Publications

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.

Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation

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Type: Journal article

Reference: Schraven, A.L., McLennan, E.A., Farquharson, K.A., Lee, A.V., Belov, K., Fox, S., Grueber, C.E. and Hogg, C.J. (2025), Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation. Mol Ecol e17671. https://doi.org/10.1111/mec.17671

Abstract

Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, in situ actions like supplementations (releasing individuals into an existing population) are often restricted to a singular site. Considerable research and management effort have been dedicated to conserving the Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence of management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild-supplemented sites to four monitoring-only sites (not supplemented; control sites) over 9 years (2014–2022). At the study completion, genetic differentiation among supplemented sites had significantly decreased compared to among not-supplemented sites. We found statistically significant variation in genetic change over time between sites using linear mixed-effects modelling with random slopes. Investigating this among-site variation showed that three of the supplemented sites conformed to predictions that supplementations would have a positive impact on the genetic diversity of devils at these sites. We predicted no change over time at our fourth site due to the observed relatively high gene flow, however, this site did not align with predictions, instead showing decreased genetic diversity and increased relatedness. Amongst not supplemented sites, there was no consistent pattern of temporal genetic change, suggesting devil sites across Tasmania are highly heterogeneous, likely reflecting variation in site connectivity and genetic drift. Our study demonstrates that long-term concurrent monitoring of multiple sites, including controls, is necessary to contextualise the influence of management interventions on natural species fluctuations.

Global meta-analysis shows action is needed to halt genetic diversity loss

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Type: Journal article

Reference: Shaw, R.E., Farquharson, K.A., Bruford, M.W. et al. Global meta-analysis shows action is needed to halt genetic diversity loss. Nature 638, 704–710 (2025). https://doi.org/10.1038/s41586-024-08458-x

Abstract

Mitigating loss of genetic diversity is a major global biodiversity challenge. To meet recent international commitments to maintain genetic diversity within species, we need to understand relationships between threats, conservation management and genetic diversity change. Here we conduct a global analysis of genetic diversity change via meta-analysis of all available temporal measures of genetic diversity from more than three decades of research. We show that within-population genetic diversity is being lost over timescales likely to have been impacted by human activities, and that some conservation actions may mitigate this loss. Our dataset includes 628 species (animals, plants, fungi and chromists) across all terrestrial and most marine realms on Earth. Threats impacted two-thirds of the populations that we analysed, and less than half of the populations analysed received conservation management. Genetic diversity loss occurs globally and is a realistic prediction for many species, especially birds and mammals, in the face of threats such as land use change, disease, abiotic natural phenomena and harvesting or harassment. Conservation strategies designed to improve environmental conditions, increase population growth rates and introduce new individuals (for example, restoring connectivity or performing translocations) may maintain or even increase genetic diversity. Our findings underscore the urgent need for active, genetically informed conservation interventions to halt genetic diversity loss.

AMPed Up Immunity: 418 Whole Genomes Reveal Intraspecific Diversity of Koala Antimicrobial Peptides

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Type: Journal article

Reference: Petrohilos C, Peel E, Silver LW, Belov K, Hogg CJ. AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides. Immunogenetics. 2025 Jan 8;77(1):11. doi: 10.1007/s00251-024-01368-2.

Abstract

Characterising functional diversity is a vital element to understanding a species’ immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species’ range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.

A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi

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Type: Journal article

Reference: Nelson, H.V., Georges, A., Farquharson, K.A., McLennan, E.A., DeGabriel, J.L., Belov, K. and Hogg, C.J. (2025), A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi. Ecol Evol, 15: e70798. https://doi.org/10.1002/ece3.70798

Abstract

Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger-sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152-base-pair-long fragment of the cytochrome oxidase 1 (CO1) gene and a 186-base-pair-long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.

A reference genome for the eastern bettong ( Bettongia gaimardi)

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Type: Journal article

Reference: Silver, L. W., Edwards, R. J., Neaves, L., Manning, A. D., Hogg, C. J., & Banks, S. (2025). A reference genome for the eastern bettong ( Bettongia gaimardi). F1000Research, 13, 1544. https://doi.org/10.12688/f1000research.157851.1

Abstract

The eastern or Tasmanian bettong ( Bettongia gaimardi) is one of four extant bettong species and is listed as ‘Near Threatened’ by the IUCN. We sequenced short read data on the 10x system to generate a reference genome 3.46Gb in size and contig N50 of 87.36Kb and scaffold N50 of 2.93Mb. Additionally, we used GeMoMa to provide and accompanying annotation for the reference genome. The generation of a reference genome for the eastern bettong provides a vital resource for the conservation of the species.

Beyond nutrition: Exploring immune proteins, bioactive peptides, and allergens in cow and Arabian camel milk

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Type: Journal article

Reference: M.W. Jayamanna Mohottige, A. Juhász, M.G. Nye-Wood, K.A. Farquharson, U. Bose, M.L. Colgrave. 2024. Beyond nutrition: Exploring immune proteins, bioactive peptides, and allergens in cow and Arabian camel milk. Food Chemistry, 467. 142471, 10.1016/j.foodchem.2024.142471.

Abstract

Bovine milk has dominated the dairy segment, yet alternative milk sources are gaining attention due to perceived superior health benefits, with immune proteins and bioactive peptides (BPs) contributing to these benefits. Fractionation affects protein recovery and composition. Here, the cream fraction resulted in the highest yield of proteins, identifying 1143 camel and 851 cow proteins. The cream fraction contained a significantly higher concentration of immune system-related proteins. Straightforward filtration and protein precipitation methods achieved average BP detections of 170 and 177, compared to 31 by a solvent-solvent extraction method. Considering potentially allergenic proteins, 53 (camel) and 52 (cow) were identified. Of these, 62 % of the potential allergens in cow, had orthologous counterparts in camel milk. However, the major milk allergen β-lactoglobulin (β-Lg) was not detected in camel milk. Our results provide a comprehensive proteomic resource of camel and cow milk products, mapping potential allergens and BPs that affect health.

Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution

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Type: Journal article

Reference: Cui J, Batley KC, Silver LW, McLennan EA, Hogg CJ, Belov K. Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution. Immunogenetics. 2024 Nov 30;77(1):5. doi: 10.1007/s00251-024-01365-5

Abstract

The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species’ range, however, is not even. Toll-like receptors (TLRs) play a crucial role in innate immunity by recognising and responding to various pathogens. Variations in TLR genes can influence an individual’s susceptibility or resistance to infectious diseases. The aim of this study was to identify koala TLR diversity across the east coast of Australia using 413 re-sequenced genomes at 30 × coverage. We identified 45 single-nucleotide polymorphisms (SNP) leading to 51 alleles within ten TLR genes. Our results show that the diversity of TLR genes in the koala forms four distinct genetic groups, which are consistent with the diversity of the koala major histocompatibility complex (MHC), another key immune gene family. The bioinformatics approach presented here has broad applicability to other threatened species with existing genomic resources.