Tag Archives: Parice Brandis

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

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Type: Journal article

Reference: Hogg, C.J., Edwards, R.J., Farquharson, K.A. et al. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8, 1311–1326 (2024). https://doi.org/10.1038/s41559-024-02436-2

Abstract

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

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.

Parice Brandies

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Brandies, P. A. (2021). Conserving Australia’s iconic marsupials; one genome at a time. The University of Sydney.

In the midst of a global sixth mass extinction event, conservation initiatives are now more crucial than ever. Australia houses the most diverse range of marsupial species in the world; however, the number that are threatened is growing every year. Genetic management of threatened populations is vital in species recovery, yet incorporation of genetic data in conservation management is currently limited. International and national genome sequencing consortia are currently producing reference genomes for a large variety of species, though there is currently a gap between the creation of these genomic resources and their downstream applications, particularly in conservation contexts. One of the major drivers of this gap is due to the bioinformatic expertise and resources that are required to analyse genomic datasets and to translate the findings into conservation management. This PhD employs a variety of bioinformatic and sequencing approaches to develop genomic resources for threatened Australian Marsupials and demonstrates how these resources can be used as a tool to assist species conservation. The value of genomic data for conservation is demonstrated for a range of species under varying scenarios including: i) using existing genomic datasets for the endangered Tasmanian devil to answer new conservation questions relating to reproduction, ii) creating a reference genome for the common brown antechinus, to act as a model species for its threatened congeneric counterparts and iii) generating and uniting a suite of genomic resources to assist in the management of the vulnerable greater bilby. In addition, ten simple rules for getting started with command-line bioinformatics are presented to facilitate the use of genomic data in wildlife conservation. Bridging the research-implementation gap is essential for harnessing the power of genomic resources for the conservation of threatened species. The findings from this PhD provide crucial steps into bridging this gap.

https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991032543896605106