How to catch a koala

Posted on 6 June 2024 by admin

by Dr. Luke Silver

Until recently, the majority of research in the Australasian Wildlife Genomics Group occurred on the Tasmanian devil and trapping these marsupial carnivores is quite a straightforward process. Setting a trap overnight baited with a tasty piece of fresh meat to lure the devils inside. Recently, I was lucky enough to be invited to Kangaroo Island to help out on a koala field trip. It turns out trapping herbivorous marsupials is a far more demanding task as unfortunately you cannot lure a koala with a fresh branch of Eucalyptus leaves.

Firstly, you have to actually find the koala in their environment, which can range of extremely tall Eucalyptus trees to highly dense shrubbery regions of bush. Fortunately, n Kangaroo Island koalas are so numerous locating one is not as difficult a task in areas such as NSW and QLD where koala numbers a much lower. After finally locating a koala the real work begins, coaxing the individual out of its comfortable and safe perch within the tree. This is best achieved by using an extendable pole with a piece of fabric attached to the end and simply waving this in front of the koala, who in ideal circumstances slowly backs down the tree trunk to height where they can be captured. Often, this is not the case, with koalas using any avenue possible to escape, including jumping to another nearby branch or tree. Being able to go into the field and see the animals we work up close is just one of the perks of working in wildlife research.

Author

Luke Silver (PhD Student) is using genomic data to
investigate immune genes in Australian marsupials with a focus on koalas where he is using resequenced genomes to examine patterns of diversity in functional and neutral regions of the genome across the entire east coast of Australia. This work will be used to inform conservation and management decisions in the fight to save our threatened species.

LukeSilver20

The error in your way: a beginner’s guide to troubleshooting command error messages

Posted on 7 May 2024 by admin

by Adele Gonsalvez

As a bioinformatic newbie, there is a lot to wrap your head around – from understanding basic programming language to what commands you need to use. In my experience, one particular gem is when you are trying to run a command and you receive one in a series of often uninformative error messages. Troubleshooting will end up dominating your time when you are doing any kind of coding, and it can be incredibly frustrating. So, instead of swearing at your computer (although that can be therapeutic at times), here’s some handy tips I’ve picked up that can be more effective in addressing that pesky error message.

Simple spell check

It may seem like a minor issue, but in my experience most command errors come from typos, and they can be tricky to spot. Step through your command or script to ensure there aren’t any spelling mistakes or extra spaces at the end of commands. Also ensure file paths are correct, and input files exist and are correctly named.

Have a chat with ChatGPT

ChatGPT is an incredibly useful tool for troubleshooting both error messages and general command generation. Specifying the error code, ChatGPT can outline the various causes for that error message and suggests how to go about addressing the issue.

Take a break

Leave it for a couple hours. The human version of “Did you try turning it off and on again?”. Like any form of editing, if you have been staring at the same bit of text for too long, it is easy to gloss over misspelt words or extra spaces. Revisiting it later can help you find issues that you previously overlooked.

Phone a friend

Ask your co-workers to look over your command or script. It’s likely that some of them will be more experienced in bioinformatics and can shed some light on what’s going wrong. Even if none of your coworkers are familiar with coding, a fresh set of eyes can often spot little mistakes much better than your own. I once spent hours trying to solve an error in a script, which only took for my friend 30 seconds to solve (it was an extra space at the end of a command).

Happy troubleshooting!

Adele Gonsalvez (2022 Honours Student) is investigating the expression and the antimicrobial activity of defensins from the platypus and short-beaked echidna

IT’S MOVING DAY: Threatened Species Edition

Posted on 9 April 2024 by admin

by Andrea Achraven (PhD Student)

Moving house, city, or country always has its challenges, from adapting to a new environment to establishing connections with unfamiliar neighbours. For threatened species, the concept of moving from one area to another is no less daunting.

However, in the realm of conservation management, ‘moving day’ can be the difference between survival and extinction of endangered animals. Translocations are defined as the “intentional movement of living organisms from one are to another” by the International Union for Conservation of Nature (IUCN), and they represent a strategic effort to give struggling species a fighting chance.

Translocations come in many forms, each serving a unique purpose in species conservation management:

Re-introduction involves moving individuals back in areas where they use to exist but have disappeared, thereby giving them a second chance to thrive in their historical habitat.
Reinforcements help already existing populations of a species that are currently struggling by moving in additional individuals from another population to boost their chances of persisting.

Assisted Colonisations will introduce a species to a new and suitable habitat where they can establish themselves, often occurring when a species is unable to survive in its original habitat.

Releasing Tasmanian Devil on Maria Island, Australia. © Luke Silver

Deciding on where to move a species to is more than just merely picking the best house in the neighbourhood. Managers of a species must carefully consider numerous factors when choosing their new home. This includes evaluating the availability of resources, identifying potential threats that may jeopardize long term sustainability, and understanding behavioural dynamics such as competition among individuals.

Moreover, determining the effectiveness of translocations necessitates continued monitoring and assessment after the release. Population viability in the long term requires documenting a translocated individual’s ability to acclimate to their new environment and monitoring their survival. Additionally, managers need to monitor the reproductive output and analyse population growth trends to determine if the population is sustainable, or if continued interventions are required.

So next time you here about a species being relocated or released into the wild, remember – it’s not just a new home, but a translocation that could be a potential lifeline for the survival of an entire species.

Author

Andrea Schraven (PhD Student; co-supervised with Dr Catherine Grueber) is projecting the long-term impacts of supplementation to improve the status of wild Tasmanian devil populations with the ongoing threat of DFTD. By evaluating population genetic and fitness data before and after translocations, she is comparing how populations change over a few generations, and then feeding the data into computational models to simulate “evolutionary time”. The results will directly inform conservation management decisions for the species long-term recovery.

Andrea_Schraven

Australia’s best kept secret: the dunnart

Posted on 5 March 2024 by admin

by Kiara Jones (Honours Student)

Since starting my Honours research project last year, the question I have been asked the most is: “What is a dunnart? How have I never heard of this adorable Australian native?”

These little predators resemble a small European mouse, but they are actually marsupials and therefore more closely related to the kangaroos and koalas than they are to any mouse. During their breeding season, their teeny-tiny pouch that can change from being the size of a tic tac, to being packed with 8-10 dunnart joeys within just a few weeks. There are nineteen known dunnart species found across Australia, in a variety of habitats such as woodlands, dry sclerophyll forest, grasslands and deserts. The fat-tailed dunnart is widespread and found in most of inland Southern Australia, and this is the species involved in my research. But don’t be disheartened – these cute creatures are of minimal conservation concern. Dunnarts are a great animal model for research and are instead being used to help us better understand marsupial biology.

So, it sounds like dunnarts are found practically everywhere and you may find yourself wondering a new question: “Why haven’t I seen them or heard of them before?” Firstly, like most members of the Dasyuridae family, dunnarts are nocturnal. They emerge at nighttime to hunt down their prey, feasting on crickets, beetles, spiders, lizards, and even small frogs. Although they may be a scary predator to some smaller species, dunnarts are the perfect meal for larger predators like birds, feral foxes, and cats. This means that during the day, they’ll often be tucked away in hollow logs or nesting in clumps of tall grass where they can be well-hidden. For these reasons, it’s unlikely that you’ll see a wild dunnart unless you’re actively looking for them. And if you do accidentally disturb a nesting dunnart on your weekend hike, it’ll probably scurry away so quickly and quietly that you wouldn’t even notice.

Dunnarts also exhibit a cool behaviour called ‘torpor’, which is like hibernation’s younger cousin. Torpor is a physiological adaptation that helps the animal conserve energy. In torpor, metabolic rate and body temperature drops significantly and they become as still as a statue. Interestingly, dunnarts often rely on the external environment to bring them out of torpor. For example, some may position themselves in a spot (such as a rock crevice) where they know the sun will hit. That way they can time the end of their torpor and warm their body back up without requiring any effort. But they have to be careful to get moving quickly, because that direct sunlight will make them especially vulnerable to a soaring predator overhead!

When Cells Rebel: the dark side of evolution

Posted on 15 February 2024 by admin

by Patra Petrohilos (PhD Student)

I love dystopian horror. I love to relish in the thrill of disgust from the comfort of safety – a comfort bolstered by the knowledge that such grotesquerie could never actually happen in real life. Zombies don’t exist. Monsters aren’t trying to escape from the underworld. Cancer isn’t contagious. Actually, maybe scratch that last one. . .

You see, nature may not have the imagination of Stephen King, but it does have something even more powerful in its arsenal: mutations. Mutations are to evolution what creativity is to horror writers – the raw material that allows them to conjure up new and wondrous forms. From the most beautiful (buttercups, butterflies, butter yellow bumblebees) to the most horrific (flesh eating bacteria, pandemic inducing viruses, cancer cells).

Evolution favours the fittest individuals, be they butterflies or bacteria. In this case, “the fittest” just means the ones that are most successful at reproducing. If we are talking about koalas, reproduction means making cute little baby koalas. Everyone likes those. But when we’re talking about cancer cells, reproduction means growing and spreading and killing one’s host. Nobody likes that. Even the cancer cells probably wouldn’t like it – because killing their host also means killing themselves in the process. Kind of like a suicide bomber without the political motivation. But evolution is blind to morality and selects for the cute little baby koalas and murderous cancer cells equally – whatever is most efficient at making more copies of itself. Survival of the fittest.

Mutations are constantly arising in nature. Sometimes these make more successful versions of things, sometimes less successful. It’s a bit of a trial-and-error process. And somewhere in that trial-and-error process, a handful of cells have stumbled across the secret to become the most successful cancer cells ever. Super-cancers! How? By finding a sneaky way around that whole unfortunate dying-when-your-host-dies bit.

They do this by taking a leaf out of the life history book of parasites. Like cancer cells, many parasites are reliant on a host to survive. But unlike cancer cells, many parasites have the power to survive the death of their host by simply finding a new host – a power that evolution has also bestowed upon these super-cancers.

Yes, nature has managed to take one of the most awful diseases known to humanity and done perhaps the only thing that could make it worse. It has made it contagious.

Thankfully, such contagious super-cancers are mercifully rare and none of them affect humans (yet). But the rest of the animal kingdom has not fared quite so well. Leukaemia cells drift through the sea like hidden assassins, spreading from one unsuspecting clam to the next. Dogs can get mushroom shaped tumours on their penises from sex with a poorly chosen partner. And one of our most iconic Australian animals, the Tasmanian devil, is at risk of extinction from not only one but two contagious cancers (creatively named Devil Facial Tumour Disease 1 and Devil Facial Tumour Disease 2). Sometimes lightning really does strike twice.

The good news is, this is where we come in. By researching Devil Facial Tumour Disease – one of the most uniquely horrifying and bizarre diseases to ever arise – we aim to understand how it works, how it spreads, how it evolves and, hopefully one day, how we can stop it.

Follow me for more fun and uplifting facts about the animal world!

Author:

Patra Petrohilos (PhD Student) is researching the evolution of devil facial tumour disease (DFTD). By investigating anticancer properties of naturally occurring peptides, she is aiming to identify novel agents with therapeutic potential against DFTD. Patra Petrohilos is a PhD student with the Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science (CIPPS). Follow their exciting research at https://cipps.org.au.

patra_petro

How to catch a Tasmanian devil

Posted on 15 August 2023 by admin

by Dr Elspeth McLennan (Post-doc)

Tasmanian devils are nocturnal. We set traps during the day and overnight curious devils will come to investigate. The traps we use are made of strong PVC plastic fashioned into a cylinder with a spring trap door (see cover picture). The traps are baited with a devil’s favourite treat, a piece of fresh lamb or wallaby. The meat is tied onto the end of a string, fed through the trap, and tied to a pin which holds the door open.

When a devil comes investigating the smell of the meat, they walk to the end of the trap and take the bait. When the meat is pulled and eaten, the pin holding the door open is pulled free and the door swings shut. A second pin slides forward as the door closes and locks it. Devils spend the night in a cosy enclosed space with a full belly. The field biologists begin checking the traps as soon as the sun is up. As its daylight, we often find devils snoozing in their traps.

To perform a health check on the devil, we place a hessian sack over the opening of the trap, gently tilt the trap and the devil slides forward into the sack. The sack is used to keep the devil’s eyes covered to keep them calm making them easier to handle while we check them over. We take their weight, check their body condition, look for wounds and record pouch young in females. For populations suffering from devil facial tumour disease (DFTD), the disease status of each animal is also recorded. Once the devil has been processed, they are released. On a single trapping trip, we will often see the same devils a few times. The free food and somewhere to crash is clearly a good draw.

Author

Dr Elspeth McLennan (Post-doc) is working the on the Koala Genome Survey, investigating both neutral and functional diversity across the koala’s range to better understand the impacts of a changing climate. Elspeth has expertise in conservation genetics and using translocation and assisted colonisations as a conservation management tool.

@ellemclennan

Koalas and Chlamydia: How can genomics help?

Posted on 15 July 2023 by admin

by Luke Silver (PhD Student)

The mention of a koala infected with Chlamydia will often be met with rounds of laughter or even concern, “can I get Chlamydia from touching a koala?” For koalas, Chlamydia is no laughing matter with up to 100% of individuals in some populations infected with the bacteria. In many cases infection will lead to blindness, “wet bottom” as a result of bladder infection, infertility and eventually death. Unfortunately, unlike humans, koalas are unable to go to the doctor and receive treatment for the infection. Often koalas are taken to veterinary hospitals after a human interaction (such as vehicle strike or a dog attack) and it is there the infection is noticed and treatment can be administered.

Genomics is the study of the genes and nucleotides contained within an individual’s genome. By studying the genomics of koalas, we have been able to identify important genes which play a vital role in helping a koala clear a Chlamydia infection. One of these genes is a part of the major histocompatibility complex, or MHC, known for its vital role in recognition of pathogens. We are now using the whole genomes of over 400 koalas to investigate how diverse the MHC genes of koalas are across their entire range from northern Queensland to South Australia. A high level of genetic diversity in the MHC results in an individual or population being able to recognise a wider array of pathogens and may be linked to the health of this endangered marsupial. Scientists in other labs are attempting to develop a vaccine which can prevent koalas from contracting the infection in the first place which has shown promising results in early phase testing.

Finally, fortunately you are unable to catch Chlamydia from holding or touching a koala as the species which infects koalas is different from the species which infects humans.

Author

lukesilver20

Making bioinformatics more accessible

Posted on 15 June 2023 by admin

by Dr. Kate Farquharson (Post-doc)

In the AWGG lab, we are generating genomic resources for diverse Australian vertebrates, including birds, marsupials, amphibians and reptiles. However, following bioinformatics instructions can sometimes feel a bit like this:

And for non-model organisms, it can feel like being asked to draw an owl when you don’t even know what one looks like (or worse, imagine being given a picture of a human as a reference point). So, how do we make bioinformatics more accessible to people getting started? We have been working hard to carefully document our in-house workflows and contribute to public how-to guides, such as the Genome Assembly with Galaxy guide.

Documenting your work not only helps others but can be a useful way to remember what you have done before! Good documentation can help you to train others, present your methods and ensure your analysis is reproducible. Some tips for documenting your work include:

Always keep track of the software and versions used
Try out an editor such as Visual Studio Code, which allows you to easily insert code and scripts and integrates well with Github
Don’t forget your science brain! It can be very easy to follow a tutorial from start to finish but have no idea what the end result means. A few sentences to justify your approach and explain how you interpret your results will help others use your guide correctly

Good documentation is just one step we are working on as part of the Threatened Species Initiative and ARC Centre of Excellence in Peptides and Protein Science to make genomics and bioinformatics more accessible to conservation end-users.

Author

Dr Kate Farquharson is a Postdoctoral Research Associate in Bioinformatics within the ARC Centre of Excellence for Innovations in Peptide & Protein Science. She applies bioinformatic approaches to the assembly and annotation of genomes and transcriptomes of Australian species to identify targets for peptide discovery. Kate completed her PhD in the AWGG lab in 2020, where she used statistical and molecular genetic approaches to investigate adaptation to captivity in conservation breeding programs. Kate specialises in synthesising, analysing and interpreting data, and in communicating results clearly to a range of audiences.

@FarquharsonKate

My Favorite Culture Shock: Australia’s Wildlife

Posted on 15 May 2023 by admin

by Meadhbh Molloy (PhD Student)

I remember when I learned about the Tasmanian devil and DFTD in my Conservation Medicine textbook as a new master’s student in Virginia, USA. Since I was a child, I loved learning about different animals from all over the world but admittedly, I did know little about the Tasmanian devil. I was inspired by the many amazing researchers that were working on their conservation. I kept thinking about the Tasmanian devil throughout my master’s program and thought that maybe…I can go to Australia…and research Tasmanian devils as well for my PhD (I remember my first Zoom meeting with Carolyn…I was so excited!). After many more Zoom meetings, proposal drafts, a scholarship offer (thank you American Australian Association!), and a pandemic, I finally arrived in Sydney in August 2022. While I was eagerly looking forward to the first time I would see a Tasmanian devil, I have some honorable mentions of the other wildlife I have seen.

The mammals. This is my favorite taxonomic group, so I was most excited to see the mammals of Australia. I’ve seen potoroos scampering about, fruit bats flying at dusk, koalas at a sanctuary in Brisbane, an echidna crossing the road near Royal National Park, and of course the iconic kangaroo grazing right by my camping site in Jervis Bay. The Virginia opossum is our only native marsupial in North America. I was delighted to see brushtail possums (the arguably cuter cousin) in trees and sidewalks in the city, and digging through our food while camping. We also have a mammal that likes to dig through our stuff at campsites- the American black bear. It’s ok! You can put all your food up in a “bear bag” and it (mostly) helps.

The spiders. When I was researching my move to Australia, I came across a blog post titled “Every American remembers their first huntsman spider”. I thought “oh, well I’ll be in a city, they probably don’t get that big, assuming they are even there!”. Wrong. Listen, I appreciate spiders and their ecological role. I know they are probably “more scared of me than I am of them”. That does not mean I was calm and collected when I saw my first huntsman on the bathroom floor. Back at home we have big spiders (mainly wolf) that roam around, but they are no match for a huntsman’s speed! While I’m still a little scared of spiders, my definition of what a large spider is has certainly changed.

All the birds! It’s hard to pick a favorite Australian bird, but I would have to go with the kookaburra (even though one stole the sausage right out of my hands at a barbecue). The first time I heard one, it was 5:30am and I thought a monkey was outside my apartment window. We also don’t have wild parrots where I am from, so my phone is now filled with photos of beautiful white cockatoos and rainbow lorikeets. I remember going on a walk around my new neighborhood within the first few days of arriving. I saw a magnificent bird and told my roommate, Kimberley, about it when I returned. The bird had long legs, a beautifully contrasting white and black body, and was strutting around a park. Upon showing her a photo she said “oh yeah, a bin chicken”. A bin chicken? Not the nicest name. I now understand why they are called that.

I’ve seen many other amazing animals while traveling around Australia, including saltwater crocodiles near Port Douglas, stunning marine life while snorkeling at the Great Barrier Reef, and even a camel when I visited Uluru (it was well-timed that I read “Tracks” by Robyn Davidson before my trip). I happened to feel particularly homesick when I went to Taronga Zoo on a nice spring day, only a couple months after I landed in Sydney. I arrived at the enclosure that I was most excited to see. I have waited a long time to come to Australia, and The Tasmanian devil has morphed from being the topic of one of my research chapters, to being a symbol of resilience and patience for my entire PhD. Immediately, the Tasmanian devil got up from a shady spot and walked across the enclosure to lie down in front of me. Did this little devil know it would be the first devil I would see in person, and knew the weight of this moment? Obviously not, it just wanted to sunbathe. Of all the animals I have seen so far, the Tasmanian devil remains to be my favorite. I look forward to seeing more of Australia’s wildlife before I return to the United States.

Author

Meadhbh Molloy (PhD Student) is characterising the gut microbiome profile of Tasmanian devils at multiple locations across Tasmania

@MeadhbhMolloy

What my PhD has taught me: Turtles are awesome

Posted on 15 April 2023 by admin

by Holly Nelson (PhD Student)

So, you probably think Tasmanian Devils are adorable and Koalas are super cute. Well, let me tell you about turtles and four quick reasons why they’re awesome.

Person holding turtle - Shane Ruming NSW DPE

1. Free rent: Imagine having a portable, self-contained home acquired at birth, the Sydney housing market would be the least of your worries. Unlike hermit crabs, the shells of these little keratin caravans are an extension of their spine and are the equivalent of a ribcage.

2. Solar panel: A turtle’s shell is more than its home. Not only is it a protective barrier against predators, turtles also use it to synthesise vitamin D from UV light which is needed for bone and shell growth. Not only this, turtles have nerve receptors in their shells, making them suckers for butt scratches.

3. Mixed signals: If you’ve ever seen a turtle slapping another turtle, one word, foreplay. Yes, turtles slap each other’s faces to convey affection and to attract a mate. A male turtle will slap a females face multiple times to make it clear he digs her. No mixed signals in the turtle world.

4. Realer than Jurassic World: Who needs CGI when you have real life dinosaurs still roaming the earth? These little guys date back over 220 million years to the time of the dinosaurs – woah! So don’t waste your time watching the new Jurassic world movie (wasn’t that good anyway), enjoy some turtle videos instead.

Although there’s a never-ending list of intriguing facts about turtles, hopefully one of these points has made you appreciate these underrated little critters a bit more.

Author

Holly Nelson (PhD Student) is working on how we can use genomics to revolutionise threatened species management. From genome assembly to downstream analyses using whole-genome data, Holly is using her work to answer genetic questions on the Bellinger River Snapping Turtle, Koala, and other threatened species. Her work, in partnership with the NSW Governments Saving Our Species program, aims to create more robust conservation strategies that can be developed and applied together with wildlife managers.

@hollyvnelson