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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.

Andrea_Schraven

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Australia’s best kept secret: the dunnart

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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!

Multi-omics resources for the Australian stuttering frog (Mixophyes balbus) reveal assorted antimicrobial peptides

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Type: Journal Article

Reference: Tang, S., Peel, E., Belov, K., Hogg, C. J., & Farquharson, K. A. (2024). Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides. Scientific Reports, 14(1), 3991. https://doi.org/10.1038/s41598-024-54522-x

Abstract

The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two β-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.

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When Cells Rebel: the dark side of evolution

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by Patra Petrohilos (PhD Student)

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

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

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

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

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

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

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

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

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

Author:

Patra Petrohilos

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

patra_petro

Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape

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Type: Journal Article

Reference: de Visser, R. S., Hall, M., Ottewell, K., Pierson, J. C., Sanders, A., Friend, J. A., Berry, L., Hogg, C. & Catullo, R. A. (2024). Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape. Conservation Genetics, 1-15. https://doi.org/10.1007/s10592-024-01603-z

Abstract

Kenngoor (Phascogale calura) persist in < 1% of their original distribution, occupying highly fragmented remnant habitat in south-west Western Australia, with very little known of the genetic diversity of the remaining wild populations. Recently, the species has been translocated to managed reserves to improve its conservation. Understanding genetic structure and patterns of genetic diversity is crucial to inform conservation translocations for species recovery. This study aims to (1) assess genetic structure and genetic diversity across remaining wild locations, (2) assess long-term genetic outcomes of a mixed-source wild-to-wild translocation, and (3) estimate global effective population size. We genotyped 209 samples from 13 locations of fragmented remnant habitat using reduced representation sequencing. An isolation by distance model best explained genetic structure across the survey areas, with evidence of fine scale divergence of two northern locations. Allelic richness and autosomal heterozygosity measures indicated that diversity is spread uniformly across locations, and no locations showed signs of inbreeding or strong genetic drift. The mixed-source translocation has retained the diversity of the wider species ten years post-translocation. Overall, our results suggest that connectivity between survey areas has largely been maintained and that no location has substantially lower genetic diversity, despite the highly fragmented nature of remnant kenngoor habitat. Future translocations should aim to represent a mixture of genetically divergent locations to maintain the diversity present at the species level. Ongoing conservation management will be required to ensure the long-term viability of the species in this fragmented landscape.

A chromosome-level genome assembly for the dugong

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Type: Journal Article

Reference: Dorothy Nevé Baker, Linelle Abueg, Merly Escalona, Katherine A Farquharson, Janet M Lanyon, Diana Le Duc, Torsten Schöneberg, Dominic Absolon, Ying Sims, Olivier Fedrigo, Erich D Jarvis, Katherine Belov, Carolyn J Hogg, Beth Shapiro, A chromosome-level genome assembly for the dugong (Dugong dugon), Journal of Heredity, Volume 115, Issue 2, March 2024, Pages 212–220, https://doi.org/10.1093/jhered/esae003

Abstract

The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage.

Translating genomic advances into biodiversity conservation

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Type: Journal Article

Reference: Hogg, C.J. Translating genomic advances into biodiversity conservation. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00671-0

Abstract

A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.

Sydney Science in Instagram: Meet PhD Student Holly Nelson

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Meet PhD student Holly Nelson. Her research with the USYD Australian Wildlife Genomics group and NSW Department of Planning and Environment focuses on using genomic data to help provide tools for the management of threatened species, especially the critically endangered Bellinger River snapping turtle.

Watch the full video here: https://www.instagram.com/sydney_science/reel/Cw1FG6-hhD8/