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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

Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies

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Type: Journal article

Reference: Silver LW, Crates R, Stojanovic D et al. Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies. F1000Research 2024, 13:337 (https://doi.org/10.12688/f1000research.145788.1)

Abstract

The brown thornbill (Acanthiza pusilla) is a songbird endemic to eastern Australia with five recognised subspecies within the brown thornbill. The most notable is the King Island brown thornbill (Acanthiza pusilla magnirostris) of which there are less than 100 remaining and based on expert elicitation are the most likely Australian bird to become extinct in the next 20 years. We sequenced PacBio HiFi reads of the brown thornbill to generate a high-quality reference genome 1.25Gb in size and contig N50 of 20.1Mb. Additionally, we sequenced mRNA from three tissues to generate a global transcriptome to aid with genome annotation. The generation of a reference genome for the brown thornbill provides an important resource to align additional genomic data which will be produced in the near future.

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

A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot

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Type: Journal article

Reference: Silver LW, Stojanovic D, Farquharson KA et al. A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor). F1000Research 2024, 13:251 (https://doi.org/10.12688/f1000research.144352.2)

Abstract

The swift parrot (Lathamus discolor) is a Critically Endangered migratory parrot that breeds in Tasmania and winters on the Australian mainland. Here we provide a reference genome assembly for the swift parrot. We sequence PacBio HiFi reads to create a high-quality reference assembly and identify a complete mitochondrial sequence. We also generate a reference transcriptome from five organs to inform genome annotation. The genome was 1.24 Gb in length and consisted of 847 contigs with a contig N50 of 18.97 Gb and L50 of 20 contigs. This study provides an annotated reference assembly and transcriptomic resources for the swift parrot to assist in future conservation genomic research.

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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.