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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

Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides

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Article: Journal article

Reference: Gilding, E.K., Jackson, M.A., Nguyen, L.T.T. et al. Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides. Nat Commun 15, 6565 (2024). https://doi.org/10.1038/s41467-024-50742-x

Abstract

The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides.

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

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Type: Journal article

Reference: Hogg, C.J., Edwards, R.J., Farquharson, K.A. et al. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8, 1311–1326 (2024). https://doi.org/10.1038/s41559-024-02436-2

Abstract

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

The future is here: an easy-to-use toolkit for integrating genetics into conservation management

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Type: Journal article

Reference: Hogg, C.J., Farquharson, K.A., Brandies, P., Silver, L.W., Ottewell, K., McLennan, E.A., Richmond, S. and Belov, K. (2025), The future is here: an easy-to-use toolkit for integrating genetics into conservation management. Anim Conserv, 28: 93-103. https://doi.org/10.1111/acv.12971

Abstract

Over the past decade, the development of genetic and genomic tools for conservation management has come forward in leaps and bounds. Once considered a ‘nice to have’, genetic data are fast becoming an essential tool for informing and managing translocations. However, due to the complexity of the field, easily using genetic data for decision-making and monitoring remains beyond the reach of most managers and conservation biologists. In May 2020, we launched the Threatened Species Initiative (TSI), a programme designed to generate genomic resources for Australia’s threatened species. Critical to the project is not only the generation of reference genomes and population genetic data but an online toolkit for conservation managers. The toolkit is a ‘one stop shop’ from collecting samples, to generating and analysing genetic data, to an easily interpretable genetic management report. A series of workflows and pipelines have been developed, including the TSI Biodiversity Portal, that uses point and click web interfaces to easily transfer raw sequence data and assemble genomes, transcriptomes and soon population genetics for management decisions. Here we present how the current toolkit works and provide case study examples for how it is being used to inform translocations and the management of threatened species.

Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II

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Type: Journal article

Reference: Luke W Silver, Carolyn J Hogg, Katherine Belov, Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II, Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae156, https://doi.org/10.1093/gbe/evae156

Abstract

The major histocompatibility complex (MHC) plays a vital role in the vertebrate immune system due to its role in infection, disease and autoimmunity, or recognition of “self”. The marsupial MHC class II genes show divergence from eutherian MHC class II genes and are a unique taxon of therian mammals that give birth to altricial and immunologically naive young providing an opportune study system for investigating evolution of the immune system. Additionally, the MHC in marsupials has been implicated in disease associations, including susceptibility to Chlamydia pecorum infection in koalas. Due to the complexity of the gene family, automated annotation is not possible so here we manually annotate 384 class II MHC genes in 29 marsupial species. We find losses of key components of the marsupial MHC repertoire in the Dasyuromorphia order and the Pseudochiridae family. We perform PGLS analysis to show the gene losses we find are true gene losses and not artifacts of unresolved genome assembly. We investigate the associations between the number of loci and life history traits, including lifespan and reproductive output in lineages of marsupials and hypothesize that gene loss may be linked to the energetic cost and tradeoffs associated with pregnancy and reproduction. We found support for litter size being a significant predictor of the number of DBA and DBB loci, indicating a tradeoff between the energetic requirements of immunity and reproduction. Additionally, we highlight the increased susceptibility of Dasyuridae species to neoplasia and a potential link to MHC gene loss. Finally, these annotations provide a valuable resource to the immunogenetics research community to move forward and further investigate diversity in MHC genes in marsupials.

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

Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females

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Type: Journal article

Reference: Ockert, L.E., McLennan, E.A., Fox, S. et al. Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females. Sci Rep 14, 15188 (2024). https://doi.org/10.1038/s41598-024-66097-8

Abstract

Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female’s pouch, pouch young skin, and through the milk, are thought to boost the neonate’s immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.

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.

LukeSilver20