Endangered Macquarie Perch | Photo credit: Zeb Tonkin
Congratulations to Alexandra Pavlova, partners, and the team at the Wildlife Genetic Management Hub for their important publication, A Shift to Metapopulation Genetic Management for Persistence of a Species Threatened by Fragmentation. Revive & Restore is one of many fantastic partners on this Australian Linkage grant, aiming to develop conservation strategies informed by genomics for four at-risk species. Here, the team has used the endangered Macquarie Perch as a case study to showcase a new bioinformatic pipeline that predicts management of populations as a metapopulation achieves better conservation outcomes.
Populations of the Macquarie perch (Macquaria australasica) are highly fragmented, with declining genetic diversity. These freshwater fish once ranged widely across southeast Australia, but dams, degraded habitats, and invasive predators have left them in small, isolated populations. On-the-ground conservation now involves physically relocating fish between rivers and habitat refuges, monitoring genetic outcomes over time, and ensuring the populations are healthy and resilient.
As a strategy to “rescue” the eroded genome, the authors recommend active management that mixes fish from different remnant populations (via translocations and stocking), essentially “re-creating” a connected metapopulation.
Central to the study is the development of JeDi, an open-source genetic monitoring pipeline. JeDi is a powerful tool that enables managers to test and predict the outcomes of different mixing strategies. It revealed that combining migrants from two sources produces far higher genetic diversity than relying on one alone, a result with significant promise for guiding future restoration.
For example, many freshwater species face similar fragmentation and loss of diversity. Combining genetic insights with hands-on management provides conservation programs with a roadmap to strengthen populations and secure biodiversity across Australia and beyond.
This study immediately raises ongoing questions about genetic management for rapidly declining stony coral species in the Caribbean, particularly the elkhorn coral (Acropora palmata). In Florida, only 37 founder colonies remain after the devastating 2023 bleaching/mortality event, and devastating declines have occurred throughout the region. So far, these populations have been managed as small, fragmented, country-specific ones, restricted by jurisdiction.
Distribution of Macquarie perch populations (black, red and yellow lines) and sampling locations (colored circles). Note that some of the populations are so small that the sampling location symbol completely covers them. Populations are abbreviated by the first three letters, except King Parrot Creek is KPC and the upper Buffalo River is BufU.
These results strongly support what many coral biologists have been advocating for: that shifting to a metapopulation management approach would be far more effective. Like the Macquarie perch, elkhorn coral populations in Florida and beyond are small, isolated, and suffering from low genetic diversity and potential inbreeding depression. This recommendation to “manage a set of isolated populations by connecting them via augmented gene flow” while “establishing climate-secure populations from multiple sources” aligns well with the Caribbean-wide management approach for elkhorn corals that many envision.
This project is an excellent example of the kind of innovative science that Revive & Restore supports, demonstrating how the integration of population genomics and bioinformatics can complement and accelerate traditional conservation approaches. We’re excited to see how this approach translates across to the other species included on this grant: the Leadbeater’s possum, the Helmeted honeyeater, and the Button wrinklewort.
Project Partners:
Victorian Department of Energy Environment and Climate Action (DEECA); New South Wales Department of Primary Industries (NSW DPI); New South Wales Department of Primary Industries and Regional Development (NSW DPIRD); Diversity Arrays Technology (DArT); Commonwealth Scientific and Industrial Research Organisation (CSIRO); Zoos Victoria; Victorian Fisheries Authority (VFA); South East Local Land Services; National Landcare Program; Goulburn Broken Catchment Management Authority (GBCMA); North East Catchment Management Authority (NECMA); Australian Research Council Environment, Planning & Sustainable Development Directorate (ACT Government); Department of Biodiversity, Conservation and Attractions (Western Australia)
