Upscaling genetic management of wildlife populations
ARC Linkage Project LP220200856 started 6 Feb 2024
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Investigators listed on Australian Research Council award: Sasha Pavlova and Paul Sunnucks (Monash U), John Morgan (La Trobe U), Jarod Lyon, Zeb Tonkin, Steve Sinclair (DEECA), Dan Harley, Michael Magrath (ZoosVic), Gunjan Pandey, Tom Walsh, Rebecca Jordan (CSIRO), Andrzej Killian (DArT), Ben Novak (Revive and Restore)
Postdoc: Diana Robledo-Ruiz (Monash U)
Contributors: Rahul Rane, Heng Lin Yeap, Andy Bachler, Andrew Young (CSIRO), Luke Pearce, Meaghan Duncan, Jerom Stocks (NSW DPI), Taylor Hunt (VFA), Bruce Quin, Amy Tipton, Lily Surace, Brad Farmilo, Jian Yen (DEECA), Kim Miller, Arabella Eyre, Nick Bradsworth (ZoosVic), Mark Lintermans (Fish Fondler Pty Ltd), Ashlee Hutchinson, Elizabeth Bennett (R&R), Jesús Castrejón-Figueroa (U NSW), Chris Hardy (CSIRO), Andrew Briggs (VFA), Susan Johnston (U of Edinburgh), Katherine Harrisson (LaTrobe), Cock Van Oosterhout (University of East Anglia), Hernán Morales (University of Copenhagen), Emily Roycroft (Monash), Luis Mijangos, Andrew Kovalchek (DArT) and many others!
Students: Emily Blackburn: Honours (Monash), Aleksandra Ostrowska: BIO3990 (Monash)
Universities: Monash University, La Trobe University
Linkage project Partner Organizations: Zoos Victoria, Victorian Department of Energy Environment and Climate Action (DEECA), Commonwealth Scientific and Industrial Research Organisation (CSIRO), New South Wales Department of Primary Industries (NSW DPI), Diversity Arrays Technology (DArT), Revive and Restore (R&R, funded by R&R Catalyst Science Fund), Victorian Fisheries Authority (VFA)
Helmeted Honeyeater, photo by Paul Sunnucks
Project summary:
Australia has many unique and much-loved wildlife species, whose populations are collapsing due to habitat loss and worsening conditions, notably warming climates, droughts, wildfires and floods. Their genetic diversity and population health are declining, threatening evolutionary resilience. Cheap and quick ways to monitor and improve population health are urgently needed. This project aims to use four endangered species to develop, automate, implement, showcase and distribute innovative processes that rescue biodiversity at scale. It will provide evidence-based solutions to conservation practitioners for strengthening genetic health of wildlife species and improving their resilience to environmental change.
Our project has three main objectives:
Objective 1: Determine genetic management best practice for improving the health, adaptability and long-term fitness of wildlife populations, using four learning-by-doing test cases of ongoing augmented gene flow, with monitored fitness outcomes.
Our four species (below) are threatened by extinction through various genetic problems (i.e. inbreeding, inbreeding depression, loss of genetic diversity including self-incompatibility, Allee effect, and loss of adaptive potential) and are at different stages of genetic rescue: human-assisted mixture of different genetic lineages, aiming to improve population health, reproduction and long-term persistence. Management interventions were co-designed with our Industry Partners Zoos Victoria, DEECA, NSW DPI, Fish Fondler and VFA, and tested during our previous ARC Linkage Project Genetic Rescue. Our partners continue to monitor populations under genetic rescue and collect invaluable field data on individual health and reproductive fitness. Using whole-genome sequencing or reduced-representation DArTseq SNP datasets we will investigate which interventions are most successful, design the best indices for monitoring the outcomes and consider how best to arm population with genetic variation necessary for adaptation. A great strength of our project is the ability to use fitness data to validate the mutation-prediction and candidate loci approaches for assessing types of genetic variation that are assumed to underlie individual fitness. Our target species differ in key attributes, including major taxon, life history, geographic/environmental range, number of populations and genome size. This will allow us to generalize our findings to inform genetic management of other species. Validated genomic indicators of fitness will allow managers to rapidly and cost-effectively assess population health and augment gene flow to prevent extinctions.
Button wrinklewort Rutidosis leptorrhynchoides, photo by Steve Sinclair
This Endangered daisy of grasslands and woodlands occupies disjunct ranges in Victoria and NSW/ACT. The self-incompatible (SI) mating system in this species poses an additional genetic issue: reduced variation at SI-loci. Within- and between- population crosses were planted in grids in four environmentally-different locations, with one additional grid planned. This set up will allow us to investigate relative effects of genome-wide genetic diversity, SI diversity and local adaptation on survival and reproductive fitness in different climates.
Macquarie perch Macquaria australasica, photo by Luke Pearce
This Endangered freshwater fish was historically widespread and abundant. To prevent small remnant populations in the Murray Darling Basin from imminent inbreeding, translocations are being undertaken in several catchments of the Murray Darling Basin (inland lineage). Some evidence of success was seen in the Cotter River and Murrumbidgee River. In the Ovens River, an extinct population is being re-established using multiple sources, through translocation and captive breeding. Meanwhile, the status of the coastal lineage is still uncertain. We will monitor genetic augmentation in the inland populations and investigate history of isolation, selection, drift and recent gene flow between inland and coastal lineages via unintentional gene flow in the Cataract River.
Leadbeater's possum Gymnobelideus leadbeateri, photo by Sasha Pavlova
The single remaining lowland population of this Critically Endangered species was reduced to only 34 individuals, showing strong inbreeding depression. Genetic rescue is only starting: translocations to create populations harboring lowland and highland ancestries are being trialed, and captive breeding program has successfully produced an admixed possum. Field data on survival and reproduction of the lowland population will be used to validate genomic predictors of fitness. Meanwhile, genetic data across all highland and lowland populations will be used to identify putative locally-adapted genetic variation and develop appropriate genetic management interventions that maximize species fitness and persistence in changing climate.
Helmeted honeyeater Lichenostomus melanops cassidix, photo by Paul Sunnucks
Because this Critically Endangered subspecies of a common yellow-tufted honeyeater was reduced to a single population (Yellingbo), genetic rescue of the helmeted honeyeater necessarily involves gene flow from another subspecies. Captive breeding trials showed that benefits of such admixture outweigh the costs. From 2020, captive-bred individuals of mixed ancestry have been released into Yellingbo. Admixed birds are also part of the group of founders of the second helmeted honeyeater population, at O'Shannassy. Reproductive fitness of these birds will allow us to validate genetic proxies of fitness.
We progressed genetic management of target species:
Button wrinklewort: Glasshouse intra- and inter-population crosses have been conducted at La Trobe University. Four experimental plots with these crosses have been established in different environments (three in Victoria, one in NSW) by DEECA and other agencies. For 3 plots first sets of fitness and genetic data are being analysed.
Macquarie perch: Captive breeding programs in the Snobs Creek Hatchery, Victoria (VFA) and the Narrandera Hatchery, NSW (NSW DPI) are including two-population crosses during production of fingerlings for stocking. Wild-to wild translocations and stocking using multiple sources are ongoing in several populations (DEECA and NSW DPI). New population is being established in the Kiewa River using multiple sources (DEECA).
Using Macquarie perch as a test case, a metapopulation management approach has been developed, to ensure genetic diversity of the whole species is preserved and gene flow among populations is re-established through regular translocations to boost population adaptive potential.
Leadbeater's possum: Wild Yellingbo population went from 24 possums in 2022, 34 in 2023, 37 in 2024 down to ~20 in 2025, with evidence of low reproduction. Genetic rescue has started in captive breeding program at Healesville Sanctuary (Zoos Vic), producing 5 admixed lowland-highland young by mid-2025. New population is being planned at rehabilitated Haining Farm. Meanwhile, more possums were discovered in lowland swamp forest habitat around Buxton, embedded in highland habitats. Recently, highland possums were discovered in Kosciuszko National Park in New South Wales. Genetic study to understand evolutionary history, gene flow and relationship among highland and lowland populations is underway.
Helmeted honeyeater: Genetic rescue is progressing well: captive breeding program at Healesville Sanctuary (Zoos Vic) successfully produces admixed cassidix- gippslandicus crosses and backcrosses, which are regularly released along the cassidix - cassidix crosses. Fitness data, collected for two wild populations (remnant Yellingbo and established O'Shannassy) by DEECA and Zoos Vic (respectively), is being analyzed. Field and genetic data are being carefully curated using APV Lab&Field data sample management system. The third population of the helmeted honeyeater has been established in May 2025 after the release of the 21 genetically diverse captive-bred birds to Cardinia on Bunurong Country.
We attempted to validate genetic load proxies using helmeted honeyeater fitness data. We found that three inbreeding coefficients based on long runs of homozygosity (ROHs≥3 Mb, ≥1.3 Mb, ≥100 SNPs) predict lifetime reproductive success of honeyeaters better than genetic load proxies based on evolutionary conservation do (preprint here). This supports reduction of inbreeding as best conservation goal of the helmeted honeyeater recovery program.
Objective 2: Upscale the use of genetic management by developing data analyses workflows and implementing them through genomic analysis portals, building, testing and improving bioinformatic pipelines, and developing automated algorithms to impute genetic parameters for species with little or no genetic data, based on related species with better data.
Using our four case studies, we will develop scalable workflows for rapid detection of genetic-related fitness declines for wildlife with little or no fitness data. Through platforms developed by CSIRO (G.U.A.R.D. and/or Digital Traceability platform) and DArT (OneDart platform) we will automate and test our workflows. Automation will enable timely completion of our ambitious project. The resulting pipelines will be ready to apply in other threatened species. We will also consider a practical question: when is genome-wide diversity a sufficient conservation management proxy for fitness-conferring and climate-adaptive loci? The answers will facilitate prioritization of populations for conservation.
Paul (front) and Steve are collecting fitness data for button wrinkleworth. Photo by Sasha Pavlova
We have made a good progress:
Diana created an R package dartR.sexlinked available on CRAN as part of the dartRverse: a suite of smaller packages for analyses of SNP data in R. The dartR team that developed dartRverse, of which Diana is a member, has been announced as a finalist for the Australian Museum Eureka prize 2025, in the Excellence in Research Software category.
A telomere-to-telomere genome assembly for Button wrinklewort has been produced by Gunjan and other CSIRO collaborators. The assembly, annotated by NCBI using the RNAseq data from another individual, is available at GenBnk accession GCA_046630445.1. Complex mitochondrial and chloroplast genomes of the same individual plant as the one used for genome assembly, have been assembled and annotated by Chris (CSIRO; NCBI accession PQ762199 and PQ762215, respectively).
Chromosome-length genome assemblies produced by DNA Zoo for the helmeted honeyeater, Macquarie perch (NCBI Accession GCA_005408345.2) and Leadbeater's possum, have been polished by Gunjan (CSIRO). Gunjan and Diana corrected assemblies for chromosomes Z and 13 of the helmeted honeyeater, as verified by new linkage maps. New assemblies, all with consensus Quality > 99.999 and consensus CV > 52, will soon be available via NCBI.
Diana and Jesús led the development of the pipeline JeDi for estimating unbiased individual heterozygosity, population nucleotide diversity and population divergence from reduced-representation genome sequencing data. This pipeline reduces the problematic biases of SNP datasets by accounting for invariant, missing and multi-allelic sites and scales variation at variable site by that of all scored sites -paper featuring the approach here.
We also established the Wildlife Genetic Management Hub, to provide consultancy and services on managing genetic health of threatened wildlife. This work enables us to co-develop management recommendations together with wildlife managers based on cutting-edge research.
Sasha (front) and others releasing helmeted honeyeaters (there are three of them on this photo!). Photo by Paul Sunnucks
Diana presenting a Science Comedy talk about the genetic rescue of the Helmeted Honeyeater at the Melbourne International Comedy Festival. Video screenshot
Objective 3: Increase the uptake of genetic management through participation in recovery actions and projects, engagement with community-run, large-scale projects and international conservation initiatives, and development of outreach material showcasing successful management cases.
We have been busy:
Diana, as co-developer of the dartR package, led Module 10 at DartR training workshop (see recording here and the github tutorial here) and helped with the dartR workshop at ICCB2025.
We are contributing training material available through the Threatened Species Initiative website.
Our work on Genetic Rescue has been featured in the New York Times article 'Should We Change Species to Save Them? ' by Emily Anthes.
Paul gave a Radio National interview with Andy Park- recording here.
Diana presented a talk on genetic rescue at the Melbourne International Comedy Festival 2024- recording here, at the Pint of Science Festival at The Nott on 14/5/2024- podcast here, and at ICCB2025.
Paul was on a live-streamed panel of IUCN's World Species Congress 'Reverse the Red’ on the role of genetics in conservation on 15/05/2024.
Sasha presented a metapopulation genetic management approach for Macquarie perch at the GeoBon Genetic Composition Working Group (GCWG) online symposium 13/11/2024- talk at 1:19:57 at this link.
Our team presented many talks at national conferences, including Paul's plenary + 5 talks by our team at ESA 2024: The 2024 Conference of the Ecological Society of Australia, 2 talks and a poster at ICCB 2025: 32nd International Congress for Conservation Biology.
Paul presented a talk at an event 'Love Our National Parks' in the seat of the Victorian Minister for the Environment on 3/12/2024, highlighting the need for large, connected populations that provide genetically healthy populations.
Our Industry Partner Revive & Restore created their own webpage for our project, linked from their page on genetic rescue, to assist us in disseminating our research and linking us with wildlife agencies that could benefit from our expertise.
At the inaugural Stakeholder Meeting at 10/05/2024. Photo by John Morgan
Read about our progress in our biannual newsletters:
Newsletter 1: June 2024, Newsletter 2: December 2024, Newsletter 3: July 2025
We acknowledge the Traditional Custodians of Country throughout Australia and recognise their continuing traditions and connection to land, waters and culture. We pay our respects to their Elders past, present and emerging. Our research was undertaken on lands of the following Traditional Owners:
Button wrinklewort: diploid populations are located on Wathaurong [Wadawurrung] (St Albans), Bunurong (Truganina Cemetery), Dja Dja Wurrung (Clunes), Ngarigo (Bredbo, Michelago), Ngunnawal (ACT and Capitans’ Flat populations) and Gundungurra (Gandangara) Countries (Gundary population). Historic diploid populations between Melton and Sunbury are on Wurrundjeri Country.
Macquarie perch: populations of the Murray-Darling Basin origin occur on Traditional Lands of Ngunnawal (Cotter population), Ngarigo (upper Murrumbidgee), Ngambri (mid Murrumbidgee), Yorta Yorta (Ovens), Taungurung (Broken, Goulburn, Buffalo, Yea, Seven Creeks, Hughes Creek, King Parrot Creek, Hollands Creek, part of Ovens populations, Snobs Creek Hatchery), Wiradjuri (Lachlan [Gulari] and Adjungbilly) and Duduroa Dhargal (lower Kiewa and Dartmouth) Countries. Populations of the Hawkesbury-Nepean lineage are on Darkinung and Dharug Countries. Translocated populations of the MDB origin are on Wurundjeri (Yarra), Tharawal (Cataract Reservoir) and Yuin (Mongalowe) Countries. Shoalhaven lineage (extinct Kanagroo River population) was located on Tharawal and Yuin Countries.
The Macquarie perch is called Gubay in the Ngunnawal language, Gubir in Wiradjuri and Wunnumberu (Wanambiyu) in Dhudhuroa.
· Leadbeater's possum: the remnant populations are located on Traditional Lands of Wurundjeri Woi Wurrung (Yellingbo population), Taungurung and Gunaikurnai Countries (Buxton and highlands). A new population just discovered in Kosciuszko National Park is on the Country of the Wiradjuri, Wolgalu, Ngunnawal and Monaro Ngarigo people.
The Leadbeater's possum is called Wollert in Woiwurrung.
Helmeted honeyeater: the Yellingbo and O’Shannassy populations are on Wurundjeri Woi Wurrung Country, Cardinia (established in 2025)- on Bunurong [Boonwurrung] Country. Gippslandicus is collected in Wurundjeri and Gunaikurnai Countries.
No indigenous name has been identified for the helmeted or yellow-tufted honeyeater.
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