Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

Processes responsible for population structuring across spatial and temporal scales represent key components in understanding speciation and evolution. We use a hierarchical approach to investigate the degree and mechanisms of structuring in landlocked and diadromous populations of the facultatively amphidromous fish Galaxias brevipinnis across various temporal and spatial scales in southern New Zealand. To determine long-term structuring, multiple lakes and coastal sites were compared genetically. Short-term structuring was assessed using otolith microchemistry for a subset of sites, and behavioural mechanisms driving population structuring were assessed via larval distributions. Genetic data show that lakes foster divergence of lake-developing populations from each other and from coastal stream populations, whereas there is relatively little structuring within coast or lake populations. However, otolith analyses indicate that on a shorter time scale, most larvae do not disperse, i.e. recruitment is local. Thus, lake and coastal populations show a distinct meta-population structure based on catchment, in contrast to the prevailing assumption of widespread dispersal, with implications for management. Most larvae were distributed in river plumes, suggesting that a simple larval behavioural mechanism, e.g. positive rheotaxis, may result in larval retention within catchments and lakes. However, not all larvae were retained in plumes, creating opportunities for genetic exchange within-lake or among coastal sites. Genetic divergence of lake populations as a consequence of landscape and behaviour provides an insight into the potential of G. brevipinnis to diversify and speciate, when landscape and circumstances align, and also has implications for the management of this and other facultatively amphidromous species.

There is increasing interest in the health of waterways in Aotearoa New Zealand. The National Policy Statement for Freshwater Management 2020 (NPS-FM) places a greater onus on resource managers to report on the state of freshwater ecosystem health, including fish. Routine fish monitoring is time intensive and is principally conducted in 'wadeable' stream reaches. In comparison, environmental DNA (eDNA) sampling is a relatively recent and rapid technique that likely detects fish and other vertebrate and invertebrate taxa over a broader spatial scale. In this study, we present data for five wadeable streams comparing diversity derived from multi-year standardised electrofishing with eDNA samples collected from the same reaches. Further, we explore whether the number of eDNA monitoring 'reads' for species at a site may provide an approximate (semi-quantitative) indication of their 'near field' relative abundance based on one-pass electrofishing captures. Results indicated that while some aspects of the methodology require fine-tuning, eDNA sampling shows substantial promise for complimenting state of the environment (SOE) reporting for describing fish diversity in wadeable streams. The use of aquatic eDNA monitoring to provide a cost-effective indication of broader catchment scale biodiversity (e.g. birds and exotic pests) in wadeable and non-wadeable streams is also discussed.

Partial migration, or variation in migratory propensity within populations, has been reported across a range of taxa, including fish. Otolith microchemistry has revealed a high degree of life history plasticity in many amphidromous species, with diadromous and non-diadromous recruitment occurring. We examined this plasticity and its effect on population structure, dispersal and recruitment in Galaxias brevipinnis, an amphidromous fish widespread around New Zealand. We used otolith microchemistry analyses to examine recruitment sources and fish surveys to assess abundance and size structure in two large river systems, each containing naturally formed lakes and no obvious physical barriers to migration. Otolith analyses revealed discrete recruitment sources for stream-resident populations, with marine recruitment supporting populations downstream from lakes and exclusively lake-derived recruitment for populations upstream of lakes. Although diadromous G. brevipinnis were abundant within 10km of the sea, the abundance and relative proportion of younger fish declined as distance upstream increased, until a lake was reached, at which point abundance and the proportion of small individuals increased. The results provide a strong indication that supply is limiting recruitment for G. brevipinnis as distance from pelagic larval habitat increases, and that discrete recruitment sources and population structuring exist even within drainages.

There have been increasing calls for the holistic assessment of river condition, moving beyond the traditional focus on water quality and biology alone. Legislation in New Zealand now requires integrated assessments of freshwater ecosystem health. In this paper we report on the application of a framework for New Zealand freshwater assessment, which includes 5 core components—water quality, water quantity, aquatic biota, physical habitat, and ecological processes—in the Tukituki River catchment. Indicators of ecological processes included ecosystem metabolism and cellulose decomposition potential, which were measured and reported alongside other river-health metrics to provide an integrated picture of river ecological integrity at site, stream-type, and catchment scales. Every site in the Tukituki catchment failed to meet bottom-line benchmarks for at least 1 assessment metric. When aggregated by stream type, warm-wet lowland streams in the Tukituki River catchment had the poorest ecosystem health because of poor water quality and quantity. At the catchment scale, the Tukituki scored highly in overall ecosystem health despite 20% of the targeted network failing bottom-line benchmarks for 11 out of 22 metrics. This study demonstrates the value of: 1) a probabilistic sampling design for predicting the spatial extent of stream condition, 2) accounting for environmental variation through a process of data harmonization informed by site-specific reference conditions and bottom-line benchmarks, and 3) involving resource-management practitioners in the development of the assessment framework to ensure that the level of detail is achievable in practice and to provide examples of how the results can inform management actions. Applications could include directing land-use mitigations and stream restoration towards warm-wet lowland areas, where excess phosphorus and aquatic plants proliferate. Finally, we demonstrate how a report-card approach can simultaneously provide information across multiple components and avoid the loss of information. The framework is adaptable and can be used across contrasting spatial scales, it is consistent and representative, and it is easily understood.

New Zealand has a complex recent history of climatic and tectonic change that has left variable signatures in the geographic distribution and genetic structure of the region’s flora and fauna. To identify concordant patterns, a broad range of taxa must be examined and compared. In New Zealand’s North Island, a consensus is forming as to the dominant biogeographic barriers in the region although obligate freshwater taxa have not been considered in this framework. We use single-nucleotide polymorphisms to investigate phylogeography in the widespread obligate freshwater fish Gobiomorphus basalis on the North Island. Phylogeographic patterns within G. basalis reveal biogeographic disjunctions that are in some ways consistent and in other ways at odds with established patterns, providing insight into the processes that have shaped the islands’ biogeography. We also use phylogeography to delineate species boundaries within the entire New Zealand radiation of Gobiomorphus and find that it contains several morphologically cryptic species. We resolve two clades within G. basalis that correspond to areas north and south of the Taupo Volcanic Zone. We confirm the distinctiveness of Gobiomorphus alpinus relative to Gobiomorphus cotidianus, as well as the presence of two lineages within Gobiomorphus breviceps that were previously identified based on mitochondrial data.

Otolith microchemistry was used to identify marine- versus freshwater-derived recruitment of three native freshwater fish species belonging to the southern hemisphere family Galaxiidae, in New Zealand's longest river system, the Waikato River. Water chemistry data for trace elements and Sr-87/Sr-86 isotope ratios were collected from five lentic and 10 lotic water bodies throughout the lower river floodplain. Potential spawning sites for galaxiids were compared with values obtained by laser ablation inductively coupled mass spectrometry (LA-ICPMS) depth profiling of young-of-the-year otoliths sampled from fish in nine lower river catchment sites. Otolith chemical signatures from the larval rearing period indicated that catchment-scale recruitment for two species, Galaxias argenteus (Gmelin, 1789) and Galaxias fasciatus Gray, 1842, was driven predominantly by non-diadromous recruitment from one lake (Lake Waahi). In contrast, diadromous recruitment appeared to be more common for Galaxias maculatus (Jenyns, 1842); however, non-diadromous specimens were also identified for the first time from a New Zealand river. Reversing lake outlet flows linked to river stage appears be important in facilitating the dispersal of rheotactic larvae out of lakes, suggesting that lake outflow management at key times could be used to sustain this ecologically important function. This study highlights that some water bodies can supply a disproportionately large number of recruits to support fish populations within the wider riverscape. Identifying these water bodies and managing them to sustain recruitment is key to the conservation of non-diadromous Galaxiidae in this modified lowland environment

Three independent scientific lines of evidence were sought to determine the nutrient load limits to safeguard the macrophyte community of an intermittently closed and open lake/lagoon (ICOLL): (1) a literature review identified nitrogen load thresholds related to the collapse of macrophytes in similar systems in Australia, Europe and elsewhere, (2) an ICOLL expert carried out an assessment based on current local data and on data from 57 Australian coastal lakes and lagoons, and (3) a deterministic coupled hydrodynamic-ecological model was developed and applied to simulate the ecological outcomes of several nutrient loading scenarios. The three lines of evidence converged on well-defined nitrogen load estimates required to avoid the collapse of the macrophyte community. Uncertainties were slightly greater in relation to required phosphorus load limits, but the evidence still helped set a precautionary phosphorus load limit that accounted for these uncertainties. Thus, despite the challenges in setting load limits for complex ecosystems, multiple lines of evidence helped derive robust nutrient load limits for managing the ICOLL to safeguard values associated with a healthy macrophyte community.

Understanding migratory life histories is critical for the effective management and conservation of migratory species. However, amphidromous migrations (fish hatch in streams, immediately migrate to the sea for a feeding period and return to fresh water as juveniles) remain understudied owing to the difficulties of tracking tiny larval fish. Despite this, it has widely been assumed that amphidromous fish have open, resilient populations, with marine-rearing larvae dispersing widely during their pelagic phase. In the present study we tested the hypothesis that when an alternative freshwater pelagic habitat is available, non-diadromous recruitment will be the dominant process in sustaining amphidromous fish populations, with implications for their connectivity and resilience. Otolith microchemical analyses of five species (three Galaxias (Galaxiidae), two Gobiomorphus (Eleotridae)) from paired systems on the South Island of New Zealand indicated that when a suitable freshwater pelagic habitat existed downstream, non-diadromous recruitment was the primary population-sustaining process, typically contributing >90% of recruits. In addition, not all species recruited from all lakes, indicating the importance of the largely unstudied role of species-specific amphidromous larval requirements. The results of the present study emphasise the need to better understand the dynamics of individual populations of amphidromous fish, and highlight the importance of understanding species-specific early life history requirements to fully understand their distributions and management needs.

Sediment resuspension during and after mechanical excavation of macrophytes may have a significant impact on resident fish populations. Unfortunately, little is known about the influence of this sediment on the respiratory performance and feeding abilities of fishes in New Zealand waterways. We examined the effects of suspended sediment (SS) concentrations previously observed after a large-scale macrophyte removal operation on oxygen consumption (MO2) and feeding rates of brown trout (Salmo trutta). MO2 at 0 mg L-1, 150 mg L-1, 300 mg L-1, 450 mg L-1 and 600 mg L-1 of SS was measured using semi-closed respirometry. Feeding rates at the same SS concentrations were also measured using laboratory tank experiments. Results suggest that SS concentrations up to 600 mg L-1 have no effect on MO2. Conversely, feeding rates were significantly reduced at 450 mg L-1 (22% reduction) and 600 mg L-1 (31% reduction), indicating that sediment concentrations above 450 mg L-1 may negatively affect brown trout populations.

Summary Amphidromy is a widespread migratory behavioural syndrome exhibited by fish (and some aquatic invertebrates) that spawn in fresh water and whose larvae migrate to pelagic marine (or lentic) habitats for a period of early growth, followed by a return migration to adult freshwater habitats. The fitness advantage of amphidromy has been the subject of prolonged debate, and we examined the hypothesis that amphidromy mainly increases fecundity through the production of small pelagic larvae. We compared egg size (a proxy for larval size) of closely related non‐migratory and amphidromous fish species in the families C ottidae, G alaxiidae, E leotridae and G obiidae. To examine how egg size changes in relation to body size within a taxonomic group, we also compared egg size and maximum body size across most species of N ew Z ealand non‐migratory and amphidromous galaxiids. Non‐migratory species generally have relatively larger eggs than their amphidromous confamilial species. This particular trait has evolved independently several times in each of the four families of amphidromous fish that have given rise to significant freshwater radiations. Amongst the N ew Z ealand galaxiids, mean egg diameter increased with maximum body length for both non‐migratory and amphidromous species; however, despite the considerably smaller relative body size of the non‐diadromous species, the rate of increase in egg diameter relative to the increase in body size is considerably higher in the non‐migratory fish. We propose that amphidromous fish maintain a high level of fecundity by producing small pelagic larvae. In contrast, the relatively large eggs and well‐developed larvae of non‐migratory species increase larval survival in what are often relatively harsh and unproductive freshwater habitats. Consequently, amphidromous species are likely to have a competitive advantage over their non‐migratory relatives when close to a pelagic habitat in which their larvae can grow and develop and then migrate upstream, releasing them from recruitment limitation and giving them a local reproductive advantage over their less fecund non‐migratory relatives. We argue that the persistence and distribution of both life‐history strategies across the landscape depends on the relative difference in the net reproductive return for each strategy in relation to distance from a pelagic larval habitat, as mediated by the relative costs of migration and egg size/fecundity relationships.

Parasite avoidance is increasingly considered to be a potential driving factor in animal migrations. In many marine and freshwater benthic fish, migration into a pelagic environment by developing larvae is a common life history trait that could reduce exposure to parasites during a critical window of developmental susceptibility. We tested this hypothesis on congeneric fish (family Galaxiidae, genus Galaxias ) belonging to a closely related species complex sampled from coastal streams in southeastern New Zealand. Migratory Galaxias have larvae that migrate to pelagic marine environments, whereas the larvae of non-migratory species rear close to adult habitats with no pelagic larval phase. Both migratory and non-migratory fish are hosts to two species of skin-penetrating trematodes that cause spinal malformations and high mortality in young fish. Using generalized linear models within an Akaike information criterion and model averaging framework, we compared infection levels between migratory and non-migratory fish while taking into account body size and several other local factors likely to influence infection levels. For one trematode species, we found a significant effect of migration: for any given body length, migratory fish harboured fewer parasites than non-migratory fish. Also, no parasites of any kind were found in juvenile migratory fish sampled in spring shortly after their return to stream habitats. Our results demonstrate that migration spares juvenile fish from the debilitating parasites to which they would be exposed in adult stream habitats. Therefore, either the historical adoption of a migratory strategy in some Galaxias was an adaptation against parasitism, or it evolved for other reasons and now provides protection from infection as a coincidental side-effect.

Complete macrophyte removal to maintain drainage performance in lowland streams can have a negative effect on resident fish communities, but few studies have quantified this impact. Moreover, limited research has been carried out exploring alternative approaches for macrophyte removal that minimise the impact on the resident fish community. The aims of this study were (i) to determine how the current practice of removing almost 100% of available macrophyte cover affects native fish populations in lowland New Zealand streams and (ii) to see whether this impact can be reduced by limiting macrophyte removal to alternating 50-m sections of the waterway. Native fish populations were surveyed before and after experimental macrophyte removal for the following three treatments: (i) complete macrophyte removal, (ii) macrophyte removal from alternating 50-m reaches and (iii) control with no macrophyte removal. Radiotelemetry was used to monitor the behavioural response of individual giant kokopu (Galaxias argenteus) to the different treatments. The results of this study suggest that current drain management practices reduce CPUE of fish by 60%. Although limiting macrophyte removal to alternating 50-m sections did not minimise the community impacts of drain clearing, large giant kokopu did benefit from this strategy. All tagged giant kokopu remained in stream reaches partially cleared of macrophytes, while in completely cleared reaches all individuals were displaced. These results demonstrate the threat current drain management practices pose to New Zealand native fish and highlight the value of trialling alternative methods of macrophyte removal.

An increasing number of studies are uncovering considerable flexibility in migration patterns of diadromous fishes. The development of otolith microchemical techniques has largely driven this research and led to an appreciation of the significance of facultative diadromy in the life history of numerous species. However, validation experiments need to be undertaken for each species and life stage of interest before diadromous migrations can be confidently reconstructed. These validation experiments are required to establish a salinity calibration series against which the otolith microchemistry of unknown individuals can be compared. To facilitate research on facultative amphidromy in galaxiids, we reared the larvae of two species, Galaxias maculatus and G. argenteus, in five different salinities (2, 5, 10, 20, 34). We tested whether trace element signatures of fish reflected their salinity treatment, and hence whether otolith microchemistry could reconstruct diadromous migrations. Distinguishing low salinity (2 and 5) from high salinity (20 and 34) treatments was straightforward using otolith Sr:Ca alone. The five salinity treatments resulted in five distinct multi-trace element signatures for both species (DFA classification success of 85% and 92% for G. maculatus and G. argenteus, respectively). Otolith lithium showed a similar trend to otolith Sr:Ca (ie. higher in saltwater), and otolith Rb:Ca showed a surprising negative trend with salinity despite higher ambient Rb concentrations in saltwater. Our results suggest otolith Li:Ca and Rb:Ca should be considered as part of a multi-trace element approach when investigating diadromous migrations, particularly when non-marine Sr levels may be high.