Upscaling genetic management of wildlife populations
ARC Linkage Project LP220200856 started 6 Feb 2024
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 (CSIRO), Luke Pearce, Meaghan Duncan, Jerom Stocks (NSW DPI), Taylor Hunt (VFA), Bruce Quin, Lily Surace, Brad Farmilo (DEECA), Kim Miller, Arabella Eyre, Nick Bradsworth (ZoosVic), Mark Lintermans (Fish Fondler Pty Ltd), Ashlee Hutchinson (R&R) and many others!
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 leptorhynchoides, 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 three environmentally-different locations, with two additional grids 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. 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.
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
Sasha (front) and others release 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.
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- and at the Pint of Science Festival at The Nott on 14/5/2024.
Paul is 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.
Hands-on participation:
Steve and Paul have collected fitness data for the button wrinkleworth (01/2024)
Paul and Sasha participated in release of the captive-bred helmeted honeyeaters, including admixed birds, to Yellingbo population (04/2024).
Our Industry Partner Revive & Restore will 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
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.