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From Cardiff to Maria Island

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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

The Conversation: Strong progress – from a low base: here’s what’s in NSW’s biodiversity reforms

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Professor Carolyn Hogg from the Faculty of Science at the University of Sydney, Jaana Dielenberg from Charles Darwin University and Professor Hugh Possingham from the University of Queensland discuss the NSW Government’s proposed major overhaul of the Biodiversity Conservation Act.

Find the full article here: https://theconversation.com/strong-progress-from-a-low-base-heres-whats-in-nsws-biodiversity-reforms-234917

Australia’s ‘Easter bunny’, the bilby, has had its genome fully sequenced

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Under pressure from predatory foxes and cats and competing with feral rabbits, the Greater bilby has lost more than 80 percent of its habitat. Conservation work led by Professor Carolyn Hogg is designed to help save the bilby from extinction.

Read the full article here: https://www.sydney.edu.au/news-opinion/news/2024/07/01/australia-greater-bilby-genome-sequenced-marsupial-conservation.html

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How to catch a koala

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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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Genomic insights into the critically endangered King Island scrubtit

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Type: Journal Article

Reference: Crates, R., von Takach, B., Young, C.M., Stojanovic, D., Neaves, L., Murphy, L., Gautschi, D., Hogg, C.J., Heinsohn, R., Bell, P. and Farquharson, K.A., 2024. Genomic insights into the critically endangered King Island scrubtit. Journal of Heredity, p.esae029. https://doi.org/10.1093/jhered/esae029

Abstract

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

Characterisation of defensins across the marsupial family tree

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Type: Journal Article

Reference: Peel, E., Hogg, C. and Belov, K., 2024. Characterisation of defensins across the marsupial family tree. Developmental & Comparative Immunology, p.105207. https://doi.org/10.1016/j.dci.2024.105207

Abstract

Defensins are antimicrobial peptides involved in innate immunity, and gene number differs amongst eutherian mammals. Few studies have investigated defensins in marsupials, despite their potential involvement in immunological protection of altricial young. Here we use recently sequenced marsupial genomes and transcriptomes to annotate defensins in nine species across the marsupial family tree. We characterised 35 alpha and 286 beta defensins; gene number differed between species, although Dasyuromorphs had the largest repertoire. Defensins were encoded in three gene clusters within the genome, syntenic to eutherians, and were expressed in the pouch and mammary gland. Marsupial beta defensins were closely related to eutherians, however marsupial alpha defensins were more divergent. We identified marsupial orthologs of human DEFB3 and 6, and several marsupial-specific beta defensin lineages which may have novel functions. Marsupial predicted mature peptides were highly variable in length and sequence composition. We propose candidate peptides for future testing to elucidate the function of marsupial defensins.

Reinforcements in the face of ongoing threats: A case study from a critically small carnivore population

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Type: Journal Article

Reference: McLennan, E.A., Cheng, Y., Farquharson, K.A., Grueber, C.E., Elmer, J., Alexander, L., Fox, S., Belov, K. and Hogg, C.J., 2024. Reinforcements in the face of ongoing threats: a case study from a critically small carnivore population. Animal Conservation. https://doi.org/10.1111/acv.12945

Abstract

Reinforcements are a well-established tool for alleviating small population pressures of inbreeding and genetic diversity loss. Some small populations also suffer from specific threats that pose a discrete selective pressure, like diseases. Uncertainty about reinforcing diseased populations exists, as doing so may increase disease prevalence and disrupt potential adaptive processes. However, without assisted gene flow, isolated populations are at high risk of extinction. Tasmanian devils (Sarcophilus harrisii) are a useful case study to test whether reinforcements can alleviate small-population pressures where there is an ongoing disease pressure. We investigated demographic, genome-wide and functional genetic diversity, and disease consequences of reinforcing a small population (<20 animals) that was severely impacted by devil facial tumour disease. Released animals from one source population successfully bred with incumbent individuals, tripling the population size, improving genome-wide and functional diversity and introducing 26 new putatively functional alleles, with no common alleles lost and no increase in disease prevalence. Results suggest, in the case of Tasmanian devils, reinforcements can alleviate small-population pressures without increasing disease prevalence. Because no common functional alleles were lost, it is likely that any adaptive processes in response to the disease may still occur in the reinforced population, perhaps even with greater efficiency due to reduced genetic drift (due to larger population size). Our study is presented as a comprehensive worked example of the IUCN’s guidelines for monitoring reinforcements, to showcase the value of genetic monitoring in a richly monitored system and provide realistic approaches to test similar questions in other taxa.

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

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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

Tasmanian devil (Sarcophilus harrisii) gene flow and source-sink dynamics

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Type: Journal Article

Reference: Schraven, A. L., Hogg, C. J., & Grueber, C. E. (2024). Tasmanian devil (Sarcophilus harrisii) gene flow and source-sink dynamics. Global Ecology and Conservation, 52, e02960. https://doi.org/10.1016/j.gecco.2024.e02960

Abstract

Increased access to genetic data has substantially improved how we manage threatened species. The Tasmanian devil (Sarcophilus harrisii) is listed as endangered due to the ongoing threat of a highly contagious cancer, devil facial tumour disease (DFTD), causing more than 80% population reductions. To assist future management interventions (e.g. releases into wild sites) we expanded upon previous studies of gene flow for the devil by assessing more recent and broad-scale patterns. We use genome-wide single nucleotide polymorphisms generated via DArTSeq across 21 devil sites to delineate source-sink dynamics across the species’ range. Our findings revealed gene flow is stronger on the northeast and central regions of Tasmania, with high rates of bidirectional gene flow among central sites. The northwest exhibits weaker connectivity relative to other regions of Tasmania, while gene flow appears to be non-existent between the southwest and other areas. Northeast coastal sites tend to serve as ‘sources’ for inland central sites, whereas gene flow appears restricted to the coastline in the northwest. These results are consistent with genetic structure of devil sites and spatial spread of DFTD, which has yet to arrive in the southwest region of Tasmania. Southwest isolation is probably due to mountain ranges and lack of roadways. Interestingly, some waterbodies did not appear to restrict devil movement among sites. Conversely, areas of high elevation act as apparent barriers, as evidenced by limited gene flow observed between eastern and western sites. Integrating source-sink dynamics into conservation management planning will be crucial in developing effective strategies to safeguard the Tasmanian devil and other threatened species facing similar threats (i.e. disease, habitat loss).

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IT’S MOVING DAY: Threatened Species Edition

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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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