How this scientist is using genome data to help save koalas

13 Oct 2021

Image: Carolyn Hogg

Dr Carolyn Hogg is part of a team of scientists making koala genome data available on AWS to help prevent the extinction of these marsupials.

While the climate crisis has created a whole host of problems for the planet, endangered species have to contend with many other challenges as well.

As well as the rising sea levels and more intense droughts, many species also have to worry about hunting or overharvesting from humans, as well as deforestation and pollution.

That’s where conservationists come into play, working from a wide range of disciplines towards a single goal to preserve future generations of biological life and ecosystems.

There are many ways to go about this. One of which is to integrate molecular genetics into real-time conservation management decisions.

Dr Carolyn Hogg is the senior research manager for the Australasian Wildlife Genomics Group at the University of Sydney and the science lead for the Threatened Species Initiative.

She has been working on the conservation of threatened species for more than 25 years, both in Australia and overseas and her career has taken her from studying whales in the North Atlantic to leopard seals in Antarctica.

‘No matter how much we fight to save species, there are some that we will lose’

However, she said the underlying theme to her career has been a keen interest in developing new methods and tools to answer key biological questions.

“It was this that led me to genetics. I had questions about how the founding animals in the Tasmanian devil insurance population were potentially related to each other and what were the consequences of this relationship to our long-term management strategy,” she said.

“This led me to working with Prof Kathy Belov at the University of Sydney. It took us about five years to answer this question simply because the genetic technology we needed was only being developed and, due to the low levels of genetic diversity with devils, we had trouble developing a tool that would work easily.”

Saving the koalas

Hogg’s latest project involves koalas. Earlier this year, it was said that koalas could soon be listed as endangered in parts of eastern Australia, and last month the Australian Koala Foundation revealed that 30pc of Australia’s remaining koalas have been lost in the past three years. This is mainly due to major bushfires as well as drought, heat waves and lack of drinking water.

Now, as part of an initiative to double the number of koalas by 2050, Hogg is part of a team of scientists making genome data from 450 koalas available on Amazon Web Services (AWS) with the aim of accelerating efforts to prevent their extinction.

The objective is to develop a map of koala genetic diversity from all over Australia. This will allow the researchers to understand how differences in the koala genomes allow them to live in different climates, eat different food, breed at different rates and survive or succumb to different diseases.

“We are making the data available to researchers anywhere in the world through the AWS Open Data Sponsorship Program. Genomes are a powerful tool that we are only just starting to utilise to their full potential in conservation management.”

While the team’s original plan was to release batches of 96 sequenced koala genomes onto AWS every six to eight weeks, Covid-19 has pushed that timeline back. However, Hogg said the first set of genomes is now available for researchers to access.

“This means that researchers globally can start working with the data for those specific koala populations immediately without having to wait for all the sequencing to be complete.”

Expanding the research

As well as helping researchers to better understand the biology and evolution of koalas, Hogg said the outcomes of the research could potentially be used by conservation managers to help make better decisions around how to protect the species.

Not only that, but this kind of research could even be used for other endangered or threatened species. “My colleagues and I used AWS Cloud in 2020 to generate genetic information for the management of the Tasmanian devil, an endangered Australian marsupial,” said Hogg.

“In addition, the Threatened Species Initiative is aiming to develop different genomic resources for a suite of Australia’s threatened species from plants to fish, amphibians, reptiles, birds and mammals. The project, launched in May 2020, has already generated resources for 62 species, which will be available on the AWS Open Data Sponsorship Program in future.”

She added that the more genetic diversity a species has, the greater its adaptive potential is – which is critically important in a changing world.

“We may not be able to afford the type of genomic work being undertaken on koalas for other species, but the tools we develop to understand the interplay between genome-wide diversity and functional diversity using the koala genome survey will have benefits for other species as we will have a new toolset which we can use for these species.”

A different kind of wilderness

While Hogg has been primarily focused on the threatened species of Australia in recent times, her career has also taken her to the extreme ends of the world.

In late 2019, she was part of an all-women expedition to the Antarctic Peninsula with the women in STEM initiative Homeward Bound. She said visiting such a pristine and remote wilderness was one of the most humbling experiences of her life and was both breathtaking and saddening at the same time.

“Although we were at the bottom of the Earth, the impacts of humans and climate change were obvious and it made me realise that there is nowhere left on Earth that is now untouched and that the pressure on the ecosystem from humans is ever increasing,” she said.

“It also brought home the reality that no matter how much we fight to save species, there are some that we will lose. My aim is to generate new tools to study and conserve species so my children and grandchildren have the opportunity to be filled with the wonder of nature, the same way I was.”

With the very real effects of the climate crisis continuing to press down on us as a society, I asked Hogg what the key message to the general public should be.

“That every one of us has the opportunity to make a difference by the choices that we make – from the food we choose to eat, to the clothes we choose to buy, to how we reduce, reuse and recycle,” she said.

“The policymakers and governments do not make decisions until pushed to do so by the general public – if we want to see things start to change, then we need to start making the change.”

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Jenny Darmody is the editor of Silicon Republic