A systematic review of approaches to assess fish health responses to anthropogenic threats in freshwater ecosystems.

Anthropogenic threats such as water infrastructure, land-use changes, overexploitation of fishes and other biological resources, invasive species and climate change present formidable challenges to freshwater biodiversity. Historically, management of fish and fishery species has largely been based on studies of population- and community-level dynamics; however, the emerging field of conservation physiology promotes the assessment of individual fish health as a key management tool. Fish health is highly sensitive to environmental disturbances and is also a fundamental driver of fitness, with implications for population dynamics such as recruitment and resilience. However, the mechanistic links between particular anthropogenic disturbances and changes in fish health, or impact pathways, are diverse and complex. The diversity of ways in which fish health can be measured also presents a challenge for researchers deciding on methods to employ in studies seeking to understand the impact of these threats. In this review, we aim to provide an understanding of the pathway through which anthropogenic threats in freshwater ecosystems impact fish health and the ways in which fish health components impacted by anthropogenic threats can be assessed. We employ a quantitative systematic approach to a corpus of papers related to fish health in freshwater and utilize a framework that summarizes the impact pathway of anthropogenic threats through environmental alterations and impact mechanisms that cause a response in fish health. We found that land-use changes were the most prolific anthropogenic threat, with a range of different health metrics being suitable for assessing the impact of this threat. Almost all anthropogenic threats impacted fish health through two or more impact pathways. A robust understanding of the impact pathways of anthropogenic threats and the fish health metrics that are sensitive to these threats is crucial for fisheries managers seeking to undertake targeted management of freshwater ecosystems.

Statistical downscaling of GRACE terrestrial water storage changes based on the Australian Water Outlook model.

The coarse spatial resolution of the Gravity Recovery and Climate Experiment (GRACE) dataset has limited its application in local water resource management and accounting. Despite efforts to improve GRACE spatial resolution, achieving high resolution downscaled grids that correspond to local hydrological behaviour and patterns is still limited. To overcome this issue, we propose a novel statistical downscaling approach to improve the spatial resolution of GRACE-terrestrial water storage changes (ΔTWS) using precipitation, evapotranspiration (ET), and runoff data from the Australian Water Outlook. These water budget components drive changes in the GRACE water column in much of the global land area. Here, the GRACE dataset is downscaled from the original resolution of 1.0° × 1.0° to 0.05° × 0.05° over a large hydro-geologic basin in northern Australia (the Cambrian Limestone Aquifer-CLA), capturing sub- grid heterogeneity in ΔTWS of the region. The downscaled results are validated using data from 12 in-situ groundwater monitoring stations and water budget estimates of the CLA's land water storage changes from April 2002 to June 2017. The change in water storage over time (ds/dt) estimated from the water budget model was weakly correlated (r = 0.34) with the downscaled GRACE ΔTWS. The weak relationship was attributed to the possible uncertainties inherent in the ET datasets used in the water budget, particularly during the summer months. Our proposed methodology provides an opportunity to improve freshwater reporting using GRACE and enhances the feasibility of downscaling efforts for other hydrological data to strengthen local-scale applications.

Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation.

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.

New integrated hydrologic approach for the assessment of rivers environmental flows into the Urmia Lake.

Recent research has greatly focused on the environmental water supplement of rivers individually and independently. However, a comprehensive and integrated view of all rivers in the basin is simultaneously required in closed basins leading to lakes and wetlands. This has affected Lake Urmia, which is the second largest saltwater lake in the world. It has been in danger of drying up in recent years as a result of not allocating the required environmental flow (e-flow) due to the increase in water resource consumption in the agricultural sector and climate changes. In this study, a method derived from the flow duration curve shifting (FDCS) method is presented in addition to explaining the possibility of providing the e-flow of rivers leading to the lake. The method can make the least amount of change in the hydrological characteristics of rivers while providing the volume of required water by the ecosystem of lakes or downstream wetlands. Unlike the conventional method which presents the results on a monthly basis, the above-mentioned method is based on daily data of hydrometric stations and can calculate the amount of the environmental requirement of rivers in real-time according to the upstream inlet of the river. This method has been used in the Urmia Lake basin. According to the results, it can provide the environmental requirement of the lake by allocating 70.5% of the annual flow of rivers and thus can save the lake and the ecosystem of the region from the current critical conditions.

Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps.

Methane availability in freshwaters is usually associated with spatial-temporal variation in methanogenesis. Unusually, however, natural gas macro-seeps occur along the Condamine River in eastern Australia which elevate ambient water-column methane concentrations more than 3,000 times. We quantified the spatial-temporal variation in methane oxidation rates and the total microbial and methanotroph community composition (through the amplification and sequencing of 16S rRNA and particulate methane monooxygenase (pmoA) genes), and the factors mediating this variation, in reaches with and without macro-seeps. Sediment methane oxidation rates were, on average, 29 times greater, and the abundance of methanotrophs significantly higher, in the vicinity of methane macro-seeps compared to non-seep sites. Methylocystis was the most abundant methanotroph group at all sites, but type Ib methanotrophs showed the steepest increase in abundance at seep sites. pmoA gene analysis identified these as clade 501, while 16S rRNA gene analysis identified these as the closely related genus Methylocaldum. Sediment methane oxidation rates and the relative abundance and composition of benthic microbial communities were primarily influenced by methane availability which was in turn related to variation in river discharge. Methane-derived carbon may be an important energy source for the aquatic food webs in reaches affected by natural gas macro-seeps.

A national-scale dataset for threats impacting Australia's imperiled flora and fauna.

Australia is in the midst of an extinction crisis, having already lost 10% of terrestrial mammal fauna since European settlement and with hundreds of other species at high risk of extinction. The decline of the nation's biota is a result of an array of threatening processes; however, a comprehensive taxon-specific understanding of threats and their relative impacts remains undocumented nationally. Using expert consultation, we compile the first complete, validated, and consistent taxon-specific threat and impact dataset for all nationally listed threatened taxa in Australia. We confined our analysis to 1,795 terrestrial and aquatic taxa listed as threatened (Vulnerable, Endangered, or Critically Endangered) under Australian Commonwealth law. We engaged taxonomic experts to generate taxon-specific threat and threat impact information to consistently apply the IUCN Threat Classification Scheme and Threat Impact Scoring System, as well as eight broad-level threats and 51 subcategory threats, for all 1,795 threatened terrestrial and aquatic threatened taxa. This compilation produced 4,877 unique taxon-threat-impact combinations with the most frequently listed threats being Habitat loss, fragmentation, and degradation (n = 1,210 taxa), and Invasive species and disease (n = 966 taxa). Yet when only high-impact threats or medium-impact threats are considered, Invasive species and disease become the most prevalent threats. This dataset provides critical information for conservation action planning, national legislation and policy, and prioritizing investments in threatened species management and recovery.

New insights into the food web of an Australian tropical river to inform water resource management.

Rivers around the world are threatened by altered flow due to water resource development. Altered flow can change food webs and impact riverine energetics. The Fitzroy River, in northern Australia, is targeted for development but uncertainty remains about the sources of carbon supporting the food web, particularly in the lowlands-the region most likely to be impacted by water extraction. This study used stable isotopes to investigate if algal biofilm is the main carbon source sustaining fish in lowland habitats. We also sought evidence that large-bodied migratory fish were transporting remote carbon around the system. Our results revealed that local algal biofilm carbon was the dominant source of energy sustaining fish in wet season floodplain habitats, but that fish in main-channel pools during the dry season were increasingly dependent on other carbon sources, such as leaf litter or phytoplankton. We found no evidence that large-bodied fish were transporting remote carbon from the floodplain or estuary into the lower main-channel of the river. We recommend that water planners take a precautionary approach to policy until sufficient food web evidence is amassed.

Effects of a low-head weir on multi-scaled movement and behavior of three riverine fish species.

Despite providing considerable benefits to society, dams and weirs threaten riverine ecosystems by disrupting movement and migration of aquatic animals and degrading riverine habitats. Whilst the ecological impacts of large dams are well studied, the ecological effects of low-head weirs that are periodically drowned out by high flows are less well-understood. Here we examine the effects of a low-head weir on fine- and broad-scale movements, habitat use, and breeding behaviour of three species of native freshwater fish in the Nymboida River in coastal eastern Australia. Acoustic telemetry revealed that eastern freshwater cod (Maccullochella ikei) and eel-tailed catfish (Tandanus tandanus) made few large-scale movements, but Australian bass (Percalates novemaculeata) upstream of the weir were significantly more mobile than those below the weir. Within the weir pool, all three species displayed distinctive patterns in fine-scale movement behaviour that were likely related the deeper lentic environment created by the weir. No individuals of any species crossed the weir during the study period. Tandanus tandanus nesting behaviour varied greatly above and below the weir, where individuals in the more lentic upstream environment nested in potentially sub-optimal habitats. Our results demonstrate the potential effects of low-head weirs on movement and behaviour of freshwater fishes.

Coupling environment and physiology to predict effects of climate change on the taxonomic and functional diversity of fish assemblages in the Murray-Darling Basin, Australia.

This study uses species distribution modeling and physiological and functional traits to predict the impacts of climate change on native freshwater fish in the Murray-Darling Basin, Australia. We modelled future changes in taxonomic and functional diversity in 2050 and 2080 for two scenarios of carbon emissions, identifying areas of great interest for conservation. Climatic-environmental variables were used to model the range of 23 species of native fish under each scenario. The consensus model, followed by the physiological filter of lethal temperature was retained for interpretation. Our study predicts a severe negative impact of climate change on both taxonomic and functional components of ichthyofauna of the Murray-Darling Basin. There was a predicted marked contraction of species ranges under both scenarios. The predictions showed loss of climatically suitable areas, species and functional characters. There was a decrease in areas with high values of functional richness, dispersion and uniqueness. Some traits are predicted to be extirpated, especially in the most pessimistic scenario. The climatic refuges for fish fauna are predicted to be in the southern portion of the basin, in the upper Murray catchment. Incorporating future predictions about the distribution of ichthyofauna in conservation management planning will enhance resilience to climate change.

Understanding invasion success of Pseudorasbora parva in the Qinghai-Tibetan Plateau: Insights from life-history and environmental filters.

Understanding mechanisms of fish invasion success is crucial to controlling existing invasions and preventing potential future spread. Despite considerable advances in explaining successful fish invasions, little is known about how non-native fish successfully invade alpine freshwater ecosystems. Here, we explore the role of fish life history and environmental factors in contributing to invasion success of Pseudorasbora parva on the Qinghai-Tibet Plateau. We compared life history trait differences between native populations in lowland China with introduced populations in lowland Europe and the high elevation Qinghai-Tibet Plateau. Linear mixed-effects models were used to analyse life-history trait variation across elevation gradients. A random forest model was developed to identify the key environmental filters influencing P. parva invasion success. Life history characteristics differed substantially between native and introduced populations. Compared with native Chinese populations, introduced populations in lowland Europe had smaller body size, higher fecundity, smaller oocytes and earlier maturation. Introduced populations in the Qinghai-Tibet Plateau had smaller body size, lower fecundity, smaller oocytes and later maturation compared with native populations. 1-Year-Length and fecundity in all age classes of females significantly increased with increasing elevation. 2-Year-Length and 3-Year-Length of male significantly increased while maximal longevity and length at first maturity were significantly decreased with the elevation gradient. Habitat type, annual mean temperature, elevation, annual precipitation and precipitation seasonality, were the 5 most important predictors for the occurrence of the P. parva. Our study indicates that invasive P. parva adopt different life history strategies on the plateau compared with invasive populations at low elevations, highlighting that more studies are required for a better understanding of biological invasion under extreme conditions. Considering the ongoing hydrologic alteration and climate change, our study also highlighted that P. parva may expand their distribution range in the future on the Qinghai-Tibet Plateau.

Does a bigger mouth make you fatter? Linking intraspecific gape variability to body condition of a tropical predatory fish.

In gape-limited predators, gape size restricts the maximum prey size a predator is capable to ingest. However, studies investigating the energetic consequences of this relationship remain scarce. In this study, we tested the hypothesis that gape-size variability influences individual body condition (a common proxy for fitness) in one of the largest freshwater teleost predators, the barramundi. We found that individual barramundi with larger gapes relative to body size had higher body condition values compared to conspecifics with smaller gapes. Body condition was highest soon after the wet season, a period of high feeding activity on productive inundated floodplains, and body condition decreased as the dry season progressed when fish were restricted to dry season remnant habitats. The increased condition obtained during the wet season apparently offsets weight loss through the dry season, as individuals with large gapes were still in better condition than fish with small gapes in the late-dry season. Elucidation of the links between intraspecific variability in traits and performance is a critical challenge in functional ecology. This study emphasizes that even small intraspecific variability in morphological trait values can potentially affect individual fitness within a species' distribution.

Age structure of the Australian lungfish (Neoceratodus forsteri).

The Australian lungfish has been studied for more than a century without any knowledge of the longevity of the species. Traditional methods for ageing fish, such as analysis of otolith (ear stone) rings is complicated in that lungfish otoliths differ from teleost fish in composition. As otolith sampling is also lethal, this is not appropriate for a protected species listed under Australian legislation. Lungfish scales were removed from 500 fish from the Brisbane, Burnett and Mary rivers. A sub-sample of scales (85) were aged using bomb radiocarbon techniques and validated using scales marked previously with oxytetracycline. Lungfish ages ranged from 2.5-77 years of age. Estimated population age structures derived using an Age Length Key revealed different recruitment patterns between river systems. There were statistically significant von Bertalanffy growth model parameters estimated for each of the three rivers based on limited sample sizes. In addition, length frequency distributions between river systems were also significantly different. Further studies will be conducted to review drivers that may explain these inter-river differences.

Climate-driven synchrony in growth-increment chronologies of fish from the world's largest high-elevation river.

Understanding how sensitive aquatic ecosystems respond to climate change is essential for effective biodiversity conservation and management. The Tibetan Plateau (TP) is one of the most globally sensitive areas to climate change with potentially serious implications for resident fish populations and aquatic food webs. However, how the growth of TP fish responds to climate change, and how this response varies with the trophic level of different species remain unknown. We established growth-increment chronologies of two important Schizothoracinae fishes that are endemic to the TP (e.g., the omnivorous Schizopygopsis younghusbandi and the carnivorous Oxygymnocypris stewartii) from the Yarlung Tsangpo River, using otolith increment width measurements and dendrochronological methods. These growth chronologies were correlated with key indicators of environmental variation (temperature, precipitation, and river discharge) to examine the potential effects of climate change. The two chronologies displayed synchronous responses to recent climate change. In this glacial-fed river, the growth of both fish species was significantly and negatively correlated with the mean annual air temperature, while it was positively but not significantly correlated with precipitation and discharge. The higher trophic level species O. stewartii was more sensitive to climate than was the lower trophic level species S. younghusbandi, with temperature variables explaining a higher proportion of growth variability in O. stewartii (64.6%) than in S. younghusbandi (46.4%). The results collectively indicate that both species are highly sensitive to climate change, which may affect fish growth by altering water environment, fish physiological fitness and food availability. This study provides further empirical evidence of the utility of growth-increment chronologies for investigating the effects of climate change on aquatic ecosystems across different basins and water body types of the TP. These findings can inform conservation and management actions related to addressing climate change on the TP and other high-elevation temperate systems found worldwide.

Monitoring age-related trends in genomic diversity of Australian lungfish.

An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old postreproductive individuals, potentially resulting in a small and declining breeding population. Here, we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb radiocarbon dating method to age lungfish nonlethally, based on 14 C ratios of scales. A total of 15,201 single nucleotide polymorphic (SNP) loci were genotyped in 92 individuals ranging in age from 2 to 77 years old. Standardized individual heterozygosity and individual inbreeding coefficients varied widely within and between riverine populations, but neither was associated with age, so perceived problems with recruitment have not translated into genetic erosion that could be considered a proximate threat to lungfish populations. Conservation concern has surrounded Australian lungfish for over a century. However, our results suggest that long-lived threatened species can maintain stable levels of intraspecific variability when sufficient reproductive opportunities exist over the course of a long lifespan.

Strong evidence for changing fish reproductive phenology under climate warming on the Tibetan Plateau.

Phenological responses to climate change have been widely observed and have profound and lasting effects on ecosystems and biodiversity. However, compared to terrestrial ecosystems, the long-term effects of climate change on species' phenology are poorly understood in aquatic ecosystems. Understanding the long-term changes in fish reproductive phenology is essential for predicting population dynamics and for informing management strategies, but is currently hampered by the requirement for intensive field observations and larval identification. In this study, a very low-frequency sampling of juveniles and adults combined with otolith measurements (long axis length of the first annulus; LAFA) of an endemic Tibetan Plateau fish (Gymnocypris selincuoensis) was used to examine changes in reproductive phenology associated with climate changes from the 1970s to 2000s. Assigning individual fish to their appropriate calendar year class was assisted by dendrochronological methods (crossdating). The results demonstrated that LAFA was significantly and positively associated with temperature and growing season length. To separate the effects of temperature and the growing season length on LAFA growth, measurements of larval otoliths from different sites were conducted and revealed that daily increment additions were the main contributor (46.3%), while temperature contributed less (12.0%). Using constructed water-air temperature relationships and historical air temperature records, we found that the reproductive phenology of G. selincuoensis was strongly advanced in the spring during the 1970s and 1990s, while the increased growing season length in the 2000s was mainly due to a delayed onset of winter. The reproductive phenology of G. selincuoensis advanced 2.9 days per decade on average from the 1970s to 2000s, and may have effects on recruitment success and population dynamics of this species and other biota in the ecosystem via the food web. The methods used in this study are applicable for studying reproductive phenological changes across a wide range of species and ecosystems.

High rates of organic carbon processing in the hyporheic zone of intermittent streams.

Organic carbon cycling is a fundamental process that underpins energy transfer through the biosphere. However, little is known about the rates of particulate organic carbon processing in the hyporheic zone of intermittent streams, which is often the only wetted environment remaining when surface flows cease. We used leaf litter and cotton decomposition assays, as well as rates of microbial respiration, to quantify rates of organic carbon processing in surface and hyporheic environments of intermittent and perennial streams under a range of substrate saturation conditions. Leaf litter processing was 48% greater, and cotton processing 124% greater, in the hyporheic zone compared to surface environments when calculated over multiple substrate saturation conditions. Processing was also greater in more saturated surface environments (i.e. pools). Further, rates of microbial respiration on incubated substrates in the hyporheic zone were similar to, or greater than, rates in surface environments. Our results highlight that intermittent streams are important locations for particulate organic carbon processing and that the hyporheic zone sustains this fundamental process even without surface flow. Not accounting for carbon processing in the hyporheic zone of intermittent streams may lead to an underestimation of its local ecological significance and collective contribution to landscape carbon processes.

Freshwater fishes of northern Australia.

Northern Australia is biologically diverse and of national and global conservation signicance. Its ancient landscape contains the world's largest area of savannah ecosystem in good ecological condition and its rivers are largely free-flowing. Agriculture, previously confined largely to open range-land grazing, is set to expand in extent and to focus much more on irrigated cropping and horticulture. Demands on the water resources of the region are thus, inevitably increasing. Reliable information is required to guide and inform development and help plan for a sustainable future for the region which includes healthy rivers that contain diverse fish assemblages. Based on a range of information sources, including the outcomes of recent and extensive new field surveys, this study maps the distribution of the 111 freshwater fishes (excluding elasmobranches) and 42 estuarine vagrants recorded from freshwater habitats of the region. We classify the habitat use and migratory biology of each species. This study provides a comprehensive assessment of the diversity and distribution of fishes of the region within a standardised nomenclatural framework. In addition, we summarise the outcomes of recent phylogeographic and phylogenetic research using molecular technologies to identify where issues of taxonomy may need further scrutiny. The study provides an informed basis for further research on the spatial arrangement of biodiversity and its relationship to environmental factors (e.g. hydrology), conservation planning and phylogentic variation within individual taxa.

Testing Three Species Distribution Modelling Strategies to Define Fish Assemblage Reference Conditions for Stream Bioassessment and Related Applications.

Species distribution models are widely used for stream bioassessment, estimating changes in habitat suitability and identifying conservation priorities. We tested the accuracy of three modelling strategies (single species ensemble, multi-species response and community classification models) to predict fish assemblages at reference stream segments in coastal subtropical Australia. We aimed to evaluate each modelling strategy for consistency of predictor variable selection; determine which strategy is most suitable for stream bioassessment using fish indicators; and appraise which strategies best match other stream management applications. Five models, one single species ensemble, two multi-species response and two community classification models, were calibrated using fish species presence-absence data from 103 reference sites. Models were evaluated for generality and transferability through space and time using four external reference site datasets. Elevation and catchment slope were consistently identified as key correlates of fish assemblage composition among models. The community classification models had high omission error rates and contributed fewer taxa to the 'expected' component of the taxonomic completeness (O/E50) index than the other strategies. This potentially decreases the model sensitivity for site impact assessment. The ensemble model accurately and precisely modelled O/E50 for the training data, but produced biased predictions for the external datasets. The multi-species response models afforded relatively high accuracy and precision coupled with low bias across external datasets and had lower taxa omission rates than the community classification models. They inherently included rare, but predictable species while excluding species that were poorly modelled among all strategies. We suggest that the multi-species response modelling strategy is most suited to bioassessment using freshwater fish assemblages in our study area. At the species level, the ensemble model exhibited high sensitivity without reductions in specificity, relative to the other models. We suggest that this strategy is well suited to other non-bioassessment stream management applications, e.g., identifying priority areas for species conservation.

Measuring benefits of protected area management: trends across realms and research gaps for freshwater systems.

Protected areas remain a cornerstone for global conservation. However, their effectiveness at halting biodiversity decline is not fully understood. Studies of protected area benefits have largely focused on measuring their impact on halting deforestation and have neglected to measure the impacts of protected areas on other threats. Evaluations that measure the impact of protected area management require more complex evaluation designs and datasets. This is the case across realms (terrestrial, freshwater, marine), but measuring the impact of protected area management in freshwater systems may be even more difficult owing to the high level of connectivity and potential for threat propagation within systems (e.g. downstream flow of pollution). We review the potential barriers to conducting impact evaluation for protected area management in freshwater systems. We contrast the barriers identified for freshwater systems to terrestrial systems and discuss potential measurable outcomes and confounders associated with protected area management across the two realms. We identify key research gaps in conducting impact evaluation in freshwater systems that relate to three of their major characteristics: variability, connectivity and time lags in outcomes. Lastly, we use Kakadu National Park world heritage area, the largest national park in Australia, as a case study to illustrate the challenges of measuring impacts of protected area management programmes for environmental outcomes in freshwater systems.