Physiological and behavioural plasticity improves resilience to chronic hypoxia and warming in a dryland river fish.

Abstract Migratory fish species are highly vulnerable to stream fragmentation. Potamodromous golden perch (Macquaria ambigua) inhabit the barrier-laden Murray–Darling Basin (MDB), Australia’s largest river system, and its lifecycle includes a requirement for uninterrupted stretches of flowing water habitat. Owing to these barriers, large-scale connectivity in many regions is limited to periods of high flow events that facilitate barrier drown-out. We undertook a 3-year (2021–2024) study using telemetry to quantify the movements of 150 adult golden perch from the Barwon–Darling River over a period that encompassed numerous high flow events and flooding. Approximately 75% of tagged golden perch undertook movements > 50 km, with > 90% of movements in an upstream direction, extending up to 1500 km and associated with increased river discharge. Tributary entries were detected on multiple occasions, with an apparent preference for specific tributaries. Ten fish migrated > 1000 km upstream across multiple flow events. The results of this study (1) highlight the importance of the Barwon–Darling River and tributaries as a key migration conduit for adult golden perch, (2) demonstrate that multiple flow events are required to achieve large-scale dispersal and (3) provide quantitative flow-movement relationships that can be used to support inter-regional management actions. These management actions might include barrier removal, the construction of fishways and protection of tributary–mainstem flow events.

ABSTRACTFish population dynamics are influenced by intrinsic and environmental drivers across multiple spatial and temporal scales. A thorough understanding of these drivers is essential for maintaining fish recruitment in flow‐regulated rivers. In the Murray–Darling Basin (MDB) in Australia, golden perch (Macquaria ambigua) are an iconic species with a life history characterised by irregular, strong recruitment of year classes. In‐channel flow pulses and overbank flows are important for spawning and recruitment; however, the drivers of fluctuations in golden perch recruitment have not been sufficiently quantified to allow for full operationalisation into river and fishery management. We used long‐term standardised electrofishing data to model relationships between the relative abundance of young‐of‐the‐year (YOY) golden perch with large‐scale climate indices, local river hydrology and temperature, and river/fishery management actions. While consistent recruitment was observed in only five rivers, there were strong, positive associations between the abundance of YOY golden perch and two broadscale climatic drivers (Australian Monsoonal Index and total rainfall across the northern MDB). The driver of these relationships is likely to be the effects of climate on local river discharge and temperature. YOY abundance increased with temperature and generally increased with river discharge to an optimum before declining at a very high discharge. We also found positive but variable effects of stocking, suggesting that stocking of fish can augment natural populations but that outcomes are spatially and temporally inconsistent. Our results have the potential to enable proactive management targeted towards supporting the hydrological conditions necessary for self‐sustaining golden perch populations.

Modification of river flows is a major cause of freshwater fish population declines in many parts of the world. Identifying the precise mechanisms of these declines represents a significant challenge, as a range of stressors can simultaneously impact various components of fish health, fitness and population dynamics. Here we investigate the role of river flows and other biophysical factors on spatio‐temporal variation in freshwater fish body condition in Australia's highly modified Murray‐Darling Basin using three widely distributed native (Murray cod Maccullochella peelii, golden perch Macquaria ambigua and bony herring Nematalosa erebi) and one introduced (common carp Cyprinus carpio) species. Our aim was to uncover drivers of spatio‐temporal variation in fish condition at two spatial extents: at the basin scale, utilising a flow regime disturbance index, and at the river‐valley scale, employing individual flow gauge data to assess responses in fish condition to multiple measures of antecedent (365 day) flow. Linear mixed effects modelling revealed that at the basin scale, M. peelii and M. ambigua were in better condition in rivers with lower flow regime disturbance, and temporal trends in the condition of N. erebi, C. carpio and M. peelii reflected boom and bust dynamics related to wet and dry climate periods. At the river‐valley scale, mean antecedent daily flow magnitude was significantly positively related to the condition of M. peelii, M. ambigua and C. carpio, whereas the number of high‐flow days was negatively related to condition of N. erebi. Our study demonstrates that a simple body condition index calculated from routinely collected length–weight data is sensitive to multiple measures of hydrological disturbance in river systems that experience substantial temporal and spatial variability. We emphasise that studies considering multiple spatial scales are important for understanding complex scale‐dependent mechanisms influencing fish condition.

ABSTRACTManaging fish populations in regulated rivers requires an understanding of the spatial and temporal scale of their dispersal, the locations of key spawning and nursery habitats and the hydraulic processes that interplay with their life history. Golden perch (Macquaria ambigua), an Australian freshwater pelagic‐spawning fish, highlights the worldwide challenges of managing riverine species that rely on hydraulic conditions to sustain critical metapopulation processes. This study aimed to quantify the spatial scale of early life history golden perch dispersal after a drought‐breaking in‐channel flow event in early 2020 in a regulated lowland river. Otolith microchemistry (87Sr/86Sr) and single nucleotide polymorphisms (SNPs) determined natal origins and sibling relationships, respectively, of young‐of‐year (YOY) caught in a floodplain nursery with larval fish captured upstream. For fish collected in the floodplain nursery, dispersal distances ranged to ~1600 km. Otolith microchemistry attributed 52% of YOY as localised in origin, 44% as originating in the midcatchment and 4% from the most upstream sample locations. Genetic analyses identified a full‐sibling pair captured 900 km apart and 31 half‐sibling pairs that linked YOY to larval fish captured at a diversity of upstream sites. Our study highlights the range of spatial scales over which ELH dispersal can occur for golden perch and emphasises the importance of interconnected flowing river habitats in sustaining metapopulation processes. We illustrate the positive results that increased riverine connectivity can yield for fish with similar life history strategies.

Variation in somatic growth plays a critical role in determining an individual's body size and the expression of its life history. Understanding the environmental drivers of growth variation in mobile organisms such as fishes can be challenging because an individual's growth expression integrates processes operating at different spatial and temporal scales. Traditionally, otolith (ear stone) based growth analyses have focussed on temporal environmental variation by assuming an individual spends its whole life at its capture location. This approach ignores the movement potential of individuals and thus the role of spatio-temporal variation in conditions experienced. Here, we develop a modelling framework that incorporates individual movement information reconstructed via the analysis of chemical tracers in otoliths. We assess whether consideration of movement histories is important to estimating growth of a mobile freshwater fish, golden perch (Macquaria ambigua) at three spatial resolutions: basin-scale, reach-scale (movement-exclusive), and reach-scale (movement-inclusive). The predictive capacity of annual growth models slightly improved from the basin to the reach spatial scales (inclusive or exclusive of movement histories). Contrary to expectations, incorporating individual movement information, did not improve our ability to describe growth patterns. Golden perch growth was linked to the magnitude of and variation in spring, summer, and previous-year (antecedent) discharge, and spring temperature. The direction and magnitude of these effects was, however, dependent on life stage. Adults benefitted strongly from any increase in discharge or temperature, whereas juveniles benefitted only from increased summer discharge and grew slower in years characterised by wetter and warmer springs. We suggest that, for highly mobile fish like golden perch and in the absence of fine, 'within reach' scale biological data, coarser 'reach-scale' environmental variation may adequately describe individual growth trajectories.

ABSTRACTFreshwater ecosystems and their biota are under increasing pressure from anthropogenic stressors. In response to declining fish stocks, hatchery and stocking programmes are widely implemented as core components of restoration and management strategies, with positive outcomes for some wild populations. Despite this, stocking remains contentious due to potential genetic and ecological risks to wild populations. Monitoring and evaluation of stocking outcomes are critical to ensuring the long‐term sustainability of wild populations, but identification of stocked individuals post‐release remains a key challenge, particularly for mobile species. In this study, we combined otolith (natal origin and age) and genomic data to identify stocked individuals and evaluate the genetic implications of stocking for a culturally and socioeconomically important and mobile freshwater fish, golden perch Macquaria ambigua (family: Percichthyidae), across Australia's Murray–Darling Basin (MDB). We also generated a chromosome‐level genome assembly. Many close kin were detected across the MDB, increasing in prevalence over recent decades and mostly of hatchery origin. Rivers with many close kin were associated with low effective population sizes (Ne < 100). Genetic signatures of stocking varied according to local context, being most pronounced in but not restricted to rivers considered functionally isolated for management purposes. Where fish are stocked into rivers that are part of the connected metapopulation, there is scope to modify current stocking practices to avoid over‐representation of related stocked individuals. Increased focus on the genetic diversity of stocked fish is likely to promote the long‐term persistence of golden perch in the wild.

Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype-environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range-wide genomic diversity and genomic vulnerability in the migratory and fisheries-important golden perch (Macquaria ambigua) from Australia's expansive Murray-Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range-wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross-validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity.

Context Understanding the movement behaviour of flow-dependent fish species is a foundational principle underlying the effective management of highly modified riverscapes. Aims To determine how variations in river discharge and instream barriers affect the residency, survival and movement of golden perch (Macquaria ambigua) in the degraded Gwydir River system within the northern Murray–Darling Basin. Methods We monitored the movement of 25 acoustic-tagged golden perch for up to 3 years by using a linear array spanning ~180 km of the main river channels across the lower Gwydir system. Key results Golden perch were largely sedentary for extended periods, with movements constrained by the barrier maze that now defines the system. High flows facilitated passage over instream barriers, with the highest periods of activity occurring in spring and early summer, and to a lesser extent in autumn. Conclusion Our findings are indicative of a highly constrained and isolated population of golden perch that is now likely to be neither a source nor a sink, but is in effect a false sink perpetuated by re-stocking practices. Implications The rehabilitation of the fish community in the Gwydir and other systems in similarly poor condition throughout the Murray–Darling Basin will require major institutional and societal change.

Context Dryland rivers are unique ecosystems, where drought and flood play an important role in shaping the ecosystem. River regulation has altered the natural flow regime in many of these systems, affecting migration cues and connectivity for many species. Aims To quantify the discharge-related movements of Murray cod and golden perch within the Condamine–Balonne River subject to differing levels of river regulation. Methods We quantified flow regime variability, river regulation and fish movement to develop generalised additive mixed models to predict movement probability for Murray cod and golden perch. Results Both species showed strong positive relationships between discharge and movement. Murray cod did not show any association with river regulation; however, medium-sized individuals were significantly more likely to move than were smaller or larger fish. Golden perch movements varied among levels of regulation, were more likely to move as body weight increased and showed seasonality of movement, moving less during winter. Conclusions This study presents the largely unobserved movement behaviours of fish across a gradient of river regulation and environmental conditions in the northern Murray–Darling Basin. Implications This information is valuable for informing policy and management decisions that may affect species’ life-history requirements in analogous river systems.

Abstract We conducted an acoustic telemetry study of native golden perch (Macquaria ambigua) to examine movement behaviour in areas affected by methane seeps and hypoxia in the intermittent Condamine River, Murray‐Darling Basin (MDB), Australia. Fish were collected during periods of no flow and hypoxia (dissolved oxygen [DO] &lt;1 mg/L). Despite these conditions, 38 of 43 fish tagged with acoustic transmitters were detected for &gt;3 months post‐tagging in the study reach and 27 fish were being detected after 14 months. During periods of elevated river flow and relatively high DO, 30 fish moved away from their original tagging locations, with three undertaking movements (&gt;7 km) outside the study reach and not returning. Generalised additive mixed models showed a significant increase in the probability of movement as soon as flow commenced and when water temperatures exceeded 19°C. As flows receded, most fish that had moved exhibited accurate homing behaviour to their original tagging location. The patterns of movement and site fidelity exhibited by golden perch correspond with previous studies of the species in intermittent rivers not affected by methane seeps and severe hypoxia, suggesting that the methane seeps and hypoxia did not inhibit fish movement nor render the affected habitats unsuitable for habitation. Golden perch can survive and remain active in water with much lower DO (&lt;1 mg/L) than previously described for large‐bodied native fishes in the MDB. However, fish condition in the study reach was slightly lower than other regions of the MDB, providing preliminary evidence that fish residing in habitats affected by chronic hypoxia and methane seepage may experience sub‐lethal stress. Our results demonstrate the importance of field‐based data on the behavioural and physiological responses of fish to chronic hypoxia and methane exposure to guide appropriate management responses.

In response to the need to augment electrofishing surveys of golden perch, Macquaria ambigua (an important endemic freshwater fish in southeastern Australia), with other non-lethal survey methods, the utility of environmental DNA (eDNA) as an index of relative fish abundance/biomass was investigated. From three adjacent rivers, five sites in each were sampled for eDNA immediately before electrofishing during sequential years. Up to six individuals or 10 kg of electrofished golden perch (200–548 mm total length) were caught or observed site−1. Analyses of concurrent eDNA concentrations revealed no significant relationship with the relative abundance of golden perch, but there was with relative biomass—manifesting as increasing eDNA concentrations between 1.1 and approximately 5.5 kg biomass site−1, after which concentrations stabilized at greater biomasses. Future research warrants assessing the viability of sampling eDNA for spatio-temporally monitoring rivers where low biomasses of golden perch (1–5 kg site−1) are likely to occur.

Abstract Each year, millions of fish are extracted from Australian waterways by the pumping and diversion of water into irrigation systems. Fish protection screens can help reduce these losses but are largely untested in Australian rivers. In this study, a large, gravity‐fed irrigation offtake on Gunbower Creek, Victoria, Australia, was investigated for fish and debris entrainment. Experiments were performed under screened and unscreened conditions across various river flows. Mark–release–recapture experiments were undertaken with fingerlings of two recreationally significant fish species, Murray cod (Maccullochella peelii) and golden perch (Macquaria ambigua), together with wild fish community assessments, to determine how effective the screen was at reducing fish entrainment into the irrigation channel. The mean percentage of recaptured fingerlings was significantly lower when the irrigation channel offtake was screened compared with unscreened. Entrainment of released fish into the irrigation channel was reduced by &gt;98%. Similarly, wild fish entrainment was significantly lower when the irrigation channel was screened. When screened, fewer wild species dominated the sampled fish community, and entrained fish were generally &lt;40 mm in length. Debris loads decreased significantly in the irrigation channel owing to the screen, indicating the economic benefits of fish screens. Implementing screens could aid in native fish conservation efforts in riverine environments.

Abstract Models based on ecological processes (process‐explicit models) are often used to predict ecosystem responses to environmental changes or management scenarios. However, models are imperfect and need to be validated, ideally by testing their assumptions and outputs against independent empirical data sets. Examples of validation of process‐explicit models are rare. Recently, stochastic population models have been developed to predict the likely responses (over 10–120 years) of a riverine fish (golden perch, Macquaria ambigua) to flow management in the Murray–Darling Basin (MDB) in eastern Australia, one of the world's most regulated river basins. Declines in golden perch (and other species) are a direct consequence of altered hydrology, and managers require information to predict how fish will respond to possible future hydrological conditions to guide substantial investments in flow management. Here, we use two independent field data sets to validate our population model. We compared model predictions to observed trends to ask: (1) How do predicted population sizes and growth rates compare with observed data? (2) Does the correlation between predicted and observed population sizes and growth rates vary among populations? (3) Does the correlation between predicted and observed population sizes and growth rates vary across observed hydrological conditions? (4) How do modeled and observed fish movement rates compare? We found reasonable correlations between fish population sizes and growth rates as predicted by the model and observed in independent data sets for several populations (Aim 1), but the strength of these correlations varied among populations (Aim 2) and hydrological conditions (Aim 3). Predicted and observed fish movement rates were strongly correlated (Aim 4). Population models are frequently used in conservation decision‐making but are rarely validated. We demonstrate that: (1) validation can identify model strengths and weaknesses; (2) observed data sets often have inherent limitations that can preclude robust validations; (3) validation is likely to be more common if appropriate observed data sets are available; and (4) validation should consider the purpose of modeling. Wider consideration of these messages would contribute to more critical examinations of models, so they can be most appropriately used in conservation decision‐making.

Abstract Freshwater ecosystems are under extreme stress due to anthropogenic influences including changing climate, river regulation and water abstraction. Improving our understanding of the hydrological determinants of key life‐history processes of fish, as well as the spatial scales over which these processes occur, is fundamental to inform effective recovery actions. We monitored the spawning response of native fish to a drought‐breaking long‐distance flow pulse that was protected from extraction by a legal intervention order in Australia's northern Murray–Darling Basin. Sampling sites were distributed across &gt;1600 km of the Barwon–Darling River and three of its major tributaries. Larvae of the pelagophilic golden perch (Macquaria ambigua) were captured at all sites, with the size and age distribution indicative of both mainstem and tributary spawning. A mismatch between estimated hatch dates and river discharge at some locations suggested substantial flow‐assisted dispersal from upstream spawning sites, although this was site‐specific and more prevalent at downstream locations. Early life growth rates were the highest at tributary sites compared with mainstem sites, and within mainstem sites, golden perch grew faster in upper reaches compared with lower reaches. The present study provides insight into the environmental benefit of a post‐drought protected flow event whereby connected lotic habitats promoted fish spawning and dispersal over a large spatial scale. Protection of future flow events should occur to support the conservation of golden perch and other pelagophil species, particularly following future drought periods which are forecast to become more intense and frequent.

Context As social–ecological systems, recreational fisheries often vary temporally in response to environmental changes affecting ecological processes and human behaviour. Monitoring such variability in this ecosystem service can guide adaptive management measures for sustainability. Aims This novel research for Australian, sought to quantify interannual changes in the freshwater recreational fisheries of five key (i.e. commonly caught) finfish species (Murray cod, Maccullochella peelii; golden perch, Macquaria ambigua; Australian bass, Percalates novemaculeata; brown trout, Salmo trutta; and rainbow trout, Oncorhynchus mykiss) in relation to a series of extreme climate-related events and the COVID-19 pandemic. Methods Annual estimates during 2013–14, 2017–18 and 2019–20 of freshwater fishing effort and catch across New South Wales, Australia, were derived from off-site surveys and compared in relation to a severe drought period, the ‘Black Summer’ bushfires, widespread flooding and the COVID-19 pandemic, all of which affected fish productivity or human mobility. Key results There were significant declines in fishing effort between 2013–14, the year preceding the extreme environmental events and the pandemic, and 2017–18 and 2019–20. Catch across the five species was also significantly lower in 2019–20. Catch of species such as golden perch and rainbow trout declined from 2013–14 to 2019–20. Conclusions and implications This study can inform adaptive measures against societal and climate-related changes in weather by enabling scientists and managers to identify problematic trends.

Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species’ distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.

Context Native fish populations in Australia’s Murray–Darling Basin (MDB) have experienced severe declines since European settlement. Information on their status is needed to guide management and recovery. Aims To quantify trends in MDB fish populations in New South Wales (NSW) from 1994 to 2022. Methods Relative abundance, biomass, and size structure were examined using generalised additive mixed models at NSW MDB and river catchment (valley) scales for five native species (Murray cod, Maccullochella peelii; golden perch, Macquaria ambigua; silver perch, Bidyanus bidyanus; Macquarie perch, Macquaria australasica; freshwater catfish, Tandanus tandanus) and one alien species (common carp, Cyprinus carpio). Key results There was strong inter-annual variation in relative abundance, biomass and population structure for all species. At the Basin scale, relative abundance of Murray cod, golden perch and common carp increased across the time series, with no clear trends for silver perch, Macquarie perch or freshwater catfish. Patterns in relative abundance, biomass, and population structure were variable among valleys for most species. Conclusions and implications Although native fish populations in the MDB remain degraded and face escalating threats, recent increases in the abundance of some native species are an encouraging sign that integrated restoration efforts can improve the outlook for native fish.

Ecological responses to changing riverine flows are often evaluated by describing the relationship between river discharge and response. However, aquatic organisms experience the hydraulics (i.e. velocity, shear stress, depth) of a river, not its discharge. Hydraulic characterizations of riverine habitats may improve our ability to predict ecological responses. We used two-dimensional hydraulic models to translate river discharge into flow velocity. We used discharge and reach-averaged velocity, along with water temperature and 8 years of field observations of fish spawning, to develop predictive models of the spawning of golden perch (Macquaria ambigua) in the Goulburn River, south-east Australia. Probability of spawning was positively related to both discharge and reach-averaged velocity. Water temperature was critical for enabling the flow response, and antecedent flows prior to spawning had a weak positive effect. Against expectations, there was little difference in predictive uncertainty for the effect of flows when reach-averaged velocity was used as the main predictor rather than discharge. The lower Goulburn River has a relatively simple channel and so discharge and velocity are monotonically related over most flows. We expect that in a more geomorphically complex environment, improvement in predictive ability would be substantial. This research only explores one example of a hydraulic parameter being used as a predictor of ecological response; many others are possible. The extra effort and expense involved in hydraulic characterization of river flows is only justified if our understanding of flow-ecology relationships is substantially improved. Further research to understand which environmental responses might be best understood through different hydraulic parameters, and how to better characterize hydraulic characteristics relevant to riverine biota, would help inform decisions regarding investment in hydraulic models. Regardless, hydraulics offers a more process-based assessment of ecological responses to changing flows, has the potential to facilitate mechanistic understanding rather than just associations, and provides the opportunity to translate hydraulic metrics that drive ecological responses across river systems of differing sizes. However, while considering ecological responses in terms of river hydraulics is more physically realistic, our results suggest that average hydraulic conditions may not result in an improved ability to predict the effects of changing flows.

On the Cover: A water hole in Australia. Aridification of Australia during the Pleistocene has influenced the divergence of a migratory freshwater obligate, the golden perch (Macquaria ambigua). Photo credit: Shutterstock/Tim Pryce. For more information see “Aridification-driven evolution of a migratory fish revealed by niche modelling and coalescence simulations” by Booth et al. (DOI:10.1111/jbi.14337), a contribution to the special section on Geogenomics.