Tag Archives: Population genomics

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.

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.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

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Type: Journal article

Reference: Kosch, T.A., Torres-Sánchez, M., Liedtke, H.C. et al. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BMC Genomics 25, 1025 (2024). https://doi.org/10.1186/s12864-024-10899-7

Abstract

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.