– ABOUT
Threatened Species Initiative
The Threatened Species Initiative (TSI) is a national program aiming to assist the conservation industry in managing species recovery by using cutting-edge genomics technology and advanced computational biology.
To do this, we are 1) generating genomic resources (reference genomes, transcriptomes) and supporting generation of some population data for Australia’s threatened species, and 2) deploying this alongside fit-for-purpose tools and training materials that together create a systematic approach to integrating genomics into species recovery.
Established in 2020, the TSI has aimed to support the integration of genomics information in hands-on species recovery actions through an end-to-end systematic framework. This framework is currently being deployed across more than 60 TSI-supported projects.
For more information, visit our website dedicated to the activities and bioinformatic tools developed by the initiative.
OBJECTIVES
Through this initiative, the creation of referential data resources of Australia’s endangered species will:
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- Support conservation efforts: Directly aid various conservation programs by providing genomic resources and analytical tools.
- Develop infrastructure: Create data and analytical pipelines to enhance biodiversity conservation through species management teams.
- Address extinction: Contribute to efforts against Australia’s high mammalian extinction rate by managing and boosting genetic diversity in threatened species.
- Empower conservation managers: Develop an online tool to assist conservation managers in using genomics to make informed breeding recommendations.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Project name | Project Summary | Species name | Data strategy |
|---|---|---|---|
| Enhancing habitat restoration and recovery of Adamson’s blown grass through genomic insights | Lachnagrostis adamsonii (Adamson’s Blown Grass), an endangered species restricted to saline habitats in southern Australia, faces critical threats from habitat loss, climate change, and limited population viability. This project aims to generate a reference genome, transcriptome, and comprehensive population genomic data to inform species delimitation, assess genetic diversity, and guide conservation actions, ensuring the survival and recovery of L. adamsonii across its entire range. | Adamson's blown grass (Lachnagrostis adamsonii) | Reference genome (PacBio HiFi), Population genetics (DArT) |
| Assessing clonality and conservation strategies for the rare aenigma hakea | Hakea aenigma, a rare and enigmatic shrub endemic to Kangaroo Island, South Australia, is one of only two Hakea species entirely reliant on vegetative reproduction. With no seed production and sterile pollen, its survival depends on suckering, raising concerns about its genetic diversity and long-term viability. This project aims to determine whether remnant populations consist of a single clone or multiple genetically distinct individuals, using genetic analysis of collected samples. The findings will guide conservation actions, including potential tissue culture propagation, manual pollination, or translocation efforts to enhance the species' persistence in the wild. | Aenigma hakea (Hakea aenigma) | Population genetics (ddRAD) |
| Creating a genomic foundation for Litoria conservation and research | Currently, the Litoria genus lacks available reference genomes to be used in research and taxonomy. With many genetic projects, a good reference genome of at least a closely related species is needed. This reference genome would add valuable information and resources to the largest frog genus in Australia. This reference genome will also be utilized for conservation work being done by government, museum, and zoological agencies in both Victoria and NSW regarding this species. One of the main objectives from the creation of the reference genome will be its employment later in a population viability analysis that will be used by management organizations. | Alpine tree frog (Litoria verreauxii alpina) | Reference genome (PacBio HiFi, transcriptome), Population genetics (DArT) |
| Leveraging population genomics to protect Gossia gonoclada from myrtle rust and other threats | Myrtle rust, caused by the invasive pathogen Austropuccinia psidii, threatens Australia's biodiversity, with over 390 Myrtaceae species at risk, including the critically endangered Gossia gonoclada. This project aims to assemble a reference genome for G. gonoclada and conduct population genomics analyses to inform conservation management, supporting insurance collections and enhancing genomic resources for Myrtaceae species impacted by myrtle rust. | Angle-stemmed myrtle (Gossia gonoclada) | Reference genome (PacBio-HiFi) |
| Genomic resource in support of conservation efforts of the Baw baw frog | Baw baw frog (Philoria frosti) | Population genetics (ddRAD) | |
| Genomic resource in support of conservation efforts of the Bellinger river snapping turtle | Bellinger River Snapping Turtle (Myuchelys georgesi) | Reference genome (PacBio HiFi, transcriptome, HiC) | |
| Preserving genetic integrity of the black-eared miner | The black-eared miner (Manorina melanotis), an endangered Australian bird, faces genetic threats due to hybridisation with the more abundant yellow-throated miner, which is exacerbated by habitat loss. This project aims to develop a high-quality reference genome to characterise genetic introgression, genotype-phenotype associations, and inbreeding, providing key insights for informed conservation actions such as hybrid removal, translocations, and habitat restoration to preserve the species' genetic integrity and diversity. | Black-eared miner (Manorina melanotis) | Reference genome (PacBio HiFi) |
| Assessing genetic diversity for potential genetic rescue of Promethis sterrha | Promethis sterrha was recently recognised as a critically endangered beetle species, being present on only a single small island (Blackburn Island) in the Lord Howe Island Group. Genomic analyses are required to assess genetic diversity of the species, which is expected to be low due to small population size, and also its genetic distance from its closest relatives, of which there are 4. Knowing how closely related P. sterrha is to the other four species at the genomic level would be useful for potential genetic rescue. The 5 Promethis species are mainly seen as larvae, which are very difficult to separate morphologically. Adults are less easily seen. Genetic data on P. sterrha plus related taxa would be very useful for this purpose. | Blackburn Island Beetle (Promethis sterra) | Reference genome (PacBio HiFi, resequencing) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to protect Australia’s climate-threatened tropical mountaintop plants by establishing an ex-situ conservation reserve for 14 endemic species from the Wet Tropics Bioregion. One target species, Litsea granitica, a vulnerable tree known from five mountain tops, will undergo genomic analysis to assess its genetic diversity, which will guide conservation efforts, resource allocation, and the selection of genotypes for ex-situ conservation, while also informing strategies to mitigate the impacts of predicted climate change. | Bollywood (Litsea granitica) | Population genetics (DArT) |
| Tropical Mountain Top Plant Science project | threatened tropical mountaintop plants by establishing an ex-situ conservation reserve for 14 endemic species from the Wet Tropics Bioregion. One of the species under focus, Litsea bindoniana, a tree threatened by climate change, will be included in genetic analysis to assess its diversity, which will guide resource allocation, the selection of propagated genotypes, and future field expeditions to secure the plant’s long-term survival. | Bollywood | big-leaved bollywood (Litsea bindoniana) | Population genetics (DArT) |
| Genomic resource to assist the conservation management of the broad-toothed rat | Collaboration with The Department of Environment, Land, Water and Planning (now Department of Energy, Environment and Climate Action) | Broad-toothed rat (Mastacomys fuscus) | Reference genome (resequencing) |
| Genomic resource in support of conservation efforts of the Butterfly pea | Butterfly pea (Clitoria ternatea) | Reference genome (HiC) | |
| Assessing genetic diversity and inbreeding risk in Advena campbellii | In 2020, the presumed extinct Advena campbellii campbellii was rediscovered. There are now just 197 wild snails in 0.4 km2 area across 3 sites in Norfolk Island National Park. Thus, Taronga Zoo established zoo-bred populations based on wild-caught snails, which has increased to over 300 individuals. Some of these will be reintroduced to a suitable site in 2025. We propose assembling a reference genome for the species and use SNPs from DArTseq to assess the wild and zoo populations genetic diversity, structure, and inbreeding risk. We will also assess the kinship, relatedness and pedigree of all zoo-bred snails. These findings will be used to develop strategies to increase genetic diversity and reduce inbreeding in wild and zoo populations. | Campbell’s Keeled Glass Snail (Advena campbellii campbellii) | Reference genome (PacBio HiFi, transcriptome), Population genetics (DArT) |
| Understanding genetic diversity to conserve the Capricorn yellow chat's isolated populations | The Capricorn yellow chat (CYC), a critically endangered bird restricted to central Queensland's marine plains, faces genetic isolation across its disjunct populations in Broad Sound, the Fitzroy River delta, and Curtis Island National Park. This project aims to conduct comprehensive genetic analyses to assess gene flow, inbreeding, and genetic diversity, informing conservation actions such as translocation, captive breeding, and prioritisation of efforts to secure the species' survival against threats like climate change-induced sea-level rise. | Capricorn yellow chat (Epthianura crocea macgregori) | Population genetics (ddRAD) |
| Genetic management for Christmas Island skink and gecko | The Blue-tailed Skink and Lister's Gecko, both critically endangered species endemic to Christmas Island, have been conserved through captive breeding and successful introduction programs. This project aims to use genomic analyses to refine genetic management strategies for both species, informing future supplementation and release efforts to enhance population viability and ensure long-term conservation. | Christmas Island Blue-tailed skink (Cryptoblepharus egeriae) | Reference genome (PacBio HiFi, transcriptome), Population genetics (DArT) |
| Genetic diversity and conservation of Chuditch | The Chuditch (Dasyurus geoffroii), once widespread across Australia, is now critically endangered, with remnant populations in southern Western Australia facing threats from predators, habitat loss, and changes in land use. This project aims to assess the genetic diversity of source populations for future translocations, evaluate the genetic health of re-established populations, and optimize translocation strategies to ensure the long-term survival and success of Chuditch conservation efforts. | Chuditch (Dasyurus geoffroii) | Population genetics (ddRAD) |
| Genetic diversity and conservation of Clarence galaxias | The Clarence galaxias, restricted to three fragmented populations in Tasmania's upper Derwent catchment due to competition with introduced brown trout, faces limited population connectivity and genetic data gaps. This project aims to assess genome-wide genetic diversity, guide genetic rescue and insurance population strategies, and develop an eDNA assay for low-density detection, informing conservation and recovery efforts for this Endangered species. | Clarence galaxiid (Galaxias johnstoni) | Population genetics (ddRAD) |
| Genomic resource in support of conservation efforts of the Climbing Galaxias | Climbing Galaxias (Galaxias brevipinnis) | Population genetics (ddRAD) | |
| Genetic assessment and conservation of Corangamite water skink | The Corangamite Water Skink (Eulamprus tympanum marnieae), endemic to Victoria, faces threats such as habitat loss and fragmentation, with unclear taxonomic status and limited genetic diversity among populations. This project aims to clarify the skink’s taxonomic status, assess genetic diversity and population structure, and determine conservation needs, including potential genetic interventions and the establishment of a captive insurance population, to support the species' long-term survival. | Corangamite water skink (Eulamprus tympanum marnieae) | Reference genome (PacBio HiFi, transcriptome), Population genetics (DArT) |
| Genomic resource in support of conservation efforts of the Crater Ironwood | Crater Ironwood (Rhodomyrtus canescens) | Reference genome (resequencing) | |
| Genomic resource in support of conservation efforts of the Iron Malletwood | Iron Malletwood (Rhodamnia sessiliflora) | Reference genome (resequencing) | |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants by generating genomic data for 14 target species, including Cryptocarya bellendenkerana, a species facing a predicted 28% reduction in its climatic niche by 2055. This research will inform ex-situ conservation efforts, helping to prioritise wild populations, allocate resources for germplasm preservation, and select appropriate genotypes for propagation across conservation sites, ultimately guiding conservation actions for both Cryptocarya bellendenkerana and other co-occurring species in the Wet Tropics Bioregion. | Cryptocarya bellendenkerana (Cryptocarya bellendenkerana) | Population genetics (DArT) |
| Understanding genetic variation in Cyanothamnus inflexus populations | Cyanothamnus inflexus is a rock outcrop plant occurring in small, isolated populations, in habitats experiencing changing fire regimes. While historically small populations may be adapted to such conditions, their small area puts them at risk from local and global events. We must understand the influences on genetic variation to manage such challenges. Our work addresses a severe lack of knowledge about genetic variation in endemic rock outcrop shrubs, focusing on C. inflexus. DArTseq has been successful, but without a reference genome, analysis of inbreeding is limited. The closest reference genome is in Phebalium, which belongs to a distinct clade within the Australian radiation of Rutaceae. | Cyanothamnus inflexus (Cyanothamnus inflexus) | Reference genome (PacBio HiFi) |
| Genetic assessment to inform conservation of priority species in the MacDonnell Ranges | The MacDonnell Ranges bioregion in the Northern Territory is a high conservation priority, home to several rare and threatened species experiencing population declines. This project aims to assess the population genetic diversity, connectivity, and potential inbreeding of three priority species—Acacia undoolyana, Actinotus schwarzii, and Leucopogon sonderensis. By generating population genetic data, including clonality detection, this study will provide critical insights to guide conservation management actions. The findings will support evidence-based decision-making for species protection, potential listing of Leucopogon sonderensis, and interventions such as genetic rescue or habitat connectivity improvements. | Desert flannel flower (Actinotus schwarzii) | Population genetics (ddRAD) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants by establishing an ex-situ conservation reserve for 14 target species endemic to the Wet Tropics Bioregion in northeast Queensland. Among these is Dracophyllum sayeri, a vulnerable small tree endemic to two mountain tops, which faces a predicted 70% reduction in its climatic niche by 2055, and will benefit from genomic analysis to inform conservation strategies, including the selection of genotypes for propagation and prioritisation of wild populations for further study. | Dracophyllum sayeri (Dracophyllum sayeri) | Population genetics (DArT) |
| Connecting dugong populations with genomic tools | Dugongs are listed as “vulnerable” (a subset of “threatened”) by the IUCN, with numbers declining in most of their range. Recent studies in the Great Barrier Reef region suggest greater genetic differentiation between populations than previously thought, but we have very limited understanding of their population structure in WA and the NT. Key priorities for Traditional Owners managing sea country can be addressed using genetics, e.g. whether populations are fragmented or connected, their inbreeding levels, and whether dugongs move between different sea countries. Tackling these will enable us to advise on useful conservation units.The TSI has previously funded a dugong reference genome, which we will be able to use for assembling reads. | Dugong (Dugong dugon) | Reference genome (resequencing) |
| Genomic resource in support of conservation efforts for the Dugong | Dugong (Dugonginae dugon) | Reference genome (resequencing) | |
| Enabling effective population management of East Gippsland Galaxias through genomic resources | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | East Gippland Galaxias (Galaxias aequippinis) | Reference genome (PacBio HiFi) |
| Sequencing the hidden genomes of underground orchids | The conservation of the mysterious underground orchids of Australia, is extremely challenging since even the flowers remain hidden in the leaf litter. Currently, 5 species are recognised, with the two WA species already on the IUCN Red List. Rhizanthella slateri, is listed on both Commonwealth and State lists, while the new described R. speciosa is undergoing evaluation. Unexpectedly, preliminary genetic analysis indicates unexpected population genetic and taxonomic complexity amongst NSW populations. As a key step towards resolving these issues, we propose genome sequencing as a crucial resource for building a downstream robust and informative series of genetic markers for future population, phylogenetic and eDNA applications. | Eastern Australian Underground Orchid (Rhizanthella slateri) | Reference genome (PacBio HiFi, transcriptome) |
| Enhancing genetic diversity in eastern barred bandicoots | Extinct in the wild on mainland Australia, eastern barred bandicoots (EBBs) have experienced severe genetic bottlenecks, prompting efforts to interbreed Tasmanian and Victorian populations to enhance genome-wide diversity. This project will assess whether genetic diversity is sustained across generations of interbred populations, providing critical insights to inform future conservation management practices. | Eastern barred bandicoot (Perameles gunnii) | Reference genome (PacBio HiFi, transcriptome), Population genetics (ddRAD) |
| Enhancing genetic health for eastern chestnut mouse recovery | The Eastern Chestnut Mouse (ECM) has experienced a fragmented distribution and significant declines, with the species facing challenges in detection and translocation efforts in New South Wales. This project aims to assess the genetic health of captive and reintroduced ECM populations, identify key conservation actions for improving genetic diversity, and inform future reintroduction strategies, ultimately enhancing the species' long-term persistence. | Eastern chestnut mouse (Pseudomys gracilicaudatus) | Population genetics (ddRAD) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants by establishing an ex-situ conservation reserve for 14 target species endemic to the Wet Tropics Bioregion in northeast Queensland. One of these species, Eucryphia wilkiei, a critically endangered shrub found only in a small population on Mt Bartle Frere, faces a predicted 62% reduction in its climatic niche by 2055 and will benefit from genomic analysis to inform conservation strategies, including the prioritisation of wild populations and selection of genotypes for propagation. | Eucryphia wilkiei (Eucryphia wilkiei) | Population genetics (DArT) |
| Advancing conservation strategies for Fontainea sp. 'Coffs Harbour' using genomic sequencing | Fontainea sp. ‘Coffs Harbour’, a critically endangered rainforest tree with only seven known adult individuals, faces immediate threats due to habitat loss and isolation from the Coffs Harbour bypass project. This project aims to establish the species' genomic sequence to inform propagation, translocation, and long-term conservation efforts, ensuring genetic diversity and resilience while creating a valuable genomic resource for managing this and other threatened Fontainea species. | Fontainea sp. Coffs Harbour (Fontainea sp. Coffs Harbour) | Reference genome (PacBio HiFi, transcriptome) |
| Developing advanced genetic monitoring and genomic resources to support conservation of the ghost bat and enhance resilience to threats | This project aims to develop advanced genetic monitoring protocols and genomic resources to support the conservation of the Vulnerable ghost bat (Macroderma gigas), addressing critical actions such as assessing population sizes, disturbance impacts, and remnant population connectivity. By creating a high-quality reference genome and SNP panels, this work will enhance cost-effective monitoring, inform conservation strategies, and contribute to broader comparative genomic research, with significant implications for understanding species resilience to environmental and anthropogenic threats. | Ghost bat (Macroderma gigas) | Reference genome (PacBio HiFi, transcriptome), Population genetics (SNP multiplex) |
| Genomic foundations for understanding host plant specificity in Synemon plana | Though the Synemon genus demonstrates host plant specificity, S.plana has been found to be feeding on Chilean Needlegrass (CNG) as well as native hosts; a problem for weed management. This would become the first genome for the Castniidae, providing an opportunity to understand the evolution of host plant specificity in the family. WGS will provide a basis for the development of (currently limited) population genomic tools; sampling restrictions mean this species is not suitable for standard genomic approaches (e.g., DArT). Targeted approaches can be developed from genomic data that would be suitable for museum and minimally invasive sampling. A transcriptome from the GSM is the only available genomic resource for their genus. | Golden Sun Moth (Synemon plana) | Reference genome (PacBio HiFi, transcriptome, resequencing) |
| Investigating genetic variation and adaptation in rock outcrop Boronia species | PhD student Peter Pemberton is studying the molecular ecology of rock outcrop endemic shrubs, including several listed Boronia species • B. granitica (EPBC & Qld EN, NSW VU) • B. repanda (EPBC, Qld & NSW EN) • B. boliviensis (NSW EN) • B. amabilis (QLD Near Threatened) Peter is examining genetic variation and local adaptation to address a severe gap in knowledge about genetic structure in rock outcrop shrubs, which typically occur in small, isolated populations that are at risk from localised events such as fires. We have conducted DArTseq for these species with disappointing results. It is possible that ddRAD may provide more useful data. There is not yet a reference genome in Boronia or any close relative. | granite boronia, granite rose, Bolivia Hill boronia, Wyerba boronia (Boronia granitica, B. repanda, B. boliviensis, B. amabilis) | Reference genome (PacBio HiFi) |
| Genetic diversity and population management for GGBF reintroduction | GGBF is listed as Endangered in NSW and Vulnerable at the Commonwealth level. Once common in NSW and Victoria, the species drastically declined from 1960 due to chytrid fungus, habitat loss, and competition from introduced fish. The Saving our Species (SoS) program addresses threats to GGBF at priority sites in NSW. This includes translocation at the Molonglo site. Originally planned for 2021/22 as population augmentation, no GGBF have been detected there for three seasons. Re-introduction from another population is needed. Effective re-introduction requires understanding genetic diversity, inbreeding, and population sizes. This ensures appropriate source populations are selected, maintaining genetic integrity and maximizing diversity. | Green and Golden Bell Frog (GGBF) (Litoria aurea) | Population genetics (DArT) |
| Enhancing immunity and resilience in green and golden bell frogs | The Green and Golden Bell Frog (Litoria aurea) has suffered dramatic population declines due to chytridiomycosis, and current conservation efforts rely heavily on captive breeding, which is not a sustainable long-term solution. This project aims to generate a high-quality reference genome for L. aurea, enabling the identification of genetic regions associated with disease resistance, and will use genomic selection, gene editing, and synthetic biology to enhance amphibian immunity, providing a pathway for more resilient, self-sustaining wild populations. | Green and golden bell frog (Litoria aurea) | Reference genome (PacBio HiFi, Hi-C) |
| Enhancing population estimates for the grey nurse shark | This project aims to improve the accuracy of grey nurse shark population estimates by addressing uncertainties in previous abundance data through enhanced genomic resources, including genome sequencing and SNP discovery. The resulting data will inform decisions on the potential easing of fishing restrictions in aggregation areas and provide valuable insights into reproductive connectivity, supporting the conservation and management of the species. | Grey Nurse Shark (Carcharias taurus) | Reference genome (PacBio-HiFi) |
| Hairy marron (Cherax tenuimanus) | Reference genome (PacBio HiFi) | ||
| Improving genetic strategies for northern hairy-nosed wombat recovery | The northern hairy-nosed wombat is critically endangered, and genetic management is vital for the success of population establishment and supplementation efforts. This project aims to improve census accuracy, assess genetic health, and refine translocation strategies through SNP analysis, providing key insights to enhance reintroduction outcomes and genetic diversity. | Hairy nose wombat (Lasiorhinus krefftii) | Reference genome (PacBio HiFi) |
| Unlocking reproductive potential in Haloragodendron lucassii through comparative genomics | Haloragodendron lucassii is extensively clonal, with only 7 genets due to its very low pollen viability (<4%) resulting in no viable seed. A ReCER study revealed high diversity (HO = 0.202) and 4838 alleles shared across genets. Their limited relatedness suggests that inducing sexual reproduction could “restore” the species. Investigating genomic rearrangements or mutations can elucidate low fertility due to genomic incompatibilities. Understanding demography history and factors influencing lack of reproduction will guide conservation/translocations strategies. H. gibsonii is rare and capable of sexual reproduction, serving as a genomic model for comparison. Comparing synteny may explain differences in genome structure inhibiting crossing. | Hal (Haloragodendron lucasii) | Reference genome (PacBio HiFi, resequencing) |
| Genetic resilience of Hastings River mouse post-bushfire | This project aims to assess the genetic structure, diversity, and effective population size of Hastings River mouse populations pre- and post-bushfire to evaluate genetic changes and inbreeding. The findings will guide conservation management, ensuring the protection of genetically distinct populations and the identification of appropriate management units. | Hastings river mouse (Pseudomys oralis) | Population genetics (ddRAD) |
| Genetic connectivity and diversity in Tasmanian snow skinks | Three Tasmanian endemic snow skinks (Carinascincus) are restricted to elevations >1000m, surrounded by warmer lowland environments occupied by different Carinascincus likely at a competitive advantage. High alpine skinks are potentially threatened from climate change. Genetic diversity and connectivity between populations is unknown, including the potential for cryptic species in these morphologically conserved taxa. Two species also appear to hybridise, but the extent is unknown. We will address these knowledge gaps to assist prioritisation of populations for monitoring and conservation, including translocation and captive breeding. The C. ocellatus reference genome enables assessment of functional variation among populations. | High alpine snow skinks (northern snow skink, southern snow skink, Tasmanian mountain skink) (Carinascincus greeni, C. microlepidotus, C. orocryptus) | Population genetics (DArT) |
| Refining conservation strategies for the Hooded Plover | The eastern subspecies of Hooded Plover is nationally vulnerable, and this project aims to refine conservation strategies by identifying distinct populations and management units across its broad range in Australia. By analyzing genetic variation through sequencing and SNP analysis, the project will enhance understanding of population structure and dispersal patterns, ultimately informing targeted, evidence-based management efforts to optimize conservation actions for the species. | Hooded plover (Thinornis rubricollis) | Reference genome (PacBio HiFi, transcriptome), Population genetics (DArT) |
| Howard Springs toadlet (Uperoleia daviesae) | Reference genome (PacBio HiFi, transcriptome) | ||
| Conserving the critically endangered King Island Brown Thornbill | The King Island Brown Thornbill, a critically endangered species endemic to King Island, is facing severe population decline due to habitat loss, with fewer than 150 individuals remaining. This project aims to assess the bird’s genetic structure, population viability, and potential taxonomic status, providing crucial data to guide conservation actions and inform the development of a recovery plan to protect the species from extinction. | King Island brown thornbill (Acanthiza pusilla magnirostris) | Reference genome (PacBio HiFi, transcriptome, resequencing) |
| Genetic management for the conservation of King Island scrubtit | The King Island Scrubtit, a critically endangered subspecies, faces severe population decline due to habitat loss, fragmentation, and inbreeding, with only small, isolated subpopulations remaining. This project aims to assess the genetic diversity, structure, and inbreeding risks of the remaining populations, informing management strategies for habitat restoration, potential genetic rescue through translocation or introgression, and improving the long-term viability of the species. | King Island scrubtit (Acanthornis magna greeniana) | Reference genome (PacBio HiFi, transcriptome), Population genetics (ddRAD) |
| Kroombit Tinker Frog (Taudactylus pleione) | Reference genome (PacBio HiFi, transcriptome) | ||
| Genetic management for Christmas Island skink and gecko | The Blue-tailed Skink and Lister's Gecko, both critically endangered species endemic to Christmas Island, have been conserved through captive breeding and successful introduction programs. This project aims to use genomic analyses to refine genetic management strategies for both species, informing future supplementation and release efforts to enhance population viability and ensure long-term conservation. | Lister's gecko (Lepidodactylus listeri) | Reference genome (PacBio HiFi, Hi-C, transcriptome), Population genetics (DArT) |
| Informing genetic management of WA little penguins | This project aims to assess the genetic diversity and relatedness of captive WA provenance little penguins, which are genetically distinct from eastern and southern Australian populations, in order to inform future breeding and conservation strategies. By comparing the genetic profiles of the captive WA population to wild penguins from Penguin Island and the south coast, the project will ensure effective genetic management and contribute to the preservation of this declining species through appropriate breeding program designs. | Little penguin (Eudyptula minor) | Reference genome (PacBio HiFi), Population genetics (DArT) |
| Developing genomic resources for the little pygmy perch conservation | The little pygmy perch is a small Endangered freshwater fish localised to four rivers and three lakes/wetlands and threatened by declining habitat, salinisation, and invasive species. Low genetic diversity is also a known threat to other pygmy perches. Establishing new populations is key to persistence, and several natural and artificial water points have been identified as suitable translocation sites. Captive-breeding and translocations informed by genomics have been successful in pygmy perches, are not yet possible due to limited population genomic data. New genomic resources are urgently needed to assess genetic diversity in the species and inform captive breeding and translocation design. | Little pygmy perch (Nannoperca pygmaea) | Population genetics (ddRAD) |
| Genomic resource in support of conservation efforts of the Long-Sepaled Rhodomyrtus | Long-Sepaled Rhodomyrtus (Rhodomyrtus longisepala) | Reference genome (resequencing) | |
| Understanding genetic structure of Placostylus bivaricosus for conservation | Placostylus bivaricosus, endemic to Lord Howe Island (LHI), has four recognised subspecies but only one, P. bivaricosus bivaricosus, is known to be extant. A second subspecies may be present in very low numbers. Extreme reduction in abundance and population fragmentation is likely to have negatively impacted this species' genetic diversity. In order to improve conservation outcomes for this species, we need to understand the genetic structure of the populations, allowing for management actions such as cross-breeding between populations or translocations to new areas. While sequences are available for some members of Placostylus (including complete mitochondrial genomes for 4 species), no population genomic studies have been carried out. | Lord Howe Island Flax Snail (Placostylus bivaricosus) | Reference genome (PacBio HiFi), Population genetics (DArT) |
| Understanding genetic barriers in Lord Howe Island stick insect | We need to examine the amount of standing genetic variation in captive-bred stick insect populations and estimate the amount of heritable genetic variation in advance of reintroducing them back to Lord Howe Island. | Lord Howe Island stick insect (Dryococelus australis) | Population genetics (bait) |
| Genomic insights for Mahony’s and dusky toadlet conservation | Mahony’s toadlet is a highly range restricted, endangered frog that was discovered only recently. We will develop and assess a suite of genomic tools that will provide critical information needed to make informed decisions to enhance conservation outcomes. The current project with NSW DCCEEW addresses the following questions: • Determine population status, threatening processes, and ecological parameters required for setting management objectives • Apply genomic approaches to reconstruct population history and fragmentation, utilising a comparative approach involving a common sympatric congener, the Dusky Toadlet which is a widespread species. We will compare both species to identify genomic signals associated with species decline. | Mahony’s Toadlet, Dusky Toadlet (Uperoleia mahonyi, Uperoleia fusca) | Reference genome (PacBio HiFi, transcriptome) |
| Genomic insights for Myrtle Rust resistance in Lenwebbia | Myrtle Rust, caused by the fungal pathogen Austropuccinia psidii, has devastated numerous Australian Myrtaceae species, with several becoming Critically Endangered. This project aims to apply genomic studies to Lenwebbia sp. Main Range, a species severely impacted by Myrtle Rust, to characterize genetic variation, inform germplasm collection efforts, and enhance conservation strategies for this narrow-range endemic. | Main Range lenwebbia (Lenwebbia sp.) | Reference genome (PacBio HiFi, resequencing) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to safeguard Australia’s climate-threatened tropical mountaintop plants by establishing an ex-situ conservation reserve for 14 endemic species from the Wet Tropics Bioregion in northeast Queensland. One of these species, Flindersia pimenteliana, a vulnerable tree, will benefit from genomic analysis to assess its genetic diversity, guiding conservation actions, resource allocation, and the selection of suitable genotypes for future ex-situ conservation efforts. | Maple silkwood, red beech or rose silkwood (Flindersia pimenteliana) | Population genetics (DArT) |
| Preserving the genetic diversity of Banksia cuneata through genomic analysis and conservation planning | Banksia cuneata, an endangered Western Australian species with fewer than 700 individuals remaining across fragmented and declining populations, faces threats from habitat loss, disease, and environmental pressures. This project will use genomic resources to assess genetic diversity, evaluate the success of past conservation efforts, and inform recovery strategies to preserve the species’ genetic health and guide future translocations and seed banking initiatives. | Matchstick banksia (Banksia cuneata) | Population genetics (ddRAD) |
| utilizing genomic data to support the recovery and habitat restoration of Maugean skate | The Maugean skate, a critically restricted species found almost exclusively in Tasmania's Macquarie Harbour, faces severe threats from environmental degradation and climate change, prompting its inclusion on the Threatened Species Strategy. This project aims to establish a reference genome, evaluate genetic diversity, and inform adaptive conservation strategies, providing essential genomic tools to support recovery efforts, maintain genetic health, and guide management actions such as captive breeding and habitat restoration. | Maugean Skate (Zearaja maugeana) | Reference genome (PacBio HiFi, transcriptome, resequencing), Population genetics (DArT) |
| Genetic tools for advancing the conservation of McDowall's Galaxias | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | McDowall's Galaxias (Galaxias mcdowalli) | Reference genome (PacBio HiFi) |
| Assessing genetic diversity and population viability for Mitchell's Rainforest Snail conservation | The conservation biology of this species has been studied by Murphy (2002), Andrade et al. (2011), Parkin (2014), Parkyn et al. (2014) and Parkyn et al. (2015). Habitat loss and fragmentation are main threatening processes. The global population has been estimated to be < 500 individuals. Low dispersal ability, small population size, population fragmentation effect genetic diversity. Effective management requires knowledge of genetic diversity and viability of known isolated populations and understanding if populations in protected areas are representative of the global genetic diversity. Estimates of relative population sizes would be helpful to better prioritize management actions in specific locations. | Mitchell's Rainforest Snail (Thersites mitchellae) | Reference genome (PacBio HiFi, transcriptome) |
| Reference genomes for water monitor conservation | Varanus mitchelli and Varanus mertensi are recognised by the IUCN and EPBC Act as Critically Endangered and Endangered and undergoing population decline. Both species were added to the EPBC Act in December 2023. Continuing population declines are primarily linked to the spread of cane toads, and while official conservation advice is to “support remnant subpopulations that are resilient to cane toads” (DCCEW SPRAT Profiles) there are no population genetic assessments of these species. Genomic resources are critical to assessing population and species level genetic health, informing how they should be managed. This request for reference genomes will dovetail with future population genomic work to inform their applied conservation. | Mitchell's Water Monitor; Mertens's Water Monitor (Varanus mitchelli; Varanus mertensi) | Reference genome (PacBio HiFi, transcriptome) |
| Genomic resource to support the conservation efforts of the Mount Lidgebird pinwheel snail | Collaboration with the Australian Museum | Mount Lidgebird pinwheel snail (Pseudocharopa ledgbirdi) | Reference genome (PacBio HiFi) |
| Genetic assessment to inform conservation of priority species in the MacDonnell Ranges | The MacDonnell Ranges bioregion in the Northern Territory is a high conservation priority, home to several rare and threatened species experiencing population declines. This project aims to assess the population genetic diversity, connectivity, and potential inbreeding of three priority species—Acacia undoolyana, Actinotus schwarzii, and Leucopogon sonderensis. By generating population genetic data, including clonality detection, this study will provide critical insights to guide conservation management actions. The findings will support evidence-based decision-making for species protection, potential listing of Leucopogon sonderensis, and interventions such as genetic rescue or habitat connectivity improvements. | Mount Sonder beard-heath (Leucopogon sonderensis) | Population genetics (ddRAD) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants through an ex-situ conservation reserve. Uromyrtus metrosideros, a widespread shrub found in the Wet Tropics Bioregion, will undergo genomic analysis to understand its phylogeography, inform conservation strategies for co-occurring listed species, and help mitigate its predicted decline due to climate change. | Mountain malletwood, redbark austromyrtus, (Uromyrtus metrosideros) | Population genetics (DArT) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants through an ex-situ conservation reserve, focusing on 14 endemic species from the Wet Tropics Bioregion in northeast Queensland. One of these species, Flindersia oppositifolia, a vulnerable tree found on only two mountain tops, faces a predicted 88% reduction in its climatic niche by 2055, and genomic analysis will help inform conservation strategies and complement ongoing ecophysiological studies of its climate tolerance. | Mountain silkwood (Flindersia oppositifolia) | Population genetics (DArT) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to safeguard Australia’s climate-threatened tropical mountaintop plants through an ex-situ conservation reserve. Zieria alata, a critically endangered shrub known from only two populations on the Carbine Tableland, will be included in genetic analysis to inform conservation strategies and preserve its genetic diversity, addressing its predicted extinction due to climate change by 2055. | Mt Lewis stink bush (Zieria alata) | Population genetics (DArT) |
| Genomic insights for Murray crayfish conservation | Euastacus armatus, a threatened freshwater crayfish species endemic to the Murray-Darling Basin, has experienced severe population declines due to environmental disturbances, including blackwater events. This project aims to enhance conservation efforts by generating high-quality genomic data to assess genetic diversity, inform reintroduction strategies, and guide the protection of remaining populations, ultimately supporting the long-term recovery of the species. | Murray crayfish (Euastacus armatus) | Reference genome (resequencing) |
| Genomic insights into the ecology and conservation of Cormodes darwini | Cormodes darwini was recently recognised as a critically endangered beetle species, being present on only a single small island (Blackburn Island) in the Lord Howe Island Group. Genomic analyses are required to assess genetic diversity of the species, which is expected to be low due to small population size, and also its genetic distance from its closest relatives. Dr Chris Reid proposes that genomic data on gut contents would be highly useful to determine what this predatory beetle feeds on, because very little is known about its ecology. | n/a (known officially as "a beetle") (Cormodes darwini) | Reference genome (PacBio HiFi, resequencing) |
| Enhancing genetic diversity and resistance in native guava | Highly vulnerable to Myrtle Rust, this species is in rapid decline, necessitating the establishment of ex-situ collections to preserve genetic diversity and support translocation and recovery efforts. This project will identify and maximise genetic diversity, advance research on Myrtle Rust resistance, and contribute to broader studies on at-risk species, informing long-term conservation strategies. | Native guava (Rhodomyrtus psidioides) | Reference genome (PacBio-HiFi, resequencing) |
| Genomic resource in support of conservation efforts of the Night parrot | Night parrot (Pezoporus occidentalis) | Reference genome (resequencing) | |
| Genomic insights for the conservation of Nightcap oak | Eidothea hardeniana, a rainforest tree endemic to northern NSW, faces significant threats from habitat loss, past logging, and recent bushfires, with only a single population remaining in Nightcap National Park. This project aims to produce a high-quality reference genome for Eidothea hardeniana and compare it to the genome of the related vulnerable species Eidothea zoexylocarya, providing crucial genomic insights to inform conservation actions, including translocation, and contributing to broader research on plant genome diversity in the Proteaceae family. | Nightcap oak (Eidothea hardeniana) | Reference genome (PacBio HiFi) |
| Genetic health and breeding strategies for corroboree frogs | The northern and southern corroboree frogs, critically endangered due to disease, habitat loss, and bushfires, are undergoing intensive conservation efforts, including captive breeding programs at multiple institutions. This project aims to assess genetic diversity in both wild and captive populations using SNP genotyping, inform breeding strategies through cutting-edge conservation genetics, and integrate these findings with genomic resources to ensure the long-term survival and genetic health of these iconic species. | Northern corroboree frog (Pseudophryne pengilleyi) | Population genetics (DArT) |
| Developing a reference genome to support conservation of the orange-bellied parrot and enhance immune diversity | This project aims to develop a reference genome for the species to enhance understanding of immune diversity and address its vulnerability to disease events. By aligning existing genomic data to the reference genome, this work will provide critical insights to inform recovery team management actions and support conservation efforts. | Orange belly parrot (Neophema chrysogaster) | Reference genome (PacBio HiFi, Hi-C, transcriptome) |
| restoring the extinct-in-the-wild Pedder Galaxias through genetic diversity analysis and supplementation strategies | The Pedder galaxias, endemic to Tasmania and listed as extinct in the wild, survives in only two translocated populations isolated from its historical range. This project aims to assess genetic diversity, determine potential introgression with the closely related G. brevipinnis, and provide management strategies to guide population supplementation and establish new populations, ensuring the species' long-term conservation and genetic integrity. | Pedder Galaxias (Galaxias pedderensis, TAS) | Population genetics (ddRAD) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia's climate-threatened tropical mountaintop plants through ex-situ conservation by generating genomic data for 14 target species, including the vulnerable Cinnamomum propinquum. This project will inform resource allocation for cultivating plants, selecting propagated genotypes for distribution across conservation sites, and prioritizing wild populations for further field expeditions, ultimately helping to preserve species like Cinnamomum propinquum, which is facing a predicted 100% reduction in its climatic niche by 2055 due to climate change. | Pepperwood (Cinnamomum propinquum) | Population genetics (DArT) |
| Improving genetic diversity and population numbers in Plains-wanderer | The Plains-wanderer is one of Australia’s rarest and most unique birds. Population declines have led to small, disconnected populations across Australia. Current management is focused on improving genetic diversity and population numbers through breeding, wild release, and habitat management and improvement. Inferences from DArT-seq data for wild birds are hindered by the quality of genotyping, with high missingness across samples, likely resulting from the low-quality reference genome for the species. Analyses have failed to differentiate among populations and have recovered lower than expected heterozygosity. Whether these patterns are caused by missing data or the biology of the species remains uncertain, hindering appropriate actions. | Plains-wanderer (Pedionomus torquatus) | Reference genome (PacBio HiFi, resequencing) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project seeks to protect climate-threatened plant species endemic to Australia’s tropical mountain tops through an ex-situ conservation reserve. One of the species targeted, Polyscias bellendenkerensis, a small tree at risk of an 80% reduction in its climatic niche by 2055, will undergo genomic analysis to guide conservation efforts, resource allocation, and prioritise field expeditions to secure its genetic diversity and future survival. | Polyscias bellendenkerensis (Polyscias bellendenkerensis) | Population genetics (DArT) |
| Genomic assessment to guide conservation of the critically endangered Prostrate flame flower | Chorizema humile, the prostrate flame flower, is a critically endangered species with small, fragmented populations across Western Australia. This project will use genomic data to assess genetic diversity, population structure, and inbreeding levels, evaluating the success of past translocations and seed banking efforts. The findings will inform conservation actions, including population augmentation, optimal germplasm selection, and translocation strategies to support species recovery. | Prostrate flame flower (Chorizema humile) | Population genetics (ddRAD) |
| Genetic Analysis and Conservation of the Regent Honeyeater | This project aims to generate a reference genome for the Regent Honeyeater and evaluate the genetic diversity of captive-bred populations at Taronga Zoo. | Regent honeyeater (Anthochaera phrygia) | Reference genome (PacBio HiFi, transcriptome), Population genetics (ddRAD) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to secure the future of Australia’s climate-threatened tropical mountaintop plants through an ex-situ conservation reserve. Rhodamnia longisepala, a critically endangered tree-like shrub impacted by Myrtle Rust, will undergo genomic analysis to inform conservation strategies, improve genetic diversity preservation, and guide field expeditions to enhance its survival and resilience in the face of climate change and disease threats. | Rhodamnia longisepala (Rhodamnia longisepala) | Population genetics (DArT) |
| Genetic health and recovery strategies for the Richmond birdwing | Loss and fragmentation of the Richmond birdwing’s habitat since European settlement has resulted in a reduction in the species' range of approximately 60%. Forest fragmentation has isolated certain birdwing subpopulations, potentially leading to inbreeding and poor genetic health. Information on the species’ population’s genetic health is crucial to the development of an effective recovery strategy, but is currently lacking. Between 2010 and 2018, captive breeding and release was employed to enhance the genetic diversity of the wild population by sourcing individuals from geographically distant subpopulations then releasing the captive-bred offspring back into the wild to augment existing subpopulations or establish new subpopulations. | Richmond birdwing (Ornithoptera richmondia) | Population genetics (ddRAD) |
| Developing genomic resources for the salamanderfish conservation | The salamanderfish, Lepidogalaxias salamandroides, is a freshwater fish endemic to the far south-west of Western Australia, the sole member of a 250 million-year-old lineage. It occurs in ephemeral wetlands, where it aestivates over the dry season in moist soil. Declines in rainfall and groundwater have driven a severe range reduction, and there is an urgent need to develop strategies such as captive breeding and translocation. However, no genomic resources are available to guide such programs. Here, we propose to assemble a reference genome and undertake ddRAD sequencing and reference-guided SNP alignment across populations. These data will be used to guide sourcing of individuals for potential captive breeding or translocation. | Salamanderfish (Lepidogalaxias salamandroides) | Reference genome (PacBio HiFi, HiC), Population genetics (DArT) |
| Enhancing resistance in Rhodamnia rubescens | Rhodamnia rubescens, critically endangered due to myrtle rust, faces challenges in recruitment and survival, but a small number of resistant plants have been identified. This project aims to enhance resistance in managed populations through genetic screening, using genomic prediction models to identify resistant seedlings for translocation, while maintaining genetic diversity and supporting the species' recovery. | Scrub Turpentine (Rhodamnia rubescens) | Reference genome (resequencing) |
| Population genetics of translocated western barred bandicoots | This project aims to evaluate the population genetics of translocated western barred bandicoots (WBB) to determine interbreeding success and its impact on genetic diversity. The results will inform conservation strategies to enhance genetic health and resilience in both native and translocated populations. | Shark bay bandicoot (Perameles bougainville) | Reference genome (transcriptome), Population genetics (ddRAD) |
| conserving Shaw Galaxias through genetic diversity assessment and conservation action | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | Shaw Galaxias (Galaxias gunaikurnai) | Reference genome (PacBio HiFi) |
| Genetic assessment to inform conservation of priority species in the MacDonnell Ranges | The MacDonnell Ranges bioregion in the Northern Territory is a high conservation priority, home to several rare and threatened species experiencing population declines. This project aims to assess the population genetic diversity, connectivity, and potential inbreeding of three priority species—Acacia undoolyana, Actinotus schwarzii, and Leucopogon sonderensis. By generating population genetic data, including clonality detection, this study will provide critical insights to guide conservation management actions. The findings will support evidence-based decision-making for species protection, potential listing of Leucopogon sonderensis, and interventions such as genetic rescue or habitat connectivity improvements. | Sickle leaf wattle (Acacia undoolyana) | Population genetics (ddRAD) |
| Genetic management and conservation of spidery wattle | Spidery Wattle (Acacia araneosa ) is an endangered species of Acacia only found in two small populations in the Vulkathunha Gammon Ranges National Park. The species has an extremely restricted range and is highly vulnerable to threats such as fire, grazing, pests, disease, and climate change and the species is declining. A notable feature of the species is that it often ‘reverts’ to a form similar to the closely related Creek Wattle (Acacia rivalis) when cultivated, even when seed is collected from wild stands. We hope to sequence samples of Spidery Wattle, representing all known stands alongside a small number of Creek Wattle specimens collected from a geographically close proximity. This will allow us to develop a management plan for the species by a) identifying the genetic differences/similarities between Spidery Wattle and Creek Wattle and clarifying species boundary and b) identifying any genetic structure, levels of genetic diversity and inbreeding amongst Spidery Wattle populations and developing a genetic management plan for the species. C) identifying regions of the genome under selection and identifying their genetic function by utilising the Bioplatforms reference genome for the Golden Wattle (Acacia pycnantha). | Silver wattle (Acacia rivalis) | Population genetics (ddRAD) |
| Genomic resource to assist the conservation management of the smoky mouse | Collaboration with The Department of Environment, Land, Water and Planning (now Department of Energy, Environment and Climate Action) | Smoky mouse (Pseudomys fumeus) | Reference genome (resequencing) |
| Genomic rescue for smooth scrub turpentine | R. maideniana, is critically endangered in NSW and QLD, where has drastically declined due to its high susceptibility to Myrtle rust, showing no resistance. Hence, it is in need of urgent conservation actions. ReCER has already generated reference genomes for MR impacted species (some supported by TSI). DArT seq data is available for R. maideniana. The genomic data resulting from this project will provide unbiased and detailed analysis of the entire genome, enabling insights on resistance, inbreeding and demographic history. The research will support species survival, and progress towards securing all nationally listed species impacted by myrtle rust. | Smooth Scrub Turpentine (Rhodamnia maideniana) | Reference genome (PacBio HiFi, resequencing) |
| Genetic diversity and conservation of spidery wattle | Spidery Wattle (Acacia araneosa), an endangered species with a highly restricted range, is threatened by multiple factors including climate change, grazing, and disease, and exhibits genetic similarities to the closely related Creek Wattle (Acacia rivalis). This project aims to clarify species boundaries, assess genetic diversity, and identify regions under selection, ultimately informing a genetic management plan to guide conservation and recovery efforts for Spidery Wattle. | Spidery wattle (Acacia araneosa) | Population genetics (ddRAD) |
| Enhancing genetic diversity and propagation of spiny daisy | Acanthocladium dockeri, Critically Endangered due to its limited range, fragmented populations, and lack of genetic diversity, faces significant survival challenges, including limited seed germination and reproduction. This project aims to assess and enhance the genetic diversity of the species through translocations, establish secure populations in natural habitats, and improve propagation techniques, ultimately supporting long-term conservation efforts for this critically endangered plant. | Spiny daisy (Acanthocladium dockeri) | Population genetics (ddRAD) |
| Genetic management for spotted tree frog recovery | The Spotted Tree Frog, critically endangered and disappearing from half of its historical sites, is undergoing a comprehensive recovery project that includes captive breeding, translocations, and threat management. The project aims to manage genetic diversity, assess the contribution of released individuals to wild populations, and monitor the species’ response to conservation efforts, with anticipated outcomes including a Genetics Management Plan and a SNP panel to support long-term recovery. | Spotted tree frog (Litoria spenceri) | Population genetics (ddRAD) |
| enhancing conservation efforts for Stocky Galaxias through genetic management | The critically endangered Stocky galaxias, restricted to two isolated populations in NSW, faces significant threats from habitat loss and reduced genetic diversity, exacerbated by the 2019/20 bushfires. This project aims to use genomic analyses to inform translocations, optimise captive breeding strategies, and enhance genetic diversity, directly supporting recovery actions to secure the species' long-term survival. | Stocky Galaxias (Galaxias tantangara) | Population genetics (ddRAD) |
| Stuttering Frog (Mixophyes australis) | Reference genome (PacBio HiFi, transcriptome, HiC) | ||
| Reference genome development for conservation of Idiosoma spiders | Trapdoor spiders of the genus Idiosoma are a diverse, conservation-significant and data-deficient group across south-west WA (3 Endangered, 1 Vulnerable, 14 Priority species). Most are endemic to patchy refugial habitats, and threatened by climate change, habitat destruction, and invasive species. Conservation is hampered by a lack of population genetic data or reference genomes. Many species have such small populations that sacrificing an individual for genome construction is not feasible. Here, we propose to generate a reference genome for I. sigillatum, a Priority 3 species from the Swan Coastal Plain, which retains some locally abundant populations. This will be used for mapping of planned population genomic data across the genus. | Swan Coastal Plain shield-backed trapdoor spider (Idiosoma sigillatum) | Reference genome (PacBio HiFi) |
| Genetic structure and conservation of Swan galaxias | This project aims to assess the genetic structure and diversity of the Endangered Swan galaxias across its fragmented range, including comparisons between natural and translocated populations, to guide conservation translocations and protect genetic integrity. The findings will inform recovery efforts, ensure the preservation of unique lineages, and address hybridisation risks with other galaxiid species. | Swan galaxiid (Galaxias fontanus) | Reference genome (PacBio HiFi, transcriptome), Population genetics (ddRAD) |
| Enhancing swift parrot genetic diversity and conservation | The critically endangered swift parrot is facing significant population decline, and this project aims to use genomic analysis to assess its genetic diversity and adaptation potential. Key objectives include evaluating historical bottlenecks, genetic diversity in functional genes, and the suitability of the current captive population for breeding programs, ultimately informing strategies for species conservation and potential wild supplementation. | Swift parrot (Lathamus discolor) | Reference genome (PacBio HiFi, transcriptome) |
| improving population resilience of Tapered Galaxias through genetic insights | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | Tapered Galaxias (Galaxias lanceolatus) | Reference genome (PacBio HiFi) |
| Tropical Mountain Top Plant Science project | The Tropical Mountain Top Plant Science (TroMPS) project aims to protect Australia's climate-threatened tropical mountaintop plants through an ex-situ conservation reserve. Uromyrtus tenella, a shrub endemic to the Wet Tropics Bioregion, will be included in the project’s genomic analysis to better understand its genetic diversity, inform conservation priorities, and enhance ex-situ conservation efforts to mitigate its vulnerability to climate change. | Uromyrtus tenella (Uromyrtus tenella) | Population genetics (DArT) |
| Impacts of changing environments on south-eastern Australian dragon lizards | Grassland earless dragons (Tympanocryptis spp.) are highly vulnerable to habitat loss, fragmentation, and changing fire regimes, with several species endangered or possibly extinct. This project will use genomic analyses to assess demographic history, population structure, and hybrid zones, while also investigating the genetic basis of colour adaptation in response to fire. The findings will inform conservation strategies for wild populations and captive breeding programs, while also laying the groundwork for broader evolutionary studies on agamid lizards. | Victorian grassland earless dragon (Tympanocryptis pinguicolla) | Reference genome (PacBio HiFi), Population genetics (DArT) |
| Conserving Acacia peuce through population assessment and management | Acacia peuce, a long-lived but recruitment-limited tree, persists in three disjunct populations across arid inland Australia and faces multiple threats, including fire, grazing, and trampling. This project will use genomic data to assess population size, genetic diversity, clonality, inbreeding, and connectivity, informing the distinctiveness and origins of these isolated populations. The findings will guide conservation management by identifying sources for potential translocation, supporting seedling screening for relatedness, and enabling future provenance evaluation to aid the species' persistence. | Waddy (Acacia peuce) | Population genetics (ddRAD) |
| Assessing genetic diversity and connectivity in Watson’s tree frog | Watson’s Tree Frog (Litoria watsoni), an endangered species in southeast NSW and far eastern Victoria, faces genetic risks due to low variability and isolation of Victorian populations. This project aims to assess the genetic diversity and connectivity of Victorian populations to inform potential genetic management interventions, such as translocations, ensuring the species’ long-term persistence and resilience. | Watsons tree frog (Litoria watsoni) | Population genetics (DArT) |
| genomic-informed management for the long-term survival of West Gippsland Galaxias | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | West Gippsland Galaxias (Galaxias longifundus) | Reference genome (PacBio HiFi) |
| Supporting captive breeding and genetic management of the western ground parrot | With fewer than 150 individuals remaining in the wild and a small proof-of-concept captive population, the critically endangered western ground parrot (Pezoporus flaviventris) faces significant extinction risks. This project will assess the genetic diversity and relatedness of both wild and captive populations to inform conservation breeding strategies, optimise founder selection, and enhance genetic management for potential breed-for-release programs. Additionally, comparative genomic analyses with the eastern ground parrot and night parrot will refine species taxonomy and provide insights to guide broader conservation efforts. | Western ground parrot (Pezoporus flaviventris) | Reference genome (PacBio-HiFi, transcriptome, resequencing), Population genetics (ddRAD, SNP multiplex) |
| Western swamp tortoise genetic data for better conservation | The western swamp tortoise (Pseudemydura umbrina), is Critically Endangered and occurs in only a few ephemeral claypans on the Swan Coastal Plain. These wetlands are at risk of drying through altered hydrology and climate change. The Perth Zoo breeding program provides vital insurance for the species, by providing individuals for supplementations, translocations, and potential relocation to wetter southern sites. However, these efforts depend on the selection of captive-bred source individuals, which is hampered by the lack of genomic data. Further, individual relatedness is uncertain, given limited wild dispersal, and long-term sperm storage of females, which impacts pedigree management in the breeding program. | Western swamp tortoise (Pseudemydura umbrina) | Reference genome (PacBio HiFi, transcriptome, resequencing) |
| Enhancing conservation outcomes for White’s seahorse through genomics | The White’s seahorse, an endangered species endemic to eastern Australia, has experienced severe population declines due to habitat loss and extreme climatic events. This project aims to assess the genetic diversity, population structure, and adaptive strategies of H. whitei to inform and enhance captive-breeding programs, conservation stocking, and future eDNA monitoring, ultimately contributing to the species’ recovery and long-term survival. | White’s Seahorse (Hippocampus whitei) | Population genetics (ddRAD) |
| optimizing conservation strategies for Yalmy Galaxias through genomic analysis | Victorian Galaxias species, critically threatened by habitat disruption, invasive species, bushfires, and climate change, require urgent conservation interventions to ensure their survival. This project aims to generate high-quality reference genomes and transcriptomes for these species, enabling effective population monitoring, captive breeding management, and the identification of adaptive traits for genetic rescue and climate resilience, providing crucial tools for long-term conservation strategies. | Yalmy Galaxias (Galaxias sp. 14 'Yalmy') | Reference genome (PacBio HiFi) |
| Genetic rescue and recovery for the Yarra Pygmy Perch | The Yarra Pygmy Perch (YPP), listed as endangered and extirpated from the Murray-Darling Basin, is undergoing a genetic rescue project to restore genetic diversity and resolve potential genomic incompatibilities. This project aims to enhance recovery efforts through experimental crosses, pangenome sequencing, and captive breeding, supporting the species' reintroduction and long-term conservation as outlined in the National Recovery Plan. | Yarra Pygmy Perch (Nannoperca obscura) | Reference genome (PacBio HiFi, transcriptome) |
| Building genomic resilience in yellow scroll coral | One of Australia’s most iconic group of species, scleractinean reef corals, are on the front line of climate change impacts. For corals, the IUCN recommends numerous conservation needs (establishment of a genomic resource bank, restoration action, recovery management, and artificial propagation). Resources will be used to develop a recovery plan and genomic resource bank for future field-testing of the viability of introducing this declining species to degraded or new reefs south of its native range (translocation) or through assisted gene flow (Quigley, 2024) to curb their decline and boost resilience to the impacts of climate change. As warming pressures reefs, this data will be used to help conserve species in the wild. | Yellow Scroll Coral (Turbinaria reniformis) | Reference genome (resequencing) |
PARTNERS
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advisory committee members
Jeremy Burdon – Independent Chair
Adrian Dinsdale – The Plant Innovation Centre (PIC@PEQ)
Andrew Gilbert – Bioplatforms Australia
Brendan Rodoni – Agriculture Victoria
Deb Hailstones – NSW DPI
Kim Plummer – La Trobe University
Mark Gibberd – Centre for Crop and Disease Management, Curtin University
Markus Herderich – The Australian Wine Research Institute (AWRI)
Neena Mitter – Queensland Alliance of Agriculture and Food Innovation
Peter Langridge – University of Adelaide
Peter Solomon – Australian National University
Robert Coe – Australian Plant Phenomics Facility
Sarah Richmond – Bioplatforms Australia
CONTACT US
Project Manager
Sophie Mazard – Bioplatforms Australia
smazard@bioplatforms.com
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com