Larval behaviour for many of New Zealand’s diadromous freshwater fish is inadequately described. Diadromy for many amphidromous species is not obligatory however, and where conditions are suitable, freshwater larval rearing may be facilitated. Where this occurs in lakes, opportunities to document the composition and conditions supporting larval rearing exist. Boat trawling was undertaken across nine lowland lakes in the Lower Waikato over four consecutive winters with a focus on larval galaxiids. Galaxiid larvae were captured in surface water habitats in all but one lake, with banded kōkopu (Galaxias fasciatus) and giant kōkopu (Galaxias argenteus) the most common species detected. One lake, Lake Waahi, consistently resulted in the most galaxiid captures for effort expended. Analyses of larvae from this and other lakes indicated that two sizes predominated in catches and that larger, older larvae were predominantly G. fasciatus while smaller, younger larvae were predominantly G. argenteus. Stomach contents indicated that two non-native zooplankton species predominated in the diet of larvae, the Holarctic daphnia, Daphnia galeata, and the Australian calanoid copepod Boeckella symmetrica. This study provides new information regarding the timing, movement and predicted recruitment of native fish species in this river basin that has important implications for lake and river management.

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.

Hilsa shad (Tenualosa ilisha) is an important anadromous fish species, supporting significant commercial and subsistence fisheries throughout south Asia. Otolith Sr:Ca and Ba:Ca profiles were used along with age data to examine the migratory history of hilsa shad from two major river systems in the northwestern Persian Gulf (Karun and Zohreh). In addition, elemental ratios (Sr:Ca, Ba:Ca, and Li:Ca) were analyzed using principal component analysis to investigate regional population structure. Variation in movement patterns was observed, though all fish analyzed had spent some time in freshwater, and most otolith signatures suggested a double downstream marine/upstream freshwater migration. There were however differences among rivers: the majority of fish from Zohreh River showed a single downstream/upstream migration through their life cycle, while Karun signatures were more complex, with multiple migrations and potential estuarine or freshwater residence. When comparing stock structure during the marine phase, the otolith signatures of Zohreh River fish showed greater separation while others tended to overlap, indicating that Zohreh fish were likely to have reared in a different location than the others. Although comprising a relatively small sample size, our results provide some preliminary insights into the life-history and stock structure of Persian Gulf hilsa shad, informing the management needs of this important fishery, and suggesting further more detailed investigations of migration and stock structure are warranted.

This study addresses the primary factors driving young-of-the-year (YoY) brown trout Salmo trutta abundance and population dynamics through the Austral summer in an important spawning tributary of a large New Zealand river. We measured the key traits and spawning investment of spawners; YoY density and movement; and environmental characteristics important for juvenile trout. In comparison to their native European range, we found high rates of pre-spawning mortality, low density of deposited eggs and reduced spawning efficiency of adult brown trout. Parental spawning investment did not affect spring juvenile trout distribution, a result likely related to a mismatch between YoY abundance and densities of eggs deposited by adults at the sampled locations. Spatial differences in seasonal dynamics of YoY density were likely related to the diversity of environmental conditions affecting habitat suitability for post-larval brown trout along the stream. Significant correlations between juvenile trout loss rate and both YoY density and downstream migration were observed only for the lowland stream segments, which had the highest spawning investment from diadromous adults, indicating the importance of these locations for recruitment. This study highlights knowledge gaps in species-environment interactions and the reproductive ecology of brown trout in New Zealand.

Natal homing and straying are behavioural tactics of migratory animals that return to nursery habitats to breed as adults. Straying has evolutionary and ecological importance for species flexibility, interpopulation connectivity and success of invasive species in new environments. This study aimed to estimate the relative importance of straying and homing in introduced brown trout Salmo trutta spawning in a model coastal tributary (Silverstream) of a large New Zealand river using otolith microchemistry. The data on natal homing and straying are important for the understanding of the ecological resilience of salmonid populations and metapopulations, and the development of effective management measures at stream or catchment scales. To examine brown trout homing and straying in a river catchment, otolith microchemical analysis was applied. We used linear discriminant function analysis to compare the trace element composition in the otoliths of YoY (young-of-the-year) trout collected at spawning streams across the catchment and adult trout reproducing in Silverstream. The results showed that only six from a sample of 30 spawning adults in Silverstream originated from Silverstream. Another 14 fish likely originated from other Taieri tributaries further upstream, but the origin of the remaining 10 could not be determined. Contrary to published studies based on wild populations of brown trout in Europe, and several other species of salmonids, a large proportion of brown trout spawners collected in Silverstream were strays. The large number of strayers identified in Silverstream may be a consequence of the geomorphology of the Taieri catchment and highlights the adaptability of brown trout to different environmental contexts.

Understanding the role different habitats play in the life histories of fishes is important for the development of holistic aquatic ecosystem management plans. We used otolith trace element analysis to reconstruct the life history of estuarine triplefin Forsterygion nigripenne and infer its habitat use. Analysis of otoliths using laser ablation inductively coupled plasma mass spectrometry showed an elemental profile without prominent changes in elemental concentration. The otolith elemental profiles were not indicative of movement between waters with substantial Sr:Ca and Ba:Ca differences. The Sr:Ca and Ba:Ca profiles were indicative of within-and near-estuary movements encompassing short time periods. Overall, the otolith microchemical profile was likely indicative of a life history closely associated with estuaries. However, it is difficult to rule out brief excursions to the marine environment given that may not have been of sufficient duration to be recorded in the elemental composition of the otolith. This suggests that F. nigripenne is the only species in southern New Zealand known to be closely associated with estuarine habitat for its entire life cycle.

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.

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.

Determining the factors driving population dynamics of stream salmonids across broad landscapes is important for understanding stream ecosystem functioning and for the management and conservation of the populations of such fish. A few studies have described the determinants of the early life history of salmonids across catchments, but none of them have examined how this spatial variation develops temporally. We hypothesised that: (1) spatiotemporal dynamics of young-of-the-year (YoY) trout populations vary within the catchment, with loss rates (emigration plus mortality) being higher in lower elevation, downstream reaches than in higher elevation, upstream ones; and (2) loss rate would be density dependent, leading to reduced intra- and inter-cohort competition and supporting establishment of resident populations. We tested the first hypothesis by examining relationships between geomorphic characteristics of spawning streams and temporal dynamics of YoY brown trout density, loss rate and biological traits through an austral summer across the catchment of New Zealand's fourth-longest river, the Taieri River. To test the second hypothesis, we examined whether initial YoY density in spring and other biotic determinants affected loss rate and cohort structure dynamics, resulting in density-dependent self-thinning of YoY fish to avoid resource limitation. Spring YoY density and subsequent loss rate was higher in low elevation sites, corresponding to stream accessibility to migratory spawners. These significant correlations of YoY density and related biotic variables with elevation disappeared later in the season, indicating that regardless of their origin, brown trout YoY tend to form stream resident populations with multicohort structure and densities low enough to limit intraspecific competition. Our findings provide evidence that geomorphological features of the landscape affect temporal dynamics of YoY trout populations driven by density-dependent self-regulatory mechanisms that can control the abundance of growing fish.

Amphidromous species undertake a number of migrations throughout their life-history, migrating to sea immediately after hatching in freshwater, migrating back to freshwater after a pelagic larval period, and potentially undertaking adult spawning migrations. Amphidromous species are therefore likely to be highly susceptible to water infrastructure, having different migratory directions, objectives, and requirements at different life stages. We review the current state of knowledge on the migrations of amphidromous species, identifying the requirements for successful migrations, and potential threats from water infrastructure associated with anthropogenic activities. Newly hatched larvae migrating downstream are susceptible to numerous hazards associated with water infrastructure, including larval retention and starvation in freshwater, entrainment and impingement at water intakes, and barotrauma and physical damage associated with weirs and turbines. Distinct patterns of larval drift (spatial and temporal) may provide opportunities to alleviate mortality during larval emigration. While instream barriers inhibit the upstream migrations of amphidromous post-larvae and juveniles, climbing abilities are common, allowing for creative solutions facilitating upstream migration. Downstream spawning migrations are common in numerous amphidromous taxa, and are often associated with natural changes in flow regime, highlighting the need for bidirectional passage, and the potential for artificial flow alteration to negatively affect reproduction. Much research on the passage of amphidromous taxa has focussed on upstream migrating juveniles, while downstream migrating adults and larvae, which may be far more susceptible to water infrastructure, have largely been ignored. This life-stage bias represents a key research gap that must be addressed to safeguard amphidromous species in future.

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

Invasive fish eradication is a key management strategy in aquatic ecosystems, and is often accomplished using piscicides such as rotenone. However, the effects of piscicides on aquatic invertebrate communities are poorly understood, particularly over long time scales. We monitored invertebrate communities in two treatment and two reference streams prior to and for one year following the use of rotenone to eradicate trout in Zealandia wildlife sanctuary, Wellington. Immediately following treatment, invertebrate density and taxonomic richness declined significantly, and community composition diverged markedly relative to reference streams, with pollution sensitive taxa declining greater than more tolerant taxa. Treatment streams recovered to pre-treatment conditions within 412 months of rotenone application, indicating minor long-term impacts on invertebrate communities. Speed of recovery of individual taxa appeared to be associated with life history variables, e.g. generation times and dispersal ability. Untreated upstream reaches and nearby water bodies likely facilitated successful invertebrate community recovery. Our results demonstrate that rapid recovery of New Zealand stream invertebrate communities is possible within one year of rotenone application.

While many of New Zealand's freshwater fishes undertake larval migrations as part of their amphidromous life-history, little is known of the larval stages of these fish. Torrentfish (Cheimarrchthys fosteri), a New Zealand endemic, amphidromous, riffle specialist are particularly enigmatic; their spawning sites and behaviours are unknown, and larvae have never been collected either emigrating from freshwater or during their marine feeding phase. During summer drift sampling, we captured unidentified fish larvae emigrating downstream in the Waianakarua River, South Island, New Zealand. Based on multiple lines of evidence (meristic comparisons with adults, morphology, time of capture, and adult fish populations of the Waianakarua) we identify these larvae as torrentfish. This represents the first time torrentfish larvae have been captured or identified, laying the foundations for future studies into the early life-history and ecology of this unique and threatened fish.

Knowledge of stock structure is key for the effective management of any fish species. Amphidromous fish, which live and spawn in freshwater but spend a pelagic larval period at sea, have typically been assumed to disperse widely during their larval phase, resulting in populations being sourced from a single unstructured larval pool. We used otolith microchemical analysis to examine the stock structure of bluegill bully (Gobiomorphus hubbsi), a declining amphidromous eleotrid endemic to New Zealand, along the west coast of South Island, New Zealand. Some drainages - even those in close proximity (c. 20 km) - were readily distinguishable based on otolith trace element concentrations, while little structure was evident between other geographically disparate locations. These results indicate that, at least in some cases, locally retained larvae, rather than a single unstructured larval pool, dominates recruitment. Management of bluegill bully and other amphidromous species must therefore consider the possibility of regionally distinct populations.

Fish assemblages of New Zealand estuaries are poorly studied, and knowledge of the effects of estuary–ocean connections on the ichthyofaunal composition of estuaries remains limited. Understanding the status of fish composition of estuaries is crucial for planning for sustainable management of aquatic ecosystems. In the present study we sampled fish using a seine net from lower reaches of six permanently open estuaries and six intermittently closed and open lakes or lagoons (ICOLLs) along the Otago coastline during winter 2016 and summer 2017. Marked differences in ichthyofaunal composition were observed in the shallow littoral habitats of permanently open estuaries and ICOLLs. Fish assemblages reflected estuary–ocean connection status of estuaries during both seasons. ICOLLs showed greater fish abundance than permanently open systems. Fish abundance was higher in summer than in winter in both estuary types. Fish species with marine–estuarine opportunist and estuarine–migrant life histories dominated permanently open estuaries. Conversely, species with a diadromous life history but known to form landlocked populations were abundant in ICOLLs. Salinity and temperature were correlated with fish abundance in both estuary types.

The larval stage of fishes is critical in determining their dispersal, survival and recruitment, but little is known of the larval behaviours and tolerances of amphidromous fishes, particularly in New Zealand. We report the results of a series of observational and experimental studies on bluegill bully (Gobiomorphus hubbsi), including spawning sites and behaviours, larval characteristics at hatch, phototactic responses of larvae, and larval survival at different salinity levels. Spawning primarily occurred in the lower reaches of the river, and larvae from different nests exhibited marked differences in, and trade-offs between, larval characteristics at hatch, potentially affecting larval success. Larvae were positively phototactic to intense light, an unexpected result based on diel drift patterns and international research. Finally, larvae exhibited markedly higher survival rates when reared at intermediate salinities compared to freshwater or seawater, suggesting estuaries may play an important role as nursery grounds for bluegill bully and other amphidromous fish.

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.

Amphidromy is a distinct form of diadromy, involving a downstream migration (drift') to a pelagic feeding habitat undertaken by exceptionally small, undeveloped larvae immediately after hatch. Identifying patterns of larval drift may indicate critical periods within which conservation measures can be targeted to protect migrating larvae. This study utilised diel and spatial drift sampling to examine patterns of larval drift in two of New Zealand's endemic eleotrid species, the bluegill bully (Gobiomorphus hubbsi) and the common bully (G. cotidianus) in the Waianakarua River, South Island, New Zealand. A distinct spatial and temporal window was identified within which the vast majority of larvae were migrating to sea, extending only a few hours after sunset and < 10km inland. Similar diel patterns of larval drift have been found in other amphidromous species, suggesting this may be a widespread migratory behaviour. Managing water takes to minimise impacts on migrating larvae within this relatively small spatial and temporal window potentially represents a management strategy that could provide safe passage to the vast majority of larval fish while minimising disruption to human activities.