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.

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.

Consequences of hydrological alteration for beta diversity of fish assemblages at multiple spatial scales.

Effects of dam operation and extraction of water from rivers on spatial variation in hydrological regimes, and consequences for freshwater biodiversity, are widely predicted but seldom assessed empirically. Evidence of linkages between hydrology and beta diversity contributes to water-management decisions to support landscape-scale biodiversity and avoid inadvertently contributing to further biodiversity decline. Using six lowland rivers in Australia's Murray - Darling Basin that formed a gradient of hydrological alteration, we examined (1) spatial variation in hydrology under modelled scenarios of low water-resource development and flow modification by dams and extraction, (2) how beta diversity of fish among and within rivers was associated with spatial hydrological variation and whether patterns of overall beta diversity differed between native and non-native species, and (3) the associations of spatial and environmental variables and both recent and long-term hydrology with beta diversity. Spatial variation in hydrology among rivers was higher under the modified scenario than under the low-development scenario yet change in the magnitude of within-river (longitudinal) variation was inconsistent between rivers. Beta diversity among rivers was significantly associated with spatial variation in hydrology only in certain circumstances (native species assemblages in specific years). Within-river beta diversity varied among rivers yet was unrelated to longitudinal variation in modified hydrological regimes. Patterns of beta diversity did not differ appreciably if non-native species were included in or excluded from analyses. These findings contradict predictions adopted in ecohydrological science that water resource development homogenises hydrological regimes, in turn causing biotic homogenisation in lowland rivers.

Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod.

Age-based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life-history parameters such as length, maturity, mortality and fecundity. These age-based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age-associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochella peelii) and Mary River cod (Maccullochella mariensis). Age estimation models were calibrated using either known-age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.

Cholesterol-lowering activity of natural mono- and sesquiterpenoid compounds in essential oils: A review and investigation of mechanisms using in silico protein-ligand docking.

Mono- and sesquiterpenoids are the main chemical constituents of essential oils. Essential oils and their constituents have received increasing attention for lipid-lowering properties in both cell and animal models. Despite the chemical diversity of essential oil compounds, the effects of many of these compounds on cholesterol metabolism are highly similar. In this report, we review the literature regarding the effects of essential oils and their terpenoid constituents on cholesterol homeostasis, and explore likely mechanisms using protein-ligand docking. We identified 98 experimental and seven clinical studies on essential oils, isolated compounds, and blends; 100 of these described improvements either in blood cholesterol levels or in sterol metabolic pathways. Our review and docking analysis confirmed two likely mechanisms common to many essential oil compounds: (1) direct agonism of peroxisome-proliferator-activated receptors, and (2) direct interaction with sterol-sensing domains, motifs found in key sterol regulatory proteins including sterol regulatory element binding protein cleavage activating protein and HMG-CoA reductase. Notably, these direct interactions lead to decreased transcription and accelerated degradation of HMG-CoA reductase. Our work suggests that terpene derivatives in essential oils have cholesterol-lowering activity and could potentially work synergistically with statins, however, further high quality studies are needed to establish their clinical efficacy.

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.

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.

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.

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.