The University of Sydney
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
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
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.
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
Bilbies have the biggest genome of any marsupial, which could be down to how it evolved its incredible sense of smell.
Find the full article here: https://www.theguardian.com/environment/article/2024/jul/01/bilby-genome-sequencing-endangered-species
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.
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.
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.
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
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.
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
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.
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
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.
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
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)
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.