. Displaying advanced knowledge of river hydrology and fish ecology, the traps were designed to catch Murray cod, golden and silver perch and other fish, but allow breeding stock to pass through.
When a city rises
THAT FEBRUARY 2011 earthquake, which struck during the city’s lunch hour, was the most destructive in a series. It was the one that broke so many of the Central Business District’s verticals and horizontals – its buildings and the roads, sewers, water and gas pipes. It was shallow and ferocious. Its peak vertical ground acceleration of 2.2G (more than twice the acceleration of gravity) momentarily lifted parts of Christchurch to the sort of face-distorting speeds astronauts experience when they ascend into space.
Grantham’s road to recovery
IT WAS 10 JANUARY 2011 and once again it was pouring with rain. Queensland had already endured its wettest spring and December on record, and yet still the rain kept coming. I was working at the time as a freelance photographer for Queensland’s main newspaper, The Courier Mail. And weary of capturing “wet weather photos”, I’d decided to stay dry inside my Toowoomba office.
Conservation canine-style
IN 2004, THERE WAS no way David Williams, then an environmental science student at Deakin University, in Victoria, could have predicted the chain reaction a last-minute assignment submission would create. A paper he’d written outlined an environmental management plan that suggested using trained Maremma sheepdogs to protect little penguins from fox predation on Middle Island, off the coast of Warrnambool, in south-western Victoria.