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Baby’s First Big Conference: SMBE 2024 in Puerto Vallarta

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by Toby Kovacs

One of the most exciting (and nerve-wracking) milestones in a PhD is dressing your project up, which is often still a little rough around the edges, for a presentation at an international conference. While I’d previously attended several local Australian meetings, last year I had the first opportunity to take my work global at the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE) in Puerto Vallarta, Mexico. It was daunting, inspiring, tiring and fun all tied into one, but I’ll try and summarise some of the highs and lows.

After scouring the internet for conferences that were relevant, logistically feasible, and ideally located somewhere with good food (and maybe some tequila), I settled on SMBE. After applying, I was nervously hoping to have my abstract accepted as a poster presentation. SMBE hosts large daily poster sessions, where over a hundred students and researchers present the beautiful lovechild of their scientific insights and graphic design passion. However, these plans were thwarted when I was *upgraded* to a symposium talk. I knew this was going to really test my public speaking confidence. However, choosing SMBE came with some added bonuses: my supervisor and a fellow PhD student attended too, providing invaluable support throughout the week.

From the outset, the scale of the conference was slightly overwhelming. On day one, we took the shuttle from our hotel to the convention centre and wandered around to get our bearings. I accidentally walked into the main hall, a cavernous space big enough to seat the entire conference, believing it was the venue for my talk. Glancing around, I turned to my labmate and muttered, “I’ve made a huge mistake.” Thankfully, to my relief, my actual session was scheduled for a much smaller room next door.

Each symposium at SMBE brought together leading researchers, early-career scientists, and a handful of wide-eyed PhD students, like me. I was just another Australian who had travelled around the world to talk about our unique endemic marsupials, classic. The session setup was impressively professional. There was a team dedicated to handling the microphones, projectors, clickers, and livestream recording. Unfortunately, technology still had its say. The first speaker discovered that the clicker was not working, marooning him on his title slide, which, despite his fantastic public speaking skills, could only get him so far through his talk. As three support staffers frantically dissected the clicker, a temporary solution was implemented, where the speaker had to wave their hand to signal for the next slide. The other presenting PhD student turned to me in panic, realising how she would have to continuously wave her hand to get through the hundreds of animations in her talk. She dashed up to the support table to quickly simplify her slides in the hope of not wearing her arm out.

Accepting the forced exercise that had been thrust upon us, I sat nervously through the talks before mine, regretting the jalapeños I had added to my breakfast gordita. When it was finally my turn, the host announced my last name with the correct Hungarian pronunciation, which led me to open with an off-script anecdote about its anglicisation when my family moved to Australia. The nerves were evident, but we rolled with it. I waved through most of my talk (very royal family-esque) until, with one minute to go, a staff member heroically handed me a newly functional clicker. A small but powerful victory.

One of the benefits of travelling for a conference is being able to meet people working in similar fields from around the world. After our symposium the speakers were invited to an impromptu waterside dinner, where we learned what “¡Peligro: Cocodrilos!” means, which is important in Mexico. That evening sparked what later became my first collaborative review paper, which developed (via 5 am zoom calls) over the following year. And, of course, the food was phenomenal: octopus ceviche, birria, mole, table-made guacamole, elotes, and more tacos than I could count. My mouth was delighted; my stomach, less so.

After the conference, I squeezed in some scuba diving and was lucky enough to swim alongside a pod of dolphins and spectate a manta ray flash mob. I capped off the trip with a visit to Mexico City, where I toured the botanical and entomological collections at UNAM and connected with evolutionary biologists at Mexico’s largest university. All in all, attending SMBE 2024 was an incredible experience. The people I met, the research I saw, and the tacos I ate made it all worthwhile. If you are a PhD student looking for fresh ideas or new collaborations, I highly recommend taking the plunge at an international conference, especially in a country you have never been to.

Next up: SMBE 2025 in China, where I will finally be living my poster presentation dream.

Toby Kovacs

Toby Kovacs (PhD Student) I am using historical and modern Koala genomes to assess shifts in functional diversity over time, estimate genomic mutation rates, and test for signatures of local adaptation. I have a background in phylogenetics and molecular evolution and am completing my PhD in the Molecular Ecology, Evolution and Phylogenetics Lab in collaboration with the Australian Wildlife Genomics Group and the Center for Evolutionary Hologenomics (University of Copenhagen).

@tobykovacs

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The mother of monsters chooses love not war

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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.

Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease

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Type: Journal Article

Reference: Nelson, H.V., Silver, L., Kovacs, T.G.L. et al. Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease. Immunogenetics 77, 21 (2025). https://doi.org/10.1007/s00251-025-01378-8

Abstract

Small, isolated populations are often vulnerable to increased inbreeding and genetic drift, both of which elevate the risk of extinction. The Bellinger River turtle (Myuchelys georgesi) is a critically endangered species endemic to a single river catchment in New South Wales, Australia. The only extant wild population, along with the breeding program, face significant threats from viral outbreaks, most notably a nidovirus outbreak in 2015 that led to a 90% population decline. To enhance our understanding of genomic characteristics in the species, including genome-wide and functional gene diversity, we re-sequenced, assembled, and analysed 31 re-sequenced genomes for pure M. georgesi (N = 31). We manually annotated the major histocompatibility complex (MHC), identifying five MHC class I and ten MHC class II genes and investigated genetic diversity across both classes in M. georgesi. Our results showed that genome-wide diversity is critically low in pure M. georgesi, contexualised through comparison with opportunistically sampled backcross animals—offspring of F1 hybrids (M. georgesi × Emydura macquarii) backcrossed to pure M. georgesi (N = 4). However, the variation observed within the core MHC region of pure M. georgesi, extending across scaffold 10, exceeded that of all other macrochromosomes. Additionally, no significant short-term changes in either genome-wide or immunogenetic diversity were detected following the 2015 nidovirus outbreak (before; N = 19, after; N = 12). Demographic history reconstructions indicated a sustained, long-term decline in effective population size since the last interglacial period, accompanied by more recent steep declines. These patterns suggested that prolonged isolation and reduced population size have significantly influenced the dynamics of genome-wide diversity. It is likely that contemporary stressors, including the recent nidovirus outbreak, are acting on an already genetically depleted population. This study offers new insights into genome-wide and immune gene diversity, including immune gene annotation data with broader implications for testudines. These findings provide crucial information to support future management strategies for the species.

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Why do men exist?

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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.

@SoleilleM

Range-Wide Assessment of the Tasmanian Devil Gut Microbiome

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Type: Journal Article

Reference: Molloy, M.M., McLennan, E.A., Fox, S., Belov, K. and Hogg, C.J. (2025), Range-Wide Assessment of the Tasmanian Devil Gut Microbiome. Ecol Evol, 15: e71196. https://doi.org/10.1002/ece3.71196

Abstract

The gut microbiome is an important component of host health and function and is influenced by internal and external factors such as host phylogeny, age, diet, and environment. Monitoring the gut microbiome has become an increasingly important management tool for wild populations of threatened species. The Tasmanian devil (Sarcophilus harrisii) is the largest extant carnivorous marsupial from the island state of Tasmania, Australia. Devils are currently endangered due to devil facial tumor disease. Previous assessments have shown differences between captive and wild devil gut microbiomes and changes during translocations. However, wild gut microbiome variability across Tasmania and the drivers of these differences are not well understood. We conducted a range-wide assessment of gut microbiomes at 10 locations across Tasmania, via 16S rRNA sequencing, and tested the influence of diet (12S vertebrate sequencing), location, sex, and cohort. We show that the five most abundant phyla and genera were consistent across all 10 locations. Location, cohort, and sex impacted bacterial richness, but location did not impact diversity. While there were differences in diet across the state, there was no strong evidence of differences between juveniles and adults, nor between males and females. Contrary to our hypothesis, the vertebrate diet explained a small amount of variation in microbial communities. We suspect that other variables, such as environmental factors and immune system development, may have a stronger influence on gut microbiome variability. Dietary components missed by our 12S primer, including invertebrates and plants, may also contribute to these patterns. Adjustments to dietary supplementation are not recommended when preparing devils for translocation to different sites. Future research should prioritize collecting environmental samples for microbial analysis and integrating metabolomics to elucidate functional differences associated with Tasmanian devil gut microbiome variability.

Marsupial cathelicidins: characterization, antimicrobial activity and evolution in this unique mammalian lineage

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Type: Journal Article

Reference: Peel Emma , Gonsalvez Adele , Hogg Carolyn J. , Belov Katherine. 2025. Marsupial cathelicidins: characterization, antimicrobial activity and evolution in this unique mammalian lineage. Frontiers in Immunology, 16 – 2025. https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1524092

Abstract

Introduction: Cathelicidins are a family of antimicrobial peptides well-known for their antimicrobial and immunomodulatory functions in eutherian mammals such as humans. However, cathelicidins in marsupials, the other major lineage of mammals, have received little attention despite lineage-specific gene expansions resulting in a large and diverse peptide repertoire.

Methods: We characterized cathelicidins across the marsupial family tree and investigated genomic organisation and evolutionary relationships amongst mammals. Ancestral sequence reconstruction was used to predict ancestral marsupial cathelicidins, which, alongside extant peptides, were synthesized and screened for antimicrobial activity.

Results: We identified 130 cathelicidin genes amongst 14 marsupial species representing 10 families, with gene expansions identified in all species. Cathelicidin genes were encoded in a highly syntenic region of the genome amongst all mammals, although the number of gene clusters differed amongst lineages (eutherians one, marsupials two, and monotremes three). 32 extant and ancestral marsupial cathelicidins displayed rapid, potent, and/or broad-spectrum antibacterial and antifungal activity. Phylogenetic analysis revealed that marsupial and monotreme cathelicidin repertoires may reflect both mammals and birds, as they encode non-classical cathelicidins found only in birds, as well as multiple copies of neutrophil granule protein and classic cathelicidins found only in eutherian mammals.

Conclusion: This study sheds light on the evolutionary history of mammalian cathelicidins and highlights the potential of wildlife for novel bioactive peptide discovery.

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Imitation is the best form of flattery

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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.

https://www.learnbiomimicry.com/blog/best-biomimicry-examples

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.

https://www.bbc.com/news/uk-scotland-highlands-islands-37428214

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.

Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot

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Type: Journal article

Reference: Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol. 2025 Mar 25:e17746. doi: 10.1111/mec.17746.

Abstract

Loss of genetic diversity threatens a species’ adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.

The current status of genetic monitoring in conservation introductions

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Type: Journal article

Reference: McLennan, E. A., Grueber, C. E., Belov, K., & Hogg, C. J. (2025). The current status of genetic monitoring in conservation introductions. Conservation Science and Practice, e70036. https://doi.org/10.1111/csp2.70036

Abstract

Conservation introductions, translocating species beyond their native range, are increasingly necessary. Because genetic diversity is essential for species to respond to novel environments, understanding whether establishing populations can maintain genetic diversity is crucial to the long-term success of conservation introductions. Using a systematic review, we quantified conservation introductions globally and assessed whether genetic monitoring is occurring. We found that, despite extensive discussion, conservation introductions were rare. Of 167 examples, most were performed in North America, Australia, and China, with megadiverse developing nations underrepresented. Plants were disproportionately represented (74%), and climate change was the primary motivator of conservation introductions (40%). Survival and reproduction were the most frequently measured outcomes (71% and 37%, respectively). Ten works (5.9%) reported genetic monitoring, of which only two considered temporal genetic data and showed a worrying trend of rapid negative genetic change post-establishment. With limited genetic evidence, it remains unclear whether conservation introductions can establish self-sustaining populations. As these translocations may be the only option for some species, we recommend conservation practitioners trial conservation introductions with temporal genetic monitoring to assess the maintenance of founding genetic diversity and inbreeding. Only through scientifically derived applications of conservation introductions will we learn how to establish self-sustaining populations in an uncertain future.

Low genetic diversity and high inbreeding in one of the last chlamydia-free strongholds for New South Wales koalas

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Type: Journal article

Reference: McLennan, E.A., Wilmott, L., Madden, K. et al. Low genetic diversity and high inbreeding in one of the last chlamydia-free strongholds for New South Wales koalas. Conserv Genet (2025). https://doi.org/10.1007/s10592-025-01682-6

Abstract

The genetic consequences of population isolation include inbreeding, genetic diversity loss and loss of adaptive potential. Koalas across south-western Sydney (New South Wales, Australia) may be vulnerable to isolation due to major roads and cleared forest. A few sites within south-western Sydney are some of the last chlamydia-free sites for koalas. Low genetic diversity and potentially low adaptive potential could lead to local extinction of these chlamydia-free sites. Using reduced representation sequencing, we assessed population differentiation, genetic diversity, relatedness, inbreeding, and gene flow across seven sites in south-western Sydney and the Southern Highlands. We found south-western Sydney koalas had significantly lower diversity, higher relatedness and inbreeding than Southern Highlands koalas. There was no evidence of contemporary gene flow from the more genetically diverse Southern Highlands sites into south-western Sydney. The separation between south-western Sydney and the Southern Highlands likely explains the lower genetic diversity among south-western Sydney sites. It may also explain why chlamydia is yet to reach these sites. However, there is evidence of a disease-front movement of chlamydia from Wingecarribee up into Wollondilly which has high gene flow with Campbelltown, a chlamydia-free site. While gene flow from south to north is low, the risk of chlamydia entering the chlamydia-free sites from a few migrants is notable. With possible low adaptive potential of south-western Sydney sites, a new threat of chlamydia entering the system may lead to population declines in these stronghold areas.