Reinforcements in the face of ongoing threats: A case study from a critically small carnivore population

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.


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.


How to catch a Tasmanian devil

by Dr Elspeth McLennan (Post-doc)

Tasmanian devils are nocturnal. We set traps during the day and overnight curious devils will come to investigate. The traps we use are made of strong PVC plastic fashioned into a cylinder with a spring trap door (see cover picture). The traps are baited with a devil’s favourite treat, a piece of fresh lamb or wallaby. The meat is tied onto the end of a string, fed through the trap, and tied to a pin which holds the door open.

Tasmanian devil inside trap

When a devil comes investigating the smell of the meat, they walk to the end of the trap and take the bait. When the meat is pulled and eaten, the pin holding the door open is pulled free and the door swings shut. A second pin slides forward as the door closes and locks it. Devils spend the night in a cosy enclosed space with a full belly. The field biologists begin checking the traps as soon as the sun is up. As its daylight, we often find devils snoozing in their traps.

To perform a health check on the devil, we place a hessian sack over the opening of the trap, gently tilt the trap and the devil slides forward into the sack. The sack is used to keep the devil’s eyes covered to keep them calm making them easier to handle while we check them over. We take their weight, check their body condition, look for wounds and record pouch young in females. For populations suffering from devil facial tumour disease (DFTD), the disease status of each animal is also recorded. Once the devil has been processed, they are released. On a single trapping trip, we will often see the same devils a few times. The free food and somewhere to crash is clearly a good draw.


Dr Elspeth McLennan

Dr Elspeth McLennan (Post-doc) is working the on the Koala Genome Survey, investigating both neutral and functional diversity across the koala’s range to better understand the impacts of a changing climate. Elspeth has expertise in conservation genetics and using translocation and assisted colonisations as a conservation management tool.

The genome sequence of the critically endangered Kroombit tinkerfrog

Type: Journal Article

Reference: Farquharson, K., McLennan, E., Belov, K., & Hogg, C. (2023). The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione). F1000Research, 12(845).


The Kroombit tinkerfrog (Taudactylus pleione) is a stream-dwelling amphibian of the Myobatrachidae family. It is listed as Critically Endangered and is at high risk of extinction due to chytridiomycosis. Here, we provide the first genome assembly of the evolutionarily distinct Taudactylus genus. We sequenced PacBio HiFi reads to assemble a high-quality long-read genome and identified the mitochondrial genome. We also generated a global transcriptome from a tadpole to improve gene annotation. The genome was 5.52 Gb in length and consisted of 4,196 contigs with a contig N50 of 8.853 Mb and an L50 of 153. This study provides the first genomic resources for the Kroombit tinkerfrog to assist in future phylogenetic, environmental DNA, conservation breeding, and disease susceptibility studies.

Koala Genome Survey: an open data resource to improve conservation planning

Type: Journal Article

Reference: Hogg, C. J., Silver, L., McLennan, E. A., & Belov, K. (2023). Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes, 14(3), 546. doi: 10.3390/genes14030546


Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.

See all our publications HERE!

Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities

Type: Journal Article

Reference: Stojanovic, D., McLennan, E., Olah, G., Cobden, M., Heinsohn, R., Manning, A. D., Alves, F., Hogg, C. & Rayner, L. (2023). Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities. Animal Conservation. doi: 10.1111/acv.12855


Reproductive skew occurs when a few individuals monopolize breeding output, which can act as a mechanism of natural selection. However, when population sizes become small, reproductive skew can depress effective population size and worsen inbreeding. Identifying the cause of reproductive skew is important for mitigating its effect on conservation of small populations. We hypothesized that superb parrots Polytelis swainsonii, which strongly select for the morphology of tree cavity nests, may be reproductively skewed toward pairs that monopolize access to nests. We use SNP genotyping to reconstruct a pedigree, estimate molecular relatedness and genetic diversity of wild superb parrot in the Australian Capital Territory. We successfully genotyped 181 nestlings (a census between 2015–2019) and showed they were the progeny of 34 monogamous breeding pairs. There was a strong reproductive skew – 21 pairs bred only once producing 40% of the nestlings, whereas 13 pairs bred two to four times, producing 60% of the total nestlings. Five of these repeat-breeders produced 28% of all nestlings, which was nearly triple the productivity of one-time breeders. Repeat breeders usually monopolized access to their nest cavities, but the few pairs that switched nests did not differ in fecundity from those that stayed. The cause of nest switching was unknown, but uninterrupted access to a suitable nest (not minor variations in morphology between nests) better predicted fitness of breeding superb parrots. Pedigrees offer powerful insights into demographic processes, and identifying reproductive skew early provides opportunities to proactively avoid irreversible loss of genetic diversity via conservation management. We identify new research questions based on our results to clarify the relationship between access to resources and breeding success.

See all our publications HERE!