Publications

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.

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.

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).

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.

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.

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.

Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates

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Type: Journal article

Reference: Toby G L Kovacs, James Walker, Simon Hellemans, Thomas Bourguignon, Nikolai J Tatarnic, Jane M McRae, Simon Y W Ho, Nathan Lo, Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates, Systematic Biology, Volume 73, Issue 3, May 2024, Pages 532–545, https://doi.org/10.1093/sysbio/syae002

Abstract

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analyzed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all 13 major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.