Riverine Fish Communities Research Articles

Disentangling the simultaneous effects of habitat degradation and introduced species on naturally depauperate riverine fish communities

Disentangling the simultaneous effects of habitat degradation and introduced species on naturally depauperate riverine fish communities

Correction to “eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada”

Correction to “<scp>eDNA</scp> metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada”

Past and recent anthropogenic pressures drive rapid changes in riverine fish communities

Understanding how and why local communities change is a pressing task for conservation, especially in freshwater systems. It remains challenging because of the complexity of biodiversity changes, driven by the spatio-temporal heterogeneity of human pressures. Using a compilation of riverine fish community time series (93% between 1993 and 2019) across the Palaearctic, Nearctic and Australasia realms, we assessed how past and recent anthropogenic pressures drive community changes across both space and time. We found evidence of rapid changes in community composition of 30% per decade characterized by important changes in the dominant species, together with a 13% increase in total abundance per decade and a 7% increase in species richness per decade. The spatial heterogeneity in these trends could be traced back to the strength and timing of anthropogenic pressures and was mainly mediated by non-native species introductions. Specifically, we demonstrate that the negative effects of anthropogenic pressures on species richness and total abundance were compensated over time by the establishment of non-native species, a pattern consistent with previously reported biotic homogenization at the global scale. Overall, our study suggests that accounting for the complexity of community changes and its drivers is a crucial step to reach global conservation goals.

EDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada

AbstractClimate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling methods and is being increasingly used in areas that have been historically difficult to sample such as northern freshwater habitats. Here, we employed eDNA metabarcoding using three mitochondrial markers at 174 coastal river sites, sampled over three years (2019–2021) across a broad region in northeastern North America, Newfoundland and Labrador. We characterized current riverine fish community composition, compared it to traditional sampling records, and quantified the influence of climate on variation in fish community composition. The analysis detected 33 fish species across the region (1–13 per location), including three non‐native species, as well as several new possible range expansions. Variance partitioning with redundancy analysis indicated ~56% of the variation in community composition could be explained by spatial and climate factors (~21% and ~7%, respectively, with an additional ~28% shared). A temporal comparison across a subset of locations with both eDNA and historical records (1965–1985) revealed that more species were detected on average with eDNA sampling, and that sampling method explained a small portion of the variation (~4%) in comparison with space (~10%) and climate (~7%). Ultimately, this work is the most complete survey of freshwater and diadromous fishes present in Newfoundland and Labrador to date, highlights new detections of non‐native species including previously unknown diversity for the region, and provides future direction for the application of eDNA analysis in northern riverine habitats.

Fishways provide catchment-scale improvements to common galaxias (Galaxias maculatus) upstream of a barrier in south-eastern Australia

ABSTRACT The common occurrence of dams is a major threat to riverine fish communities globally and a common remediation technique for fragmented fish communities is fishway construction. Demonstrating the effectiveness of this technique on impacted species is required to rationalise or improve management practices. This study investigates the effects of the installation of a fishway complex on the catadromous common galaxias (Galaxias maculatus) population at a catchment scale. We used electrofishing in a before-after-control-impact design to investigate the effects of the installation of a rock-ramp and a vertical-slot fishway complex on this species. This study demonstrated an increase in the relative abundance of common galaxias of 7.6–28.1 times and a shift to higher proportions of small fish in tributaries upstream of the fishway complex (as far as 90 km upstream). These findings provide strong evidence for the efficacy of the installation of fishways to increase the number of catadromous fishes in rivers where fish migrations have been blocked by dams.

Assessing riverine fish community diversity and stability by eDNA metabarcoding

Monitoring and evaluating river ecosystems are of paramount importance in addressing ecological and environmental challenges. While eDNA (environmental deoxyribonucleic acid)-based method has emerged as a valuable tool for understanding these issues, its application in assessing phylogenetic diversity, community stability, and the identification of key species within river systems has been limited. In this study, we conducted eDNA metabarcoding to assess fish community phylogenetic diversity, species composition, assembly variations, and their relationship with hydrologic characteristics. We also explored ecological stability and the roles of key species in a river system comprising a mainstem (MS) and a tributary (TB) with distinct hydrologic features. Our findings uncovered previously unknown endemic fish species diversity, exemplified by the discovery of Triplophysa. We identified disparities in diversity, community composition, and assembly between the MS and TB. Furthermore, we established significant associations between water-level variations, water flow, and changes in community composition. Triplophysa, with its high diversity, played a pivotal role in the ecological network, contributing significantly to community stability. The loss of Triplophysa increased fragility in co-occurrence patterns. Comparing the ecological network of fish communities between the MS and TB, we found that the MS displayed greater robustness and lower vulnerability, with increased species competition likely promoting network stability. Overall, this study highlights the potential of integrating eDNA metabarcoding data for monitoring phylogenetic diversity, community structure, and variations in stability within fish communities.

Shifting taxonomic and functional community composition of rivers under land use change.

Land use intensification has led to conspicuous changes in plant and animal communities across the world. Shifts in trait-based functional composition have recently been hypothesized to manifest at lower levels of environmental change when compared to species-based taxonomic composition; however, little is known about commonality in these responses across taxonomic groups and geographic regions. We investigated this hypothesis by testing for taxonomic and geographic similarities in the composition of riverine fish and insect communities across gradients of land use in major hydrologic regions of the conterminous United States. We analyzed an extensive dataset representing 556 species and 33 functional trait modalities from 8,023 fish communities, and 1,434 taxa and 50 trait modalities from 5,197 aquatic insect communities. Our results demonstrate abrupt threshold changes in both taxonomic and functional community composition due to land use conversion. Functional composition consistently demonstrated lower threshold responses compared to taxonomic composition for both fish (urban p = 0.069; agriculture p = 0.029) and insects (urban p = 0.095; agriculture p = 0.043) communities according to gradient forest models. We found significantly lower thresholds for urban versus agricultural land use for fish (taxonomic and functional p < 0.001) and insects (taxonomic p = 0.001; functional p = 0.033). We further revealed that threshold responses of functional composition were more geographically consistent than those of taxonomic composition to both urban and agricultural land use change. Traits contributing the most to overall functional composition change differed along urban and agricultural land gradients, and conformed to predicted ecological mechanisms underpinning community change. This study points to reliable early-warning thresholds that accurately forecast compositional shifts in riverine communities to land use conversion, and highlight the importance of considering trait-based indicators of community change to inform large scale land use management strategies and policies. This article is protected by copyright. All rights reserved.

Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information

Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300–1000 m upstream transect. The potential application for other river systems is further discussed.

Alien species and climate change drive shifts in a riverine fish community and trait compositions over 35 years

Alien fish substantially impact aquatic communities. However, their effects on trait composition remain poorly understood, especially at large spatiotemporal scales. Here, we used long-term biomonitoring data (1984–2018) from 31 fish communities of the Rhine river in Germany to investigate compositional and functional changes over time. Average total community richness increased by 49 %: it was stable until 2004, then declined until 2010, before increasing until 2018. Average abundance decreased by 9 %. Starting from 198 individuals/m2 in 1984 abundance largely declined to 23 individuals/m2 in 2010 (−88 %), and then consequently increased by 678 % up to 180 individuals/m2 until 2018. Increases in abundance and richness starting around 2010 were mainly driven by the establishment of alien species: while alien species represented 5 % of all species and 0.1 % of total individuals in 1993, it increased to 30 % (7 species) and 32 % of individuals in 2018. Concomitant to the increase in alien species, average native species richness and abundance declined by 26 % and 50 % respectively. We identified increases in temperature, precipitation, abundance and richness of alien fish driving compositional changes after 2010. To get more insights on the impacts of alien species on fish communities, we used 12 biological and 13 ecological traits to compute four trait metrics each. Ecological trait dispersion increased before 2010, probably due to diminishing ecologically similar native species. No changes in trait metrics were measured after 2010, albeit relative shares of expressed trait modalities significantly changing. The observed shift in trait modalities suggested the introduction of new species carrying similar and novel trait modalities. Our results revealed significant changes in taxonomic and trait compositions following alien fish introductions and climatic change. To conclude, our analyses show taxonomic and functional changes in the Rhine river over 35 years, likely indicative of future changes in ecosystem services.

Emergent dual scaling of riverine biodiversity

A prevailing paradigm suggests that species richness increases with area in a decelerating way. This ubiquitous power law scaling, the species-area relationship, has formed the foundation of many conservation strategies. In spatially complex ecosystems, however, the area may not be the sole dimension to scale biodiversity patterns because the scale-invariant complexity of fractal ecosystem structure may drive ecological dynamics in space. Here, we use theory and analysis of extensive fish community data from two distinct geographic regions to show that riverine biodiversity follows a robust scaling law along the two orthogonal dimensions of ecosystem size and complexity (i.e., the dual scaling law). In river networks, the recurrent merging of various tributaries forms fractal branching systems, where the prevalence of branching (ecosystem complexity) represents a macroscale control of the ecosystem's habitat heterogeneity. In the meantime, ecosystem size dictates metacommunity size and total habitat diversity, two factors regulating biodiversity in nature. Our theory predicted that, regardless of simulated species' traits, larger and more branched "complex" networks support greater species richness due to increased space and environmental heterogeneity. The relationships were linear on logarithmic axes, indicating power law scaling by ecosystem size and complexity. In support of this theoretical prediction, the power laws have consistently emerged in riverine fish communities across the study regions (Hokkaido Island in Japan and the midwestern United States) despite hosting different fauna with distinct evolutionary histories. The emergence of dual scaling law may be a pervasive property of branching networks with important implications for biodiversity conservation.

Climate and land-use changes interact to drive long-term reorganization of riverine fish communities globally

As climate change unfolds, changes in population dynamics and species distribution ranges are expected to fundamentally reshuffle communities worldwide. Yet, a comprehensive understanding of the mechanisms and extent of community reorganization remains elusive. This is particularly true in riverine systems, which are simultaneously exposed to changing temperature and streamflow, and where land-use change continues to be a major driver of biodiversity loss. Here, we use the most comprehensive compilation of fish abundance time series to date to provide a global synthesis of climate- and LU-induced effects on riverine biota with respect to changes in species thermal and streamflow affinities. We demonstrate that fish communities are increasingly dominated by thermophilic (warm-water) and limnophilic (slow-water) species. Despite being consistent with trends in water temperature and streamflow observed over recent decades, these community changes appear largely decoupled from each other and show wide spatial variation. We further reveal a synergy among climate- and land use-related drivers, such that community thermophilization is heightened in more human-modified systems. Importantly, communities in which species experience thermal and flow regimes that approach or exceed their tolerance thresholds (high community sensitivity), as well as species-poor communities (low community resilience), also display faster rates of compositional change. This research illustrates that quantifying vulnerability of riverine systems to climate change requires a broadening from a narrower thermal focus to more integrative approaches that account for the spatially varying and multifaceted sensitivity of riverine organisms to the interactive effects of water temperature, hydrology, and other anthropogenic changes.

RivFishTIME: A global database of fish time‐series to study global change ecology in riverine systems

AbstractMotivationWe compiled a global database of long‐term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones.Main types of variables containedThe database includes 11,386 time‐series of riverine fish community catch data, including 646,270 species‐specific abundance records, together with metadata related to the geographical location and sampling methodology of each time‐series.Spatial location and grainThe database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins world‐wide.Time period and grainThe database encompasses the period 1951–2019. Each time‐series is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years).Major taxa and level of measurementThe database includes 944 species of ray‐finned fishes (Class Actinopterygii).Software formatcsv.Main conclusionOur collective effort provides the most comprehensive long‐term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm.

Multiple stressor effects on alpha, beta and zeta diversity of riverine fish

We examined the effects of regional scale land use and local scale environmental and biotic stressors on alpha, beta and zeta diversities of native fish communities in wadeable streams and non-wadeable rivers in the Danube basin, Hungary. Relationships among land use and local scale environmental and biotic stressors were weak both in streams and rivers, suggesting that these stressors act relatively independently. Alpha diversity decreased strongly with increasing local scale environmental stressor intensity in rivers. On the contrary, its response to stressors was more obscure in streams, where the best-fit statistical model indicated the importance of the interaction between land use, local scale environmental and biotic stressors, while the secondly ranked model highlighted the negative impact of local scale environmental stressors. Analysis of variance using distance matrices provided evidence that stressors alone and in interactions explained compositional differences of pairs of study sites (beta diversity). Considering the degree of overall degradation, both local (alpha) and among-site (beta and zeta) diversity indices responded to increasing stressor intensity, generally negatively. Riverine fish communities showed higher degrees of similarity (lower beta and higher zeta) than stream fish communities. They also showed increasing similarity (i.e. homogenization) with increasing overall stressor intensity, unlike stream fish communities, which showed no relationship with overall stressor intensity. Our results suggest that the relationships between land use and local scale environmental and biotic stressors can be complex and so do their effects on biodiversity. While stressor specific indices can provide information on the role of specific stressors in some cases, the examination of overall stressor effects is needed to assess realistically the effects of anthropogenic disturbances on native fish diversity. Diversity indices that quantify among-site changes in species composition, such as measures of beta and zeta diversity, can be fruitful for better understanding the role of multiple stressors in structuring ecological communities.

Testing the diversity–biomass relationship in riverine fish communities

AbstractAimWe examined the diversity–biomass relationship in stream fish communities and quantified direct and indirect effects of abiotic variables on this relationship.LocationFrance.Time period1992–2012.Major taxa studiedStream fishes.MethodsWe analysed the relationship between biodiversity (species richness and functional diversity) and fish community biomass at 1,357 stream sites distributed throughout France. We used piecewise path analysis to quantify effects of abiotic and biodiversity variables on biomass and assess relative contributions of native and non‐native species on the diversity–biomass relationship.ResultsBiodiversity showed a direct positive relationship with biomass after controlling for sampling effort, and direct effects of biodiversity variables on community biomass exceeded those of climate and physical habitat variables. Our analysis indicates that positive effects of species richness on biomass exceeded those of functional diversity. Indirect effects of abiotic variables mediated by biodiversity metrics indicated that biomass increased in warmer, lowland habitats. Human impact had no effect on native biodiversity but had a positive effect on non‐native biodiversity.Main conclusionsWe provide evidence that direct effects of biodiversity on community biomass outweigh those of abiotic variables in riverine fish communities, but resource partitioning alone is unlikely to drive the effects of biodiversity on biomass in this system. Quantification of the relative roles of anthropogenic impacts, biodiversity and environmental context in the regulation of ecosystem functioning will be necessary to understand the potential consequences of ongoing global change.

Threshold responses of riverine fish communities to land use conversion across regions of the world.

The growing human enterprise has sparked greater interest in identifying ecological thresholds in land use conversion beyond which populations or communities demonstrate abrupt nonlinear or substantive change in species composition. Such knowledge remains fundamental to understanding ecosystem resilience to environmental degradation and informing land use planning into the future. Confronting this challenge has been largely limited to inferring thresholds in univariate metrics of species richness and indices of biotic integrity and has largely ignored how land use legacies of the past may shape community responses of today. By leveraging data for 13,069 riverine sites from temperate, subtropical, and boreal climate zones on four continents, we characterize patterns of community change along diverse gradients of urbanization and agricultural land use, and identity threshold values beyond which significant alterations in species composition exists. Our results demonstrate the apparent universality by which freshwater fish communities are sensitive to even low levels of watershed urbanization (range of threshold values: 1%-12%), but consistently higher (and more variable) levels of agricultural development (2%-37%). We demonstrated that fish community compositional thresholds occurred, in general, at lower levels of watershed urbanization and agriculture when compared to threshold responses in species richness. This supports the notion that aggregated taxon-specific responses may better reflect the complexity of assemblage responses to land use development. We further revealed that the ghost of land use past plays an important role in moderating how current-day fish communities respond to land use intensification. Subbasins of the United States experiencing greater rates of past land use change demonstrated higher current-day thresholds. Threshold responses of community composition, such as those identified in our study, illustrate the need for globally coordinated efforts to prioritize country-specific management and policy initiatives that ensure that freshwater fish diversity is not inevitably lost in the future.

Effects of nonnative species on the stability of riverine fish communities

Despite the increasing ubiquity of biological invasions worldwide, little is known about the scale‐dependent effects of nonnative species on real‐world ecological dynamics. Here, using an extensive time series dataset of riverine fish communities across different biogeographic regions of the world, we assessed the effects of nonnative species on the temporal variability and synchrony in abundance at different organizational levels (population, metapopulation, community and metacommunity) and spatial scales (stream reach and river basin). At the reach scale, we found that populations of nonnative species were more variable over time than native species, and that this effect scaled up to the community level – significantly destabilizing the dynamics of riverine fish communities. Nonnative species not only contributed to reduced community stability, but also increased variability of native populations. By contrast, we found no effect of nonnative species dominance on local interspecific synchrony among native species. At the basin scale, nonnative metapopulations were again more variable than the native ones. However, neither native metapopulations nor metacommunities showed differences in temporal variability or synchrony as nonnative species dominance increased basin‐wide. This suggests a ‘dilution effect’ where the contribution to regional stability of local native populations from sites displaying low levels of invasion reduced the destabilizing effects of nonnative species. Overall, our results indicate that accounting for the destabilizing effect of nonnative species is critical to understanding native species persistence and community stability.

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community.

Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon codistributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four codistributed taxa of freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic coastal drainages. Based on population relationships and hierarchical genetic structure analyses, we identify all taxa share the same geographic structure suggesting the fish utilized common passages in the past to move between river basins. In contrast to this strong spatial concordance, model-based estimates of divergence times indicate that despite common routes for dispersal, these passages were traversed by each of the taxa at different times resulting in varying degrees of genetic differentiation across barriers with most divergences dating to the Upper Pleistocene, even when accounting for divergence with gene flow. Interestingly, when this temporal dissonance is viewed through the lens of the species-specific ecologies, it suggests that an ecological sieve influenced whether species dispersed readily, with an ecological generalist showing the highest propensity for historical dispersal among the isolated rivers of the Brazilian coast (i.e., the most recent divergence times and frequent gene flow estimated for barriers). We discuss how our findings, and in particular what the temporal dissonance, despite common geographic passages, suggest about past dispersal structuring coastal communities as a function of ecological and paleo-landscape sieves.

Seasonal dynamics of riverine fish communities using eDNA.

As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems.

Nature‐like fishways as compensatory lotic habitats

AbstractDamming of rivers disrupts migration of fish and results in lotic habitats being both scarcer and spaced further apart, ultimately affecting riverine fish communities. Nature‐like fishways are often designed as bypass channels, constructed with natural materials that reroute part of the water around weirs and dams, restoring longitudinal connectivity as well as forming nature‐mimicking habitats. We evaluated the potential of such bypasses to function as compensatory lotic habitats by comparing fish fauna in 23 bypasses to adjacent lotic stream habitats in a same‐river pairwise design. Bypasses were narrower, shallower, and less shaded than adjacent stream habitats, but very few significant differences could be detected in the fish communities, indicating the potential of such nature‐like fishways to constitute compensatory lotic habitats for fish. Analyses also indicated how bypass design may be altered to favour or disfavour certain target species. Generally, narrower and shallower bypasses with high gradient favoured brown trout (Salmo trutta), whereas European eel (Anguilla anguilla) were more abundant at sites with lower gradient. Finally, to increase the impact of these compensatory habitats on running water ecosystems, we suggest that the size of bypasses should be maximized in areas where natural stream habitats have been lost.