Repeated barrier drown-out is required to facilitate long-distance migration of a potamodromous fish

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.

SummaryEnvironmental rehabilitation budgets are often limited, and management actions need to be prioritised to achieve the best outcomes. Prioritisation can best be done when evidence informs the decision‐making process. We acoustically tagged twenty Golden Perch (Macquaria ambigua) in the Loddon River, Australia, and tracked their movements to gain an understanding on the requirements for fish passage at a major regulating structure, the Box Creek regulator. The movements of these fish were monitored through a network of receivers located throughout the lower Loddon River and Pyramid Creek system. Five fish moved 50–120 km upstream, four of which reached the Box Creek regulator before moving back downstream to the entrance of the Kerang Lakes system. Most long distance upstream movements were associated with an increase in river discharge. The remaining 15 fish moved <20 km, with all fish being detected at least once. This pilot study indicates that Box Creek regulator is acting as a barrier for some fish within the Loddon River system. Movement data also indicate that Golden Perch migration pathways may be influenced by river discharge. The management implications of this work includes the need to reinstate fish passage at Box Creek regulator and the potential use of environmental flows to enhance colonisation of native fish species throughout the Murray Darling Basin.

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 >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.

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] <1 mg/L). Despite these conditions, 38 of 43 fish tagged with acoustic transmitters were detected for >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 (>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 (<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.

Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.

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 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.

Effective fisheries management requires fish size, growth and mortality information representative of the population and location of interest. Golden perch Macquaria ambigua is long lived, potamodromous and widespread in the Murray–Darling Basin (MDB), Australia. Using a sample spanning 13 river systems and 10° of latitude, we examined whether the maximum size of golden perch differed by latitude and whether growth and mortality varied between northern and southern MDB regions. The length, weight and age ranges of golden perch sampled (n=873) were 52–559mm, 2–3201g and 0+ to 26+ years respectively, and maximum length and weight were unaffected by latitude. Length and age–length distributions represented by age–length keys varied by region, with greater variability in age-at-length and a larger proportion of smaller individuals in northern MDB rivers, which generally exhibit greater variability in discharge. Growth and mortality rates were similar between regions, and an MDB-wide von Bertalanffy growth model (L∞=447, k=0.32 and t0=–0.51) and instantaneous mortality rate (Z=0.20) best described the data. An MDB-wide length–weight equation also provided the best fit (W=6.76×10–6 L3.12). Our data suggest that the MDB can be treated as one management unit in terms of golden perch maximum size, growth and mortality parameters.

Golden perch, Macquaria ambigua, from the Murray-Darling Basin were aged by using transverse thin sections of their sagittal otoliths. Samples from 889 fish were obtained from riverine and lacustrine habitats and from wild and stocked populations. Error in the precision of age estimates (calculated as the mean percentage error of the independent age estimates of four readers) was 5.6% (3.9% after allowing for discrepancies in relation to the annual mark on the edge of the otolith). Validation was accomplished by using a combination of analysis of the progression of modes in length-frequency distributions, qualitative and quantitative marginal-increment analysis, and analysis of age estimates of fish from populations with a known stocking history. The technique was validated for fish up to 8 years of age (455-545 mm total length, 1695-3988 g total weight), and the greatest recorded age was 16 years (530-600 mm total length, 2607-4050 g total weight). Annual marks become visible in otolith sections in most fish of all ages in October, and 1 October was designated as the birth date. A description of our method of reading sections of golden perch otoliths, including recognition of false annual marks, is given. Otolith length, width and thickness increased linearly with fish length and with loglo(fish age), whereas otolith weight increased linearly with fish age and exponentially with fish length. The continuous growth of the otoliths and the consistency in the appearance of annual marks support the accuracy of estimates up to the maximum recorded age. The mean length-at-age and the parameters of the length-weight relationship were estimated. The von Bertalanffy growth parameters were also estimated (L∞ =507 mm, to=0.420 years, K=0.454). No significant differences were found in growth rates or length-weight relationships between males and females. However, growth (particularly in weight) was highly variable among sites and years, and slow-growing 5-year-olds may be shorter than fastgrowing 1-year-olds. Ages were estimated for a sample of 86 golden perch caught between 1949 and 1951 but a comparison of growth rates between these and more recent collections was inconclusive.

Stocking of native fishes is conducted to augment riverine fisheries in many parts of the world, yet most stocking activities are conducted without empirical information on their effectiveness or impacts. In the Murray–Darling Basin (MDB), Australia, stocking has been underway for several decades to maintain recreational fisheries. We stocked chemically tagged golden perch (Macquaria ambigua) fingerlings in three rivers to determine the proportions of stocked fish within populations of the species. Stocked sites were monitored for up to 5 years in the Murrumbidgee River, Edward River and Billabong Creek and non-stocked sites were monitored in the Murray River. Catch per unit effort of stocked year classes increased substantially in Billabong Creek, with stocked fish contributing 100 (2005), 79 (2006) and 92% (2007). Chemically tagged fish comprised 18–38% of the respective age classes in the Murrumbidgee and Edward rivers and there was little evidence of natural recruitment in the non-stocked Murray River. Tagged fish generally attained the legal minimum size within 4 years and had dispersed up to 60km from the original release location. Our results demonstrate that artificial stocking has the potential to strongly influence the abundance and population structure of golden perch in rivers of the MDB.

Aim We conducted a range‐wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins.Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia.Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations.Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (ΦST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene.Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios.

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.

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.

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.

Investigations into the feeding of the early stages of fishes can provide insights into processes influencing recruitment. In this study, we examined ontogenetic changes in morphology and feeding behaviour of two native Australian freshwater species, Murray cod, Maccullochella peelii peelii, and golden perch, Macquaria ambigua, and the alien species, common carp, Cyprinus carpio. Murray cod free embryos are large and well developed at the onset of feeding, whereas the other two species begin exogenous feeding much younger and are smaller and less-developed. Carp commence exogenous feeding 3 days earlier than golden perch, and show more advanced development of the eyes and ingestive apparatus. We conducted feeding experiments, presenting larvae of the three species with a standardised prey mix (comprising equal numbers of small calanoid copepods, large calanoid copepods, small Daphnia, and large Daphnia). Larvae of most tested ages and species showed a preference for mid-sized prey (300–500 µm wide). This was true even when their gapes substantially exceeded the largest prey offered. Daphnia were consumed more than similar-sized copepods. The results of this study suggest that survival through their larval period will be threatened in all three species if catchable prey <500 µm in width are not available throughout such time. They also suggest that interspecific competition for prey may occur, especially when larvae are very young. The precocious development of structures involved in feeding and the extended transition from endogenous to exogenous feeding of early carp larvae are likely to have contributed to the success of this species since its introduction to Australia.