Genomics help identify endangered fish populations most vulnerable to climate change
image:
The small native Australian freshwater fish, the southern pygmy perch (Nannoperca australis), has suffered major declines due to habitat loss, river regulation and prolonged droughts. Photo courtesy Michael P Hammer, a co-author of this study.
view moreCredit: Photo courtesy Michael P Hammer
Scientists have shown that genomics can help identify which wild populations are most vulnerable to climate change – offering practical guidance for the conservation of threatened species before declines become irreversible.
The study, led by researchers from Flinders University's Molecular Ecology Laboratory and published in the Journal of Heredity, examined the endangered southern pygmy perch across Australia's Murray-Darling Basin.
By combining climate modelling with genome-wide data from hundreds of fish, the researchers identified the populations most likely to struggle as climates continue to warm.
They also showed that carefully managed conservation breeding can preserve a species' capacity to adapt to future warming.
Lead author Dr Emily Booth says the research demonstrates how genomics is becoming an increasingly powerful tool to assist conservation.
"Climate change doesn't affect all populations equally. By combining genomic data with climate modelling, we can identify the populations most at risk and help conservation managers prioritise where actions are likely to have the greatest impact," she says.
The southern pygmy perch is a small freshwater fish native to south-eastern Australia that has suffered major declines due to habitat loss, river regulation and prolonged droughts. In the Murray-Darling Basin, it now survives in small, isolated populations, many with limited genetic diversity and reduced capacity to adapt to environmental change.
To assess its future prospects, the researchers analysed thousands of DNA markers from 467 fish collected at 30 sites across the species' remaining range in the basin.
The study found that populations in upland streams are generally more vulnerable to future climate change than those in lowland wetlands and rivers.
Elevation proved to be a strong predictor of this vulnerability – a finding that suggests conservation managers could use this simple landscape feature to flag high-risk populations in other freshwater ecosystems, without needing detailed genomic data for every case.
The researchers also evaluated one of Australia's best-known freshwater fish recovery programs.
During the Millennium Drought, the southern pygmy perch disappeared from the Lower Lakes region of the Murray River, prompting a genetically informed captive breeding and reintroduction program.
The new study found that the restored population retained its capacity to adapt to future climate change – providing rare empirical evidence that conservation breeding guided by genomic information can preserve long-term evolutionary resilience.
Senior author Professor Luciano Beheregaray says the findings show how conservation genomics can directly inform management decisions.
"This is another study showing that genomics has moved beyond describing biodiversity to actively helping conserve it," says Professor Beheregaray. "We can now identify the populations most vulnerable to climate change and use that information to guide actions such as captive breeding, assisted gene flow and habitat restoration."
The researchers say the findings have implications well beyond the southern pygmy perch and Australia.
Freshwater fish are among the world's most threatened vertebrates, yet receive far less conservation attention than many other animal groups. The study offers a framework for using genomic data to identify vulnerable populations and prioritise conservation investment in freshwater ecosystems facing rapid environmental change.
The article, ‘Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch (Nannoperca australis)’, by EJ Booth (Flinders University), CJ Brauer, J Sandoval-Castillo, SD Wedderburn, NS Whiterod, PJ Unmack, MP Hammer and LB Beheregaray (2026), has been published in the Journal of Heredity. https://doi.org/10.1093/jhered/esag052.
Journal
Journal of Heredity
Method of Research
Data/statistical analysis
Subject of Research
Animals
Article Title
Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch (Nannoperca australis)
Fish shape analysis guides sustainable stinging catfish breeding
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The UPGMA dendogram clustering three H. fossilis populations collected from the Farm Bogura (Kahalu) (black) Farm Dinajpur (Sadar) (blue), Farm-Mymensingh (Muktagacha) (pink) and River (green).
view moreCredit: Journal of Applied Ichthyology
A research team has identified clear body-shape differences between wild and farmed populations of the stinging catfish Heteropneustes fossilis in Bangladesh. Wild river fish displayed greater morphological variability, while farmed stocks were generally more uniform and showed distinct patterns linked to their places of origin. Among the cultured populations, fish from Bogura were the most morphologically distinctive. These findings reveal how natural habitats, geographical separation, and hatchery conditions may shape economically important fish populations.
The stinging catfish is widely cultivated in South Asia because of its nutritional value, environmental tolerance, and suitability for high-density production. Growing demand has encouraged rapid expansion of hatchery-based propagation in Bangladesh. However, restricted broodstock pools, repeated use of related parental lines, and inconsistent genetic management may reduce diversity and produce domestication-related changes in growth, morphology, and fitness. Wild populations, by contrast, experience diverse habitats, food resources, and hydrological conditions that can maintain broader phenotypic variation. Although conventional measurements can reveal general size differences, they may overlook subtle, coordinated changes in body shape. A detailed comparison was therefore needed to determine whether farmed and wild catfish populations possess distinguishable morphologies and to identify the anatomical regions driving this divergence.
A study (DOI: 10.48130/jai-0026-0001) published in Journal of Applied Ichthyology on 12 June 2026 by Imran Parvez's team, Hajee Mohammad Danesh Science and Technology University, could help hatcheries select more diverse broodstock, preserve valuable wild morphotypes, limit the loss of phenotypic diversity, and support more resilient and sustainable catfish aquaculture.
The researchers collected 114 catfish between October 2024 and June 2025 from farms in Bogura, Dinajpur, and Mymensingh and from the Garbheswari River. They photographed each specimen under standardized lighting and camera conditions, then digitized 15 anatomical landmarks covering the head, trunk, fins, and caudal region. Generalized Procrustes Analysis removed differences caused by size, position, and orientation, while regression against centroid size corrected for allometry. The team subsequently examined shape variation using the coefficient of variation, principal component analysis, relative warp analysis, Mahalanobis and Procrustes distances, multidimensional scaling, hierarchical clustering, discriminant function analysis, and canonical discriminant analysis. Permutation testing and leave-one-out cross-validation were used to evaluate statistical robustness and classification performance. Centroid size did not differ significantly among populations, indicating that the detected patterns principally represented shape rather than overall body-size variation. Wild Garbheswari River fish showed the greatest within-population variability, particularly at landmarks associated with the head and trunk. This pattern suggests greater phenotypic plasticity under heterogeneous natural conditions. Farmed fish showed narrower variation, consistent with morphological homogenization under controlled rearing environments. The first two principal components explained 94.31% of total shape variation. The first component alone accounted for 88.18% and mainly represented differences in body depth, head profile, and fin-base position; the second captured changes in caudal-peduncle tapering, opercular width, and anal-fin base length. All pairwise Mahalanobis distances exceeded 2.0, demonstrating clear differentiation among the four populations. Bogura fish occupied the most distinctive position in multivariate analyses, while clustering placed the Garbheswari River and Dinajpur populations together and grouped Bogura with Mymensingh in a separate major cluster. Discriminant analysis produced minimal overlap and classified 96.7% of wild river specimens correctly. Canonical discriminant analysis further identified one dominant axis of separation, with a canonical correlation of 0.844. Variation in the anterior body, trunk depth, and caudal peduncle contributed strongly to population discrimination. Because the study assessed morphology rather than DNA, the patterns may reflect environmental effects, domestication, geographic separation, or potential genetic structuring.
Overall, the study demonstrates that landmark-based geometric morphometrics can efficiently distinguish farmed and wild H. fossilis populations and detect biologically meaningful changes that conventional measurements may miss. The greater variability retained by river fish highlights the conservation value of wild morphotypes, while differences among farms indicate that hatchery management practices can produce distinct morphological outcomes. Incorporating carefully evaluated wild broodstock, broadening breeding populations, and routinely monitoring body-shape diversity could help preserve adaptive traits and strengthen the long-term sustainability of stinging catfish production.
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References
DOI
Original Source URL
https://doi.org/10.48130/jai-0026-0001
About Journal of Applied Ichthyology
Journal of Applied Ichthyology (e-ISSN 1439-0426; p-ISSN 0175-8659) is an open-access, peer-reviewed journal dedicated to publishing high-quality research on applied ichthyology, aquaculture, and marine fisheries, including management of fisheries resources, fisheries ecology, fish health and pathology.
Journal
Journal of Applied Ichthyology
Subject of Research
Not applicable
Article Title
Geometric morphometric assessment of shape divergence in farmed and wild populations of Heteropneustes fossilis
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