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The mother of monsters chooses love not war

by Adele Gonsalvez

In Greek mythology, Echidna is known as the “mother of monsters” and is a feared half-woman/half-serpent. However, her possession of mammalian and reptilian traits may be the only similarity between her and her animal namesake. In fact, even when provided with all the weaponry for chemical warfare, the short-beaked echidna has opted for a different route.

The short-beaked echidna is one of five extant monotreme species, and as the evolutionary offshoot of mammals, monotremes possess a suite of unique and interesting features. From being egg-laying mammals to electroreception, the book on monotreme fun facts practically writes itself. One particularly cool feature of the monotreme lineage, is the possession of a crural system – a system used to deliver venom that consists of a hollow keratinous spur connected to a crural gland on their hind limbs. These spurs regress in female platypuses and echidnas but are retained in adult males of both species. The monotreme ancestor of the platypus and echidna also possessed this crural system and venom production. The ability to produce venom has been maintained in the platypus, who is one of only fifteen experimentally confirmed venomous mammals globally. Platypus venom is used by males against other male platypuses during the breeding season, to cause paralysis in their competition and give them a reproductive edge.

But the echidna?
Not so much.

Despite being gifted the capabilities of venom production from their monotreme ancestor, these walking pin cushions have chosen a less toxic approach to their sister lineage. Echidnas have instead repurposed their crural system to aid in chemical communication. The chemical cues produced assist their social interactions and help with mate attraction. Chemical communication is renowned across many taxa as a great tool for finding a buddy in the breeding season, and echidnas are known to use cloacal odours for this purpose as well. So yes, echidnas really did repurpose a system capable of paralysis and immense pain just to up their scent game.

Echidna spur secretions appear as a milky substance at the base of the spur (for males) or in the pit previously occupied by the spur (in females). Spur secretions also differ between the sexes, with a greater quantity and number of compounds found in those produced by males. And just like the seasonal upregulation of platypus venom, secretions produced by the echidna crural system are also upregulated during their breeding season.

So, add it to the list of fun facts: echidnas choose love not war. Even when handed the ancestral capabilities of venom production, the echidna has chosen a more peaceful approach to aid their reproductive fitness. Saying “no thanks” to being toxic and producing attractive chemical cues instead? I don’t know about you, but to me, that sounds like a monster of a good idea.


Author

Adele Gonsalvez  (PhD Student) is using a variety of ‘omics resources to investigate the unique genes, peptides and traits of Australia’s monotremes. This work particularly focuses on the characterisation and functional investigation of platypus venom and monotreme-specific genes, aiming to discover novel components and their functions to better understand these animals.


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Why do men exist?

by Soleille Miller

This remains one of the oldest unanswered questions in biology, pondered by the earliest philosophers in recorded history. Aristotle explored this very question in his seminal book “On the Generation of Animals”. While his theory (i.e. the male parent contributes the form and the female parent contributes the matter) leaves much to be desired, it marked the beginning of a long journey of discovery into the evolution of two sexes.

As a female, reproducing sexually comes with a whole list of costs. First, you have to find a mate — which takes time, uses resources, and increases your chances of becoming someone’s lunch. Then there are the physical costs of mating itself, which can hurt and potentially kill you (e.g. elephant seal mating, which sometimes results in the death of the female). And let’s not forget the genetic gamble: you’re diluting your genome with someone else’s, potentially disrupting a combination of alleles that made you successful in your environment. Asexual reproduction sidesteps all these costs. No need for a mate, no wasted energy, and every offspring is a full-genome copy. Plus, you’re not producing males that can’t reproduce themselves, which alone doubles your reproductive output. So, if sex is such a costly and risky strategy, why is it nearly universal across the animal kingdom?

This is the question I sought to address during my PhD. To add my own piece to this big evolutionary puzzle, I focused on a particularly fascinating native Australian stick insect called the Peppermint Stick Insect, Megacrania batesii. What makes this species so special is that it can successfully reproduce both sexually and asexually — a rare ability in the animal world. Out in the wilds of the Daintree Rainforest, this creates a patchwork of populations: some with both males and females reproducing the usual way, and others that have shifted to a more Amazonian-style existence (i.e. entirely female, reproducing without sex). For my PhD, I compared the ecology and genetics of these populations to figure out what actually happens — genetically and physically — when a species makes the switch to asexuality. By understanding what’s gained or lost in that transition, we can get closer to figuring out why sex is still so common in animals, despite all its costs.

What I found was that switching to asexual reproduction usually leads to a sharp and immediate drop in genetic diversity. Surprisingly though, this didn’t seem to affect the insects physically or reduce their reproductive output. In fact, most asexual populations in the wild appeared just as large, healthy, and happy as their sexual counterparts. However, this advantage may not last forever. In environments with stronger selective pressures — such as higher parasite loads or environmental stress — signs of physical damage from ectoparasites were more common in asexual populations compared to their sexual neighbours. It seems that the genetic diversity provided by sex might offer an edge in these tougher conditions, acting as extra ammunition in the evolutionary arms race against parasites. But in more stable, low-stress habitats — like peaceful beachside areas — the asexuals seemed to be doing just fine.

By exploring the evolutionary tug-of-war between sexual and asexual lineages of stick insects in the wild, we start to see a broader picture of why sexual reproduction persists, even in species like ours. It’s likely that sex gave our ancestors the flexibility to adapt to unpredictable and changing environments by generating more genetic variation for natural selection to work with. Without it, there would have been no Aristotle — or at least far fewer philosophers sitting around pondering why we have two sexes in the first place.


Author

Dr. Soleille Miller (Post-doc) utilizes genomic resources to aid the conservation of Australia’s most endangered bird species. Her work centers on understanding genomic diversity, with a focus on disease resistance in both wild and captive populations. Soleille has expertise in using population and evolutionary genomics to support the effective management of these threatened species.


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Imitation is the best form of flattery

by Iris Milligan

Nature often inspires innovation, with many of us looking to the natural world for solutions in our studies and beyond. This approach is known as biomimicry, and it’s commonly used in fields like architecture and structural engineering. For example, researchers have studied dragonfly wings for their unique design (cells by the name of nanopillars), which naturally prevents bacteria from attaching to the surface. This is also the case for Velcro, which was invented by Swiss engineer George de Mestral in 1941 after he removed burrs from his dog.

This research can be applied to not just the terrestrial realm but also the aquatic environment. We have already started this with Sharkskin-inspired swimsuits and tubercles for wind turbines. Marine mammals are similarly inspiring, such as with their blubber, which not only keeps them warm in frigid oceans but also acts like a natural buoyancy aid, allowing them to float effortlessly. Or their sheer sizes, with hearts so large they could fill a car and lungs capable of holding enough oxygen to dive deep for up to 120 minutes.

Humans have been able to train their bodies to hold their breath, with the longest hold being 24 minutes. Additionally, their ability to not only survive being deeply wounded by the propeller of a boat but heal within a few months—with nothing more than a scar—has been observed in several species. I doubt I would survive something like that without medical attention.

Before starting my PhD on wound healing in marine mammals I was aware of the basic injuries they suffer, but that they can heal and recover from even the most extreme damage shows how extraordinary they are.

Marine mammals have nailed life in the water, showing off some wild adaptations that let them dominate in harsh ocean environments. Low oxygen, high salinity, and freezing temperatures are just a few things they endure. Studying how marine mammals heal from such severe wounds could potentially revolutionize medical treatments for humans. By understanding the biology and mechanisms behind their remarkable recovery, we may uncover new ways to treat trauma, heal wounds faster, and even tackle bacterial resistance.

By imitating nature’s designs—whether it’s for improving materials or healing wounds—we can open new frontiers in science and medicine. After all, nature has had millions of years to perfect its designs, and by studying and emulating them, we’re simply giving credit where it’s due. As the saying goes, imitation is the best form of flattery.



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Academic Adventures to the Other Side of the Globe

by Luke Silver (Post-doc)

In August of 2024 I had the exciting opportunity to undertake a three-month research stay in the Institute of Evolutionary Ecology and Conservation Genomics at Ulm University. So how did this come about?

Professor Simone Sommer was one of my thesis reviewers and she reached out to Kathy and Carolyn with an opportunity to combine my skillset in genomes and MHC annotation with some newly generated bat sequences. So at the start of August, I departed Sydney for an almost 30 hour journey to the city of Ulm (about 1 hour west of Munich) in southern Germany. Upon arrival at Ulm train station, I was met by a postdoc Dr Dominik Melville who showed me to my accommodation for the next three months. With no German language knowledge, I headed to the supermarket and managed to annoy the person at the register by not pre-weighing my fruits and vegetables – just one of many times that having some German language skills would have come in handy.

The purpose of my visit was to manually annotate genes of a crucial immune gene family known as the major histocompatibility complex (MHC) in bats. These genes form molecules with are expressed on cell surfaces and are responsible for detecting self and non -self and presenting foreign pathogen derived peptides to other cells of the immune system. We were able to leverage the recently released data from phase 1 of the Bat1K project (a consortium that aims to sequence the genomes of all living bat species around the world).

I also managed to find time to sample plenty of the local delicacies of beer and pretzels  and to travel in the local area including to the beautiful Lake Konstanz, Stuttgart, Nuremberg, Vienna, Salzburg and Prague. This is just a small example of how science can lead to new and exciting experiences and opportunities.


Luke Silver

Dr Luke Silver’s research is focused on generating and using genomic and transcriptomic resources for threatened Australian species. He used these resources to investigate the evolution of the immune system and study how diversity within immune genes is linked to disease traits. He has experience in characterisation of complex immune gene families, in particular the major histocompatibility complex which is a key component of the adaptive immune system


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Making it through the final stretch of a PhD in conservation genomics and bioinformatics

by Holly Nelson (PhD Student)

Entering the final stage of a PhD is both a marathon and a sprint. After a quick 3-4 years of terminal windows, countless hours coding, latex gloves, tweaking plots to the perfect shade of maroon (#B03060), and obsessing over a turtle species that lives a world away, the world could be ending, and honestly, I wouldn’t even know.

One surprising obsession? Table spacing. Somehow, this has become the hill I’m willing to die on. Not to mention after three and a half years into postgrad education, I still don’t know whether it should be a comma or a semicolon. Who knew this was the pinnacle of academic thought? Shout-out to my colleagues who don’t blink when I send them scripts named things like “goNe_analysis__fix6_final_FINAL_v10.pbs” (you know who you are), and to my long-suffering supervisors who’ve received my manuscript drafts entitled “Manuscript_turtle_final_DEFSFinal4_v12.docx.” And Andrea—my fellow PhDer-in-crime who has joined me on the adventure. There’s something comforting in having a fellow office mate who reaches a delusion level just as unhinged as yours.

Honestly, perspective is nearly impossible when your days blur together into one big troubleshooting session, often caused by a stray space somewhere in a 94-line code. But at the end of the day the completion of a PhD is less about perfection or about how many pages are in pdf document you’ve spent years creating, and more about progress. My folders and directories may look like a chaotic labyrinth, but hey, they’re a testament to something resembling progress—90% of it’s stuff that would’ve looked like rocket science to me a couple of years ago. It’s about stepping back, handing in, disappearing, and leaving the pandora’s box of questions you opened during your thesis for the poor Honours student.

To anyone on the journey, hang in there. Or don’t, drop out and open a bakery if you feel like it. Either way, you’re not alone in those late-night bursts of productivity, never ending imposter syndrome, praying that the laptop you’ve run into the ground turns on every morning, or that compulsive need to move the plot legend just 0.5mm more to the left.

You’re the world expert in whatever obscure and niche little thing it is you do, even if no one, including you, fully understands it. Hold onto the fact that your work probably means something, and if it doesn’t, well, at least it’s given you something to do for the last few years.

As my daily reminder sticky-note says “it’s not that serious”.

Bilby release

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.

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From Cardiff to Maria Island

by Matt Spadaro

When I first arrived in Sydney from the UK, I had no idea which project I would be doing. I found out on my first day that I’d be making a stud book for the Maria Island devils- a place and a species that I was, admittedly, totally ignorant towards. Upon learning more about the two, my interest only continued to grow; when Carolyn asked me to go to the island which I had been learning so much about, I jumped at the opportunity.

Once I arrived on Maria, I realised just how special of a place it is. 10 minutes into my time, I had already seen my first Wombat and I had to take a picture despite it being dark- I had no idea that I would experience hundreds of wombat sightings over the course of the week (see below for better photos than my first).

After, we got everything sorted and began baiting the traps in the dark for the next day (for more information on how to catch a devil, see Elle’s post titled “How to catch a Tasmanian devil”).

In the morning, the processing of the devils commenced. Weight, teeth measurements, head size, pouch state (if the individual was female), number of parasites and general body condition were all taken during this processing of recaptured animals. New animals had all the preceding measurements taken with the additional processes of taking of an ear biopsy, inserting a microchip, and giving the devil a name.

As this process is quite an extensive experience for the devils, I was expecting their demeanour to be far from calm, especially when considering their given name of “devil”. Therefore, I was quite surprised when all of the first devils that we caught and processed were seemingly calm (although in retrospect many of them were likely terrified). This wasn’t the case for all devils though, with a few showing jaw popping behaviours and the low growling noises which they are well known for. Despite these exceptions, the vast majority of the devils we caught and released on Maria Island were either scared or tired, making them very easy to process.

I learnt during this trip that devils, somewhat unsurprisingly, hate the noise of anything they don’t recognise. They don’t mind the noise of your voices when speaking but they find any noise of fabric rubbing together, clanking of buckets and the sound of the bristles on brushes when they’re being used very distressing. I also learnt that devils have been a victim of a degree of fake news- not all devils have the distinctive white markings that you see on the internet. Many of the devils we processed were completely black or almost completely black (see below photos).

After-thought-

If you’re considering visiting Australia from abroad and you’re interested in seeing wildlife and nature- go to Maria Island. Maria Island is teeming with wombats, Bennet’s wallabies, sea eagles, forester Kangaroos and more. It also has the most pristine air and ocean water of anywhere I’ve visited. The landscapes are incredible, you really cannot go wrong with a visit to this Island if you’re interested in the outdoors. 

Author

Matt Spadaro

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How to catch a koala

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.

Can you spot the Koala in the trees?

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.

Koalas in trees

Author

Luke Silver

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.

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

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.

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.

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.

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.

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).

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

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IT’S MOVING DAY: Threatened Species Edition

by Andrea Schraven (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.

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Australia’s best kept secret: the dunnart

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!