Swinging back from the brink? Polygamous mating strategies revealed for an iconic threatened freshwater fish.

Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis.

Lifetime movement history is associated with variable growth of a potamodromous freshwater fish.

Directional or stabilising selection should drive the expression of a dominant movement phenotype within a population. Widespread persistence of multiple movement phenotypes within wild populations, however, suggests that individuals that move (movers) and those that do not (residents) can have commensurate performance. The costs and benefits of mover and resident phenotypes remain poorly understood. Here, we explored how the presence and timing of movements are correlated with annual somatic growth rates, a useful proxy for performance because it is easily measured and rapidly reflects environmental changes. We used otolith growth measurements and stable isotope analyses to recreate growth and among-reach movement histories of a partially migrating, long-lived freshwater fish, golden perch Macquaria ambigua. We compared the association between movement and growth at two temporal scales: (a) short-term (annual) differences in growth, in the years preceding, during or following movement; and (b) long-term (lifetime) differences in growth. Overall, 59% of individuals performed at least one among-reach movement, with these individuals subsequently more likely to move repeatedly throughout their lives. Movers grew faster than residents, with this difference most pronounced in the juvenile and early adult stages, when most movements occurred. Annual growth did not, however, change immediately prior to or following a specific movement event. Among-individual variation in growth was initially higher for residents than for movers but decreased with age, at a faster rate for residents than for movers, such that levels conformed after 5 years of age. Our results indicate that lifetime movement is linked to faster growth in the early years of a fish's life. These faster growing movers are likely to be larger at a given age, leading to numerous potential benefits. However, the persistence of resident phenotypes suggests that there is likely a cost-benefit trade-off to moving. The presence of multiple movement phenotypes may contribute to the resilience of populations by buffering against naturally and anthropogenically exacerbated environmental variability.

Erratum to: The effects of cold shock on freshwater fish larvae and early-stage juveniles: implications for river management.

[This corrects the article DOI: 10.1093/conphys/coaa092.].

The effects of cold shock on freshwater fish larvae and early-stage juveniles: implications for river management.

Temperature is essential to the maintenance of optimal physiological functioning in aquatic organisms. Fish can manage natural fluctuations in temperature; however, in freshwater ecosystems acute and rapid temperature changes can originate from sources such as large dams and industrial effluents. These rapid temperature changes may induce several physiological and behavioural responses that can result in lethal and sub-lethal consequences. The present study assessed immediate sub-lethal and short-term (10 days) lethal responses of three species of Australian freshwater fish larvae and early-stage juveniles to a range of different 'field-relevant' cold shocks (-4, -6, -8 and -10°C). Murray cod (Maccullochella peelii), silver perch (Bidyanus bidyanus) and golden perch (Macquaria ambigua) were tested at two age groups to elucidate the interaction between ontogeny and sensitivity to cold shock. Cold shock caused mortality and reductions in swimming ability (time to exhaustion and lines crossed) in all species of fish at both age groups. Sensitivity was correlated to the magnitude of cold shock; a 10°C drop in temperature caused the highest mortalities. Ontogeny interacted with the severity of cold shock; the younger fish experienced higher mortalities and greater impairment to swimming ability. This study demonstrates the potential lethal and sub-lethal impacts of cold shock on freshwater fish at a critical life-history stage. Understanding the impacts of cold shock will aid management of freshwater ecosystems for the benefit of fish populations, with the current study identifying critical life stages to be considered in remediation and guiding thresholds necessary to reduce the impact of cold shock on native fish populations.

Stage-dependent effects of river flow and temperature regimes on the growth dynamics of an apex predator.

In the world's rivers, alteration of flow is a major driver of biodiversity decline. Global warming is now affecting the thermal and hydrological regimes of rivers, compounding the threat and complicating conservation planning. To inform management under a non-stationary climate, we must improve our understanding of how flow and thermal regimes interact to affect the population dynamics of riverine biota. We used long-term growth biochronologies, spanning 34 years and 400,000 km2 , to model the growth dynamics of a long-lived, apex predator (Murray cod) as a function of factors extrinsic (river discharge; air temperature; sub-catchment) and intrinsic (age; individual) to the population. Annual growth of Murray cod showed significant, curvilinear, life-stage-specific responses to an interaction between annual discharge and temperature. Growth of early juveniles (age 1+ and 2+ years) exhibited a unimodal relationship with annual discharge, peaking near median annual discharge. Growth of late juveniles (3+ to 5+) and adults (>5+) increased with annual discharge, with the rate of increase being particularly high in adults, whose growth peaked during years with flooding. Years with very low annual discharge, as experienced during drought and under high abstraction, suppress growth rates of all Murray cod life-stages. Unimodal relationships between growth and annual temperature were evident across all life stages. Contrary to expectations of the Temperature Size Rule, the annual air temperature at which maximum growth occurred increased with age. The stage-specific response of Murray cod to annual discharge indicates that no single magnitude of annual discharge is optimal for cod populations, adding further weight to the case for maintaining and/or restoring flow variability in riverine ecosystems. With respect to climate change impacts, on balance our results indicate that the primary mechanism by which climate change threatens Murray cod growth is through alteration of river flows, not through warming annual mean temperatures per se.

Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua.

Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1-0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.

Karyotypes and Sex Chromosomes in Two Australian Native Freshwater Fishes, Golden Perch (Macquaria ambigua) and Murray Cod (Maccullochella peelii) (Percichthyidae).

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes' range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2n = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT)10 and (CGG)10 along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution.

Abiotic drivers of activity in a large, free-ranging, freshwater teleost, Murray cod (Maccullochella peelii).

The allocation of time and energy to different behaviours can impact survival and fitness, and ultimately influence population dynamics. Intrinsically, the rate at which animals expend energy is a key component in understanding how they interact with surrounding environments. Activity, derived through locomotion and basic metabolism, represents the principal energy cost for most animals, although it is rarely quantified in the field. We examined some abiotic drivers of variability in locomotor activity of a free-ranging freshwater predatory fish, Murray cod (Maccullochella peelii), for six months using tri-axial accelerometers. Murray cod (n = 20) occupied discrete river reaches and generally exhibited small-scale movements (<5 km). Activity was highest during crepuscular and nocturnal periods when water temperatures were warmest (19-30°C; January-March). As water temperatures cooled (9-21°C; April-June) Murray cod were active throughout the full diel cycle and dormant periods were rarely observed. Light level, water temperature and river discharge all had a significant, non-linear effect on activity. Activity peaked during low light levels, at water temperatures of ~20°C, and at discharge rates of ~400 ML d-1. The temporal changes observed in the behaviour of Murray cod likely reflect the complex interactions between physiological requirements and prey resource behaviour and availability in driving activity, and highlight the importance of empirical field data to inform bioenergetics models.

Swimming activity and energetic costs of adult lake sturgeon during fishway passage.

Fish migrations through riverine systems can be energetically demanding, and the presence of fishways to facilitate upstream passage can add an additional energetic cost that may directly affect fitness. Successful fishway passage is a function of the ability of fish to select appropriate paths and swimming strategies that do not exceed their swimming capacity. Triaxial accelerometers were used to estimate the energetic expenditure of adult lake sturgeon (Acipenser fulvescens) swimming through a vertical slot fishway, to determine whether individual behaviour or path selection, resulting in differences in cumulative energy use, explain fishway passage success. Most individuals attempted to pass the fishway (n=30/44; 68%), although successful passage only occurred for a subset of those attempting (n=7/30; 23%). High-speed swimming was rarely observed during upstream passage through fishway basins, and was of short duration. Two turning basins delayed passage, subsequently resulting in a higher energetic cost. The rate at which energy was expended did not differ among successful and unsuccessful individuals, although successful sturgeon exhibited higher costs of transport (42.75 versus 25.85 J kg(-1) m(-1)). Energy expenditure metrics were not predictive of successful fishway passage, leading us to conclude that other endogenous or exogenous factors influence passage success. In a practical application of field measurements of energy expenditure, we demonstrate that fishway passage through a structure designed to facilitate migration does result in an energetic loss for lake sturgeon (3249-16,331 J kg(-1)), equivalent to individuals travelling 5.8-28.2 km in a lentic system.

Behaviour and locomotor activity of a migratory catostomid during fishway passage.

Fishways have been developed to restore longitudinal connectivity in rivers. Despite their potential for aiding fish passage, fishways may represent a source of significant energetic expenditure for fish as they are highly turbulent environments. Nonetheless, our understanding of the physiological mechanisms underpinning fishway passage of fish is still limited. We examined swimming behaviour and activity of silver redhorse (Moxostoma anisurum) during its upriver spawning migration in a vertical slot fishway. We used an accelerometer-derived instantaneous activity metric (overall dynamic body acceleration) to estimate location-specific swimming activity. Silver redhorse demonstrated progressive increases in activity during upstream fishway passage. Moreover, location-specific passage duration decreased with an increasing number of passage attempts. Turning basins and the most upstream basin were found to delay fish passage. No relationship was found between basin-specific passage duration and activity and the respective values from previous basins. The results demonstrate that successful fishway passage requires periods of high activity. The resultant energetic expenditure may affect fitness, foraging behaviour and increase susceptibility to predation, compromising population sustainability. This study highlights the need to understand the physiological mechanisms underpinning fishway passage to improve future designs and interpretation of biological evaluations.

Comparative physiology and relative swimming performance of three redhorse (Moxostoma spp.) species: associations with fishway passage success.

Our understanding of biological criteria to inform fish passage design is limited, partially due to the lack of understanding of biological motivators, cues, and constraints, as well as a lack of biological performance evaluations of structures once they are built. The Vianney-Legendre vertical slot fishway on the Richelieu River, Quebec, Canada, passes large numbers of migrating redhorse (Moxostoma spp.) upriver to spawning grounds each year. We evaluated the physiological capacity and relative swimming ability of three redhorse species (Moxostoma anisurum, Moxostoma carinatum, Moxostoma macrolepidotum; silver, river, and shorthead redhorse, respectively) to determine how these biotic factors relate to variation in fishway passage success and duration. Shorthead redhorse had higher maximum metabolic rates and were faster swimmers than silver and river redhorse at their species-specific peak migration temperatures. Blood lactate and glucose concentrations recovered more quickly for river redhorse than for silver and shorthead redhorse, and river redhorse placed second in terms of metabolic recovery and swim speed. Interestingly, fish sampled from the top of the fishway had nearly identical lactate, glucose, and pH values compared to control fish. Using passive integrated transponders in 2010 and 2012, we observed that passage success and duration were highly variable among redhorse species and were not consistent among years, suggesting that other factors such as water temperature and river flows may modulate passage success. Clearly, additional research is needed to understand how organismal performance, environmental conditions, and other factors (including abundance of conspecifics and other comigrants) interact with fishway features to dictate which fish will be successful and to inform research of future fishways. Our research suggests that there may be an opportunity for a rapid assessment approach where fish chased to exhaustion to determine maximal values of physiological disturbance are compared to fish sampled from the top of the fishway, which could reveal which species (or sizes of fish) are approaching or exceeding their physiological capacity during passage.