Tag Archives: Toby Kovacs

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.

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.

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Diversity in the Dark: the hidden wonders of subterranean life

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by Toby Kovacs (PhD Student)

Australia is famous for its unique flora and fauna, harbouring some of the most unique and highly endemic groups of organisms. When I’m sitting around with my family discussing Australian biodiversity, often the first places we think of are the rainforests, the Great Barrier Reef or the hyper-biodiverse region of South Western Australia. We do unfortunately, often go without mentioning, the plethora of small, white and blind creepy crawlies living directly beneath our feet (quick have a look).

Not many people know that Australia contains an extraordinary level of subterranean (underground) life, living in the shadows. Scientists have long considered cave systems as natural ‘evolutionary laboratories’ due to the apparent simplicity of cave ecosystems. However, surprisingly few studies have contributed to our broad understanding of subterranean evolution. Subterranean fauna are characterised by their troglomorphic (cave adapted) features resulting from the loss of traits no longer required in the absence of light. These include the loss of pigment and eyes, as well as the elongation of antennae, legs and body. Although caves are the most well-known subterranean landscape, because of their accessibility and sick stalactites and stalagmites (Sydneysiders should check out the Jenolan Caves), they are not the only place you can find subterranean fauna (think a little deeper).

Modern subterranean surveys using deep bore holes and subterranean traps have found that inhabitable landscapes extend well beyond the observable caves. In the last decade a diverse array of life has been discovered in previously inaccessible non-cave subterranean landscapes. Australia, in particular the Western Australian Pilbara and Yilgarn regions, contains some of the most biodiverse non-cave subterranean landscapes known, predicted to contain ~3000 species (Halse 2014). Animals inhabit tiny, interconnected air pockets up to 150 m below the surface, where the air remains humid and relatively cool compared to the scorching surface temperatures. Here you can find spiders, cockroaches, beetles, isopods, centipedes, millipedes, pseudoscorpions, fish, crustaceans and even flies. Unfortunately, mining is abundant in these regions and conservation strategies for subterranean fauna are limited due to the vast majority of species being undescribed. However, genetic analysis provides a powerful tool for identifying species and assessing biodiversity in subterranean landscapes. If you’re interested in exploring the available specimen collections don’t hesitate to reach out, there’s so much work to be done!

 If you’re interested in visiting caves check out:

If you want to learn more about subterranean fauna check out:

  • Culver D.C., Pipan T. 2019. The Biology of Caves and Other Subterranean Habitats. Oxford University Press.
  • Halse S.A., Pearson G.B. 2014. Troglofauna in the vadose zone: Comparison of scraping and trapping results and sampling adequacy. Subterr. Biol. 13:17–34.

Author

Toby Kovacs

Toby Kovacs (PhD Student) I am using historical and modern Koala genomes to assess shifts in functional diversity over time, estimate genomic mutation rates, and test for signatures of local adaptation. I have a background in phylogenetics and molecular evolution and am completing my PhD in the Molecular Ecology, Evolution and Phylogenetics Lab in collaboration with the Australian Wildlife Genomics Group and the Center for Evolutionary Hologenomics (University of Copenhagen)

@tobykovacs