Tag Archives: Elspeth McLennan

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.

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.

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.

Genomics identifies koala populations at risk across eastern Australia

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Type: Journal article

Reference: McLennan, Elspeth A., Toby G. L. Kovacs, Luke W. Silver, Zhiliang Chen, Frederick R. Jaya, Simon Y. W. Ho, Katherine Belov, and Carolyn J. Hogg. 2025. “ Genomics Identifies Koala Populations at Risk across Eastern Australia.” Ecological Applications 35(1): e3062. https://doi.org/10.1002/eap.3062

Abstract

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega-fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future-proofed baseline genomic dataset across the koala’s range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid-coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.

Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

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Type: Journal article

Reference: Silver LW, McLennan EA, Beaman J, da Silva KB, Timms P, Hogg CJ, Belov K. Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas. Immunogenetics. 2024 Dec;76(5-6):381-395. doi: 10.1007/s00251-024-01356-6

Abstract

Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.

A genomic framework to assist conservation breeding and translocation success: A case study of a critically endangered turtle

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Type: Journal article

Reference: Nelson, H. V., Farquharson, K. A., Georges, A., McLennan, E. A., DeGabriel, J. L., Giese, M., Ormond, C., McFadden, M., Skidmore, A., Prangell, J., Belov, K., & Hogg, C. J. (2024). A genomic framework to assist conservation breeding and translocation success: A case study of a critically endangered turtle. Conservation Science and Practice, 6(10), e13204. https://doi.org/10.1111/csp2.13204

Abstract

Conservation breeding programs are an effective approach to addressing biodiversity loss. Captive populations are managed to maintain genetic diversity, yet there remains an “implementation gap” in effectively translating molecular genetic data into management. Technological advancements are facilitating rapid generation of genetic data, increasing accessibility for breeding programs. In 2010, Frankham and colleagues proposed a six-stage process for establishing successful conservation breeding and release programs. Here, we describe the conservation breeding program for the critically endangered Bellinger River turtle (Myuchelys georgesi) and characterize the value of genetic sampling for informing management actions. By generating a chromosome-level genome and population genetic data, we investigated past and present diversity and assessed relatedness among captive founders. We present a framework modeled on Frankham and colleagues six stages to assist managers in implementing genetic data into actionable conservation strategies. This framework, and worked case study, for managers aims to better guide implementation of genetic approaches into conservation breeding programs.

The future is here: an easy-to-use toolkit for integrating genetics into conservation management

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Type: Journal article

Reference: Hogg, C.J., Farquharson, K.A., Brandies, P., Silver, L.W., Ottewell, K., McLennan, E.A., Richmond, S. and Belov, K. (2025), The future is here: an easy-to-use toolkit for integrating genetics into conservation management. Anim Conserv, 28: 93-103. https://doi.org/10.1111/acv.12971

Abstract

Over the past decade, the development of genetic and genomic tools for conservation management has come forward in leaps and bounds. Once considered a ‘nice to have’, genetic data are fast becoming an essential tool for informing and managing translocations. However, due to the complexity of the field, easily using genetic data for decision-making and monitoring remains beyond the reach of most managers and conservation biologists. In May 2020, we launched the Threatened Species Initiative (TSI), a programme designed to generate genomic resources for Australia’s threatened species. Critical to the project is not only the generation of reference genomes and population genetic data but an online toolkit for conservation managers. The toolkit is a ‘one stop shop’ from collecting samples, to generating and analysing genetic data, to an easily interpretable genetic management report. A series of workflows and pipelines have been developed, including the TSI Biodiversity Portal, that uses point and click web interfaces to easily transfer raw sequence data and assemble genomes, transcriptomes and soon population genetics for management decisions. Here we present how the current toolkit works and provide case study examples for how it is being used to inform translocations and the management of threatened species.

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.