Adaptation is considered essential for species facing environmental change, but our understanding of the evolution of complex ecotypes remains limited. We show that a substantial genomic cluster of co-adapted alleles has repeatedly fuelled complex life-history shifts in fishes. Specifically, the majority of strong outlier loci underpinning repeated landlocking of formerly marine-migratory Galaxias lineages are co-located on a single chromosome. Phenotypic, behavioural and genomic comparisons reveal a strong parallel basis for multi-trait ecotype shifts (osmoregulation; musculature; locomotion; reproduction) across eight independently landlocked populations. Critically, migratory populations house 'jackpot' individuals carrying intact sequences essential for rapid multi-trait life-history switches. The observed high frequencies of these migratory jackpot carriers explain the rapid ecotype shifts detected in Galaxias populations isolated by recent catastrophic landslides in New Zealand. These findings represent a complete example of complex ecotype evolution, highlighting the key role of modular genomic variation in facilitating rapid adaptive change.

Urbanisation is a major land-use change that introduces novel disturbances and risks into ecosystems, requiring species to adjust their fear responses to avoid fitness costs associated with mismatched anti-predator behaviour. Successful urban-dwelling species often modify flight responses to balance risk avoidance with maximising access to human-associated resources. Here, we examined the impact of urbanisation on escape responses in Red-billed Gulls (Chroicocephalus novaehollandiae scopulinus), a nationally threatened species in New Zealand, using flight initiation distance (FID) as an indicator of boldness. We compared two urban sites, Dunedin and Oamaru, with one rural site, Taiaroa Head, and predicted that gulls in urban areas would exhibit shorter FIDs than those in rural environments, while adults would display shorter FIDs than juveniles and flocks. We recorded 705 FID observations across Dunedin, Oamaru, and Taiaroa Head in Otago, New Zealand. Dunedin gulls exhibited significantly shorter FIDs, while, contrary to expectations, Oamaru gulls showed longer escape distances like those in rural Taiaroa Head. Within Dunedin, FID varied across sub-habitats, with gulls in high-human-activity areas displaying shorter FIDs than those in less disturbed areas. Age and social dynamics also influenced escape responses, with juveniles and flocks exhibiting FIDs longer than adults, though this difference diminished in Dunedin. Gulls in Dunedin primarily used terrestrial escapes and anthropogenic refuges following disturbance, while rural gulls relied more on aerial escapes toward distant refuges. Our study suggests that growing Red-billed Gull populations in Dunedin are adapting risk perception and escape strategies to human-modified landscapes, reinforcing their persistence in urbanised environments. Understanding how animals modify anti-predator behaviour in response to human presence is central to behavioural ecology. We investigated flight initiation distance (FID) in the Red-billed Gull, a threatened species, across two urban and one rural site in New Zealand, focusing on age groups and social context (adults, juveniles, and flocks). While gulls in the densely populated urban centre of Dunedin exhibited reduced wariness, those in the smaller urban town of Oamaru responded more like rural birds, indicating that urban classification alone does not predict behavioural adaptation. Our findings also demonstrate that juveniles and flocks respond more sensitively than adults, highlighting the role of age and group dynamics in shaping responses to human exposure. These insights offer broader implications for understanding behavioural plasticity, urban adaptation, species persistence, and conservation in human-dominated environments.

Many aspects of the ecology, life history and distribution of fishes differ between their larval and adult life-history stages. Identifying the critical habitats and migration pathways required by each life cycle stage is crucial for effective conservation and ecological management. Using microchemical analysis of otoliths, we examined the influence of larval habitat and migration on the composition and population structure of migratory and nonmigratory Galaxias species collected from tributaries upstream of inland lakes and streams lacking downstream lake connections in the Waitaki River basin, New Zealand. Larval (core) and adult (edge) layers of each individual otolith were analysed to compare otolith trace signatures formed during larval and adult life-history stages. The results revealed considerable variation between larval and adult otolith chemical signatures of migratory (Galaxias brevipinnis) species. Classification analysis indicated that populations of G. brevipinnis upstream of each lake shared a common larval habitat, most likely the lake, with 100% of individuals from each lake-riverine system having larval signatures that were distinct from adult signatures. In contrast, relatively consistent patterns of elemental concentrations were detected across the otoliths of nonmigratory species suggesting both their larval and adult life-history stages had occurred in the same stream from which the adults were collected. These findings provide a framework for understanding how larval-rearing environments can influence the distribution of stream fish across the landscape. Furthermore, identifying the source of recruits can help to improve conservation efforts to protect naturally land-locked populations of G. brevipinnis.

Motivation: Freshwater ecosystems have been heavily impacted by land-use changes, but data syntheses on these impacts are still limited. Here, we compiled a global database encompassing 241 studies with species abundance data (from multiple biological groups and geographic locations) across sites with different land-use categories. This compilation will be useful for addressing questions regarding land-use change and its impact on freshwater biodiversity. Main Types of Variables Contained: The database includes metadata of each study, sites location, sample methods, sample time, land-use category and abundance of each taxon. Spatial Location and Grain: The database contains data from across the globe, with 85% of the sites having well-defined geographical coordinates. Major Taxa and Level of Measurement: The database covers all major freshwater biological groups including algae, macrophytes, zooplankton, macroinvertebrates, fish and amphibians.

Īnanga (Galaxias maculatus) is a widespread freshwater fish, found around coastal New Zealand, Chatham Islands, southern Australia and southern South America, exhibiting both diadromous and land-locked life history patterns. We assessed population size structure, size at maturity, timing of reproduction, and post-reproductive survival in the Waikouaiti and Kakanui rivers, two regionally important G. maculatus populations in southern New Zealand. Size at maturity varied between rivers and sexes, with males generally maturing at smaller sizes than females. The timing of reproduction and recruitment was observed to vary across a relatively small spatial scale. Population length-frequencies indicated that both populations exhibited annual population dynamics, with most individuals spawning in their first year, then apparently dying soon afterwards (as indicated by a marked drop in post-spawning abundance). However, a few individuals with recently spent or resting gonads were present over the winter months, indicating some post-spawning survival. There was a lower frequency of exceptionally large (putatively 1+) individuals than reported for other populations around New Zealand and elsewhere, suggesting over-winter survival following spawning varies. Based on the variation in life history characters over small spatial scales, we suggest that management of regionally important G. maculatus populations should be based on catchment level information.

Growing use of synthetic materials has increased the number of stressors that can degrade freshwater ecosystems. Many of these stressors are relatively new and poorly understood, such as microplastics which are now ubiquitous in freshwater systems. The effects of microplastics on freshwater biota must be investigated further in order to better manage and mitigate their impacts. Our experiment provides the first empirical evaluation of stream invertebrate community dynamics in response to microplastics of different concentrations and sizes, in combination with fine sediment, a pervasive known stressor in running waters. In a 7-week streamside experiment using 64 flow-through circular mesocosms, we investigated the effects of exposure to three simulated microplastic influxes (polyethylene microspheres at four levels between 0 and 28,800 items/event) and the addition of fine sediment (to simulate a polluted stream environment). Invertebrate drift was monitored for 48 h immediately after each microplastic influx, and benthic invertebrate communities were sampled after 28 days of microplastic and sediment manipulations. Microplastic concentration, size and fine sediment all had significant factor main effects on several invertebrate drift response metrics, whereas few microplastic main effects were seen in the benthic community. However, interactive stressor effects were common in different combinations between sediment, microplastic size and concentration, suggesting multiple-stressor relationships between microplastics and fine sediment. Microplastic ingestion was witnessed in four of 12 taxa analysed: Hydrobiosidae, Deleatidium spp., Potamopyrgus antipodarum and Archichauliodes diversus. . Our findings provide insights into how microplastics affect drift and benthic community dynamics of stream invertebrates in a field-realistic experimental setting and highlight areas requiring further study. These include investigations of invertebrate drift dynamics in response to other types of microplastics, the role invertebrate size may play in determining their vulnerability to microplastic pollution, and framing more microplastic research in a field-realistic multiplestressor context.

Although some migratory fish species are broadly distributed across large-spatial scales, they might only attain high abundance in certain areas. This can be attributed to local habitat conditions and variation in recruitment strength, which can be related to distance from spawning or larval-rearing habitats. The presence of pelagic compartments in riverine systems can enhance the abundance of some migratory fish species by providing abundant food and habitat for larval development. In this study, we examined the composition and fine-scale abundance of migratory Galaxias brevipinnis Gunther, 1866 (Teleostei: Galaxiidae) and non-migratory Galaxias spp. in relation to the presence and absence of downstream lakes and upstream distance of sites from lakes. Fish abundance and microhabitat use were estimated from randomly selected point samples (about 1 m2) from twenty-two streams in South Island, New Zealand. The total length of G. brevipinnis individuals was also measured to examine possible changes in their size-frequency distribution with increasing distance from lakes. Galaxias brevipinnis was found in almost all of the stream reaches surveyed upstream of lakes, while none were recorded in no-lake stream sites. The mean abundance of G. brevipinnis was considerably higher than non-migratory Galaxias species at sites upstream of lakes. Lotic habitats closer to the lakes also supported a higher abundance of G. brevipinnis than habitats sampled further away from the lakes, suggesting that recruitment limitation with distance from the larval supply is more important than the effect of microhabitats for this species. Furthermore, G. brevipinnis size-distribution patterns differed greatly with distance upstream, with a higher proportion of smaller (younger) individuals found mainly within 2 km upstream of lakes, suggesting strong recruitment of this species close to lake recruitment sources. Although non-migratory species made up all of the Galaxias species caught in non-lake streams, they also occurred in streams upstream of lakes, but only at low abundance in stream sites close to the lakes. However, their abundance tended to be higher at sites further away from lakes, where G. brevipinnis was less abundant. Declining recruitment of G. brevipinnis with distance inland from lake, and competitive interactions with non-migratory species, are likely the main determinants of the adult abundances and composition of these stream fish at large spatial scales, and these effects may outweigh the role of micro -habitat characteristics and preferences in such river basins.

Amphidromous fishes engage in migration to overcome the spatial mismatch between adult and larval habitat. The torrentfish (Cheimarrichthys fosteri), an endemic New Zealand amphidromous fish and only member of the Family Cheimarrichthyidae, display distinct spatial sexual segregation, but the migration assumed to overcome this segregation for reproduction is undocumented. We investigated the instream distribution of torrentfish, gaining insight into how barriers to reproduction are overcome, and how sex shapes migratory choices for the individual. We surveyed torrentfish at two spatial scales, examining the effects of sex and sexual maturity on distribution. We found that female torrentfish engage in prolonged upstream migrations, up to 100 km inland, with male torrentfish migrating upstream to a lesser extent. Both sexes return downstream to spawn, with males returning at the onset of maturity, while females may return and migrate back upstream, potentially making multiple downstream spawning migrations. Juvenile upstream migration likely results in competitive release and access to resources, but sets up a conflict between reproduction and transport of larvae into the nursery habitat in a timely manner. Adult downstream migration in torrentfish resolves this conflict and is similar to documented downstream spawning migrations in catadromous species.

Mixed-stock fisheries which simultaneously cause mortality amongst several populations of a species of fish may occur where separate stocks partially or completely overlap in the geographic area of harvest. This study aims to analyze the population-of-origin of adult and subadult adfluvial lacustrine brown trout Salmo trutta, exploited in a mixed-stock fishery in Upper Tuloma Reservoir in Eastern Fennoscandia, using otolith microchemistry. To evaluate the origin of migratory brown trout captured in these mixed-stock harvest fisheries, we undertook otolith sampling of brown trout juveniles in fluvial spawning and rearing habitats in the reservoir watershed, including 13 natal tributaries across the catchment of the reservoir in both Russia and Finland. Harvested adult and subadult brown trout otoliths were sampled from the impoundment in the central area of the reservoir and we analyzed for stock-related character differences to compare with known populations, using trace element signatures, with fish from the mixed stock fishery. The assignments-of-origin in the mixed-stock fishery-harvest samples did not follow the known distribution of populations sampled from natal streams in the watershed. For example, brown trout from the largest tributary catchments of Lotta River and Nota River were less represented in the mixed-harvest sample, which was contradictory to their contribution to the overall spawning and rearing areas of the catchment. These results point towards the importance of maintaining the diversity of different spawning and rearing tributaries required for brown trout recruitment into mixed stock fisheries, and the potential of the existence of population structure of brown trout in the reservoir catchment. Our information suggests that it is important to develop conservation and management strategies for natal habitats in multiple streams utilized by adfluvial lacustrine brown trout populations inhabiting various catchments and that are harvested in mixed-stock fisheries.

Inanga (Galaxias maculatus) are found in a range of freshwater habitats around much of the Southern Hemisphere. Although they are reasonably well studied within New Zealand, little is known about the populations found in coastal pond systems. This study focussed on inanga diet and population dynamics within a shallow pond complex in coastal Southland, investigating age, growth, distribution, and diet of juvenile inanga over a spring to autumn period. Otolith analysis indicated a three-month period (September to November) during which fish are hatching, with fish that hatched earlier growing more slowly than later fish. Inanga were found in only one location within the pond complex – a site featuring low water nutrient levels and less access by trout. Diet analysis showed high selectivity for chydorids and chironomid larvae, indicating a mixture of both benthic and pelagic foraging. Overall, this study has provided insight into inanga population dynamics in ponds, which have not previously been observed.

The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling ( Prototroctes oxyrhynchus ) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis. Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes of P. oxyrhynchus , and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa. We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling ( P. mareana ), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand. Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.

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.

Dams on rivers are known to facilitate the colonisation and spread of aquatic alien and native invasive species, but the actual mechanisms involved are poorly understood. Since the construction of the Solina Dam on the upper San River system in Poland, European perch (Perca fluviatilis) have expanded their distribution into the headwaters of this river system, becoming a native invader. In this study, we assessed the spread of perch in detail over time upstream of the Solina Reservoir, and used otolith trace element microchemistry to determine the spawning and larval rearing locations of perch in the catchment upstream of the dam. Extensive sampling over several years across the catchment upstream of the Solina Reservoir confirmed the widespread occurrence of perch into the headwaters of the tributary river systems, with smaller size classes dominating locations closer to the Solina Reservoir. Despite perch being widely distributed upstream of the Solina Reservoir, otolith microchemical analysis indicated the populations from various reservoir tributaries mostly shared the same spawning and larval rearing habitat, most likely the Solina Reservoir. Our results suggest that reservoirs can facilitate the colonisation of river systems by providing a critical habitat element that would be otherwise missing from riverine landscapes, i.e., an extensive and productive pelagic larval rearing environment. This research shows that the impacts of large dams can extend many kilometers upstream from the river reaches directly affected by the resulting impoundment.

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.

Galaxias gollumoides McDowall and Chadderton occurs in contrasting hydrological environments across Southland and Stewart Island, New Zealand. Our study experimentally investigated intraspecific variation in G. gollumoides from wetland and stream habitats, testing for phenotypic divergence in spawning substrate choice, and that spawning timing is influenced by the proximate hydrological and meteorological environments. Wetland and stream G. gollumoides displayed intraspecific behavioural divergence, utilising contrasting spawning substrates across multiple tanks, even when held in common experimental conditions. Galaxias gollumoides displayed intraspecific spawning timing differences with wetland-sourced G. gollumoides spawning earlier than stream-sourced G. gollumoides. Spawning also occurred significantly more often during peaks of warmer mean daily water temperature and barometric pressure, than during colder temperature, low-pressure periods. Interannual variation in initial spawning timing was also attributed to differences in water temperature. In combination, experimental evidence- and field-based observations support our hypothesis that G. gollumoides can utilise available substrates in habitats of contrasting hydrology and structure, while spawning timing is controlled by changes in proximate environmental conditions. These characteristics may enhance a population's recruitment success and the species persistence in the fluctuating hydrological environments of ephemeral wetlands and tributary streams that were once likely widespread in Southland.

When herbivore abundance is controlled by predators there may be an indirect positive effect on primary producers due to reduced grazing pressure, but the potential of predation refuges to modify such trophic cascades has rarely been studied. By experimentally manipulating substrate particle size and fish predation regime, we assessed the outcome of invertebrate grazer-biofilm interactions in streams. Locations at the center of larger substrate particles were predicted to pose a higher predation risk, and therefore be subjected to a lower grazing pressure. In our 52-day experiment in a New Zealand stream, small-sized substrates (terracotta tiles) remained virtually free of periphyton across their entire upper surface, whereas a thick periphyton mat was formed across large tiles with only edges remaining free. In channels containing fish (either native Galaxias vulgaris or exotic Salmo trutta), grazing on tiles was lower than in the absence of fish. A preference for grazing near to the edge of tiles was clearest in fish channels but was also evident even in the absence of fish, probably reflecting fish presence and/or fish kairomones in the stream from where the colonizing invertebrates had been derived. Total grazer density was similar across treatments with or without fish, suggesting that our results can be explained mostly by changes in the behavior of grazers. We suggest that refuge availability, interacting with grazer predator-avoidance behavior, may produce a context-dependent patchwork of trophic cascades in streams and other ecosystems.

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.

Wetland restoration or re-establishment is a common conservation goal, and the ability of a wetland community to recover from events such as drought are key to its long-term success. At the mouth of the Waiau River in Southland, New Zealand, a series of wetland ponds have been created by diverting water from the river. A period of particularly low river flows resulted in the wetland drying out entirely, except for a few deep channels. A subsequent flood inundated the ponds, creating an opportunity to study recolonisation of the system. The deep channels provided an important refuge habitat for eels (Anguilla spp.) during dry periods, with significantly higher numbers close to the channels immediately after refilling than at sites further away. Smaller fish (Gobiomorphus and Galaxias spp.) took much longer to reappear in the ponds. The macroinvertebrate community showed no significant variation over the short term or up to a year post-refill, although individually snail and water bug taxa increased and microcrustaceans decreased in abundance. Daphnia and ostracods were observed soon after refilling and dominated the community. This study highlights the importance of spatial heterogeneity in constructed wetland systems, as this habitat variation likely increases the recovery rate after drying.