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Understanding temporal changes in the composition of species communities over spatial and temporal scales relevant to conservation management is crucial for preventing further biodiversity declines. Here, we assessed patterns and potential drivers of taxonomic and functional temporal β diversity over 26 years (1991–2016) of 64 river macroinvertebrate communities, and the length of New Zealand (37°00'N, 46°00'S). We further examined changes in population size and range shifts of species pools, and related these to taxonomy and functional traits. We found increasing climate and land‐use driven differences in both the taxonomic and functional composition of communities over time, coupled with poleward species colonisations and increasing extirpations in northern locations. Increases in population and species range size were more prevalent than decreases in population and range size. Species shifted their ranges towards higher latitudes on average by 50 km per decade. Despite little to no relationship with taxonomy, we uncovered distinct relationships between functional traits and population trends and latitudinal species range shifts. Species with a high number of reproductive cycles per year and long‐life duration of adults tended to increase their population size, while larger size species with a high number of descendants per reproductive cycle tended to shift their range towards more southern latitudes. Our results suggest that the intensity of disturbances, the geographic location of individuals and communities, and species ecological and functional characteristics, are major determinants of riverine biodiversity reorganisation in the Anthropocene.

When investigating the fields of biogeography and macroecology, climate- and productivity-related variables are frequently identified as the strongest correlates of species-diversity patterns. These variables have been usually merged under the climate/productivity hypothesis and describe the direct and indirect actions of climate on species. Being among the most vulnerable ecosystems to climate change, streams and rivers are expected to be influenced both by climatic and trophic (i.e. productivity-related) factors. We propose here to distinguish the relative influence of the two processes on large-scale, long-term changes in the functional diversity of freshwater invertebrate communities over two decades in France. To this end, we designed two functional indices using invertebrate traits to surrogate the respective mechanisms: climate vulnerability and feeding specialisation. Using geographically weighted regression (GWR) models, we showed that trends in both indices, along with the initial regional species-pools, have significantly contributed to the overall long-term increase in functional diversity of invertebrate communities. In addition, we highlighted a strong geographical differentiation in the contribution patterns with the climate vulnerability effect decreasing with latitude and the feeding specialisation effect being higher in headwaters than in large rivers. Finally, taking into account this non-stationarity in the ecological processes and responses using GWR models allowed explaining about 75% of the long-term changes in the community diversity. Consequently, this study offers sound perspectives in predicting the future patterns of trends in functional diversity of communities under different scenarios of environmental changes, like climate and/or land-use.

Freshwater ecosystems are considered biodiversity hotspots, but assessing the spatial distribution of species remains challenging. One major obstacle lies in the complex geospatial processing of large amounts of data, such as stream network, sub‐catchment and basin data, that are necessary for addressing the longitudinal connectivity among water bodies. Workflows thus need to be scalable, especially when working across large spatial extents and at high spatial resolution. This in turn requires advanced command‐line GIS skills and programming language integration, which often poses a challenge for freshwater researchers. To address this challenge, we developed the package hydrographr that provides scalable hydrographic data processing in R. The package contains functions for downloading data of the high‐resolution Hydrography90m dataset, processing, reading and extracting information, as well as assessing network distances and connectivity. While the functions are, by default, tailored toward the Hydrography90m data, they can also be generalised toward other data and purposes, such as efficient cropping and merging of raster and vector data, point‐raster extraction, raster reclassification and data aggregation. The package depends on the open‐source software GDAL/OGR, GRASS‐GIS and the AWK programming language in the Linux environment, allowing a seamless language integration. Since the data is processed outside R, hydrographr allows creating scalable geo‐processing workflows. We illustrate the hydrographr functions using two workflows that focus on (i) a freshwater species distribution modelling approach, and (ii) assessing stream connectivity given the fragmentation by dams. We also provide a detailed guide for the initial installation of the required software. Windows users need to first enable the Windows Subsystem for Linux (WSL) feature, and can then follow the same software installation as Linux users. hydrographr is maintained on GitHub at https://github.com/glowabio/hydrographr. hydrographr provides a set of key functions for processing freshwater geospatial data. We expect that the package will support the freshwater‐related research communities given the easy‐to‐use wrapper functions that allow capitalizing on powerful open‐source command‐line software, which may otherwise require a steep learning curve. Users can thus perform large‐scale freshwater‐specific longitudinal connectivity and network analyses across large geographic extents while staying within the R environment.

In large-scale aquatic ecological studies, direct habitat descriptors (e.g. water temperature, hydraulics in river reaches) are often approximated by coarse-grain surrogates (e.g. air temperature, discharge respectively) since they are easier to measure or model. However, as biological variability can be very strong at the habitat scale, surrogate variables may have a limited ability to capture all of this variability, which may lead to a lesser understanding of the ecological processes or patterns of interest. In this study, we aimed to compare the capacity of direct habitat descriptors vs. surrogate environmental variables to explain the organization of fish and macroinvertebrate communities across the Loire catchment in France (10 5 km 2 ). For this purpose, we relied on high-resolution environmental data, extensive biological monitoring data (>1000 sampling stations) and multivariate analyses. Fish and macroinvertebrate abundance datasets were considered both separately and combined to assess the value of a cross-taxa approach. We found that fish and macroinvertebrate communities exhibited weak concordance in their organization and responded differently to the main ecological gradients. Such variations are probably due to fundamental differences in their life-history traits and mobility. Regardless of the biological group considered, direct habitat descriptors (water temperature and local hydraulic variables) consistently explained the organization of fish and macroinvertebrate communities better than surrogate descriptors (air temperature and river discharge). Furthermore, the organization of fish and macroinvertebrate communities was slightly better explained by the combination of direct or surrogate environmental variables when the two biological groups were considered together than when considered separately. Tied together, these results emphasize the importance of using a cross-taxa approach in association with high-resolution direct habitat variables to more accurately explain the organization of aquatic communities.

Many large European rivers have undergone multiple pressures that have strongly impaired ecosystem functioning at different spatial and temporal scales. Global warming and other environmental changes have favored the success of invasive species, deeply modifying the structure of aquatic communities in large rivers. Some exogenous species could alter trophic interactions within assemblages by increasing the predation risk for potential prey species (top-down effect) and limiting the dynamics of others via resource availability limitation (bottom-up effect). Furthermore, large transboundary rivers are complex aquatic ecosystems that have often been poorly investigated so that data for assessing long-term ecological trends are missing. In this study, we propose an original approach for investigating long-term combined effects of global warming, trophic resource decrease, predation risk, and water quality variations on the trait-based structure of macroinvertebrate and fish assemblages over 26 yr (1985–2011) and 427-km stretch of the river Meuse (France and Belgium). The study of temporal variations in biological, physiological, and ecological traits of macroinvertebrate and fish allowed identifying community trends and distinguishing impacts of environmental perturbations from those induced by biological alterations. We provide evidence, for this large European river, of an increase in water temperature (close to 1°C) and a decrease in phytoplankton biomass (−85%), as well as independent effects of these changes on both invertebrate and fish communities. The reduction of trophic resources in the water column by invasive molluscs has dramatically affected the density of omnivorous fish in favor of invertebrate feeders, while scrapers became the major feeding guild among invertebrates. Macroinvertebrate and fish communities have shifted from large-sized organisms with low fecundity to prolific, small-sized organisms, with early maturity, as a response to increased predation pressure.

Aim Invasive alien species are a growing problem worldwide due to their ecological, economic and human health impacts. The “killer shrimp” Dikerogammarus villosus is a notorious invasive alien amphipod from the Ponto‐Caspian region that has invaded many fresh and brackish waters across Europe. Understandings of large‐scale population dynamics of highly impactful invaders such as D. villosus are lacking, inhibiting predictions of impact and efficient timing of management strategies. Hence, our aim was to assess trends and dynamics of D. villosus as well as its impacts in freshwater rivers and streams. Location Europe. Methods We analysed 96 European time series between 1994 and 2019 and identified trends in the relative abundance (i.e. dominance %) of D. villosus in invaded time series, as well as a set of site‐specific characteristics to identify drivers and determinants of population changes and invasion dynamics using meta‐regression modelling. We also looked at the spread over space and time to estimate the invasion speed (km/year) of D. villosus in Europe. We investigated the impact of D. villosus abundance on recipient community metrics (i.e. abundance, taxa richness, temporal turnover, Shannon diversity and Pielou evenness) using generalized linear models. Results Population trends varied across the time series. Nevertheless, community dominance of D. villosus increased over time across all time series. The frequency of occurrences (used as a proxy for invader spread) was well described by a Pareto distribution, whereby we estimated a lag phase (i.e. the time between introduction and spatial expansion) of approximately 28 years, followed by a gradual increase before new occurrences declined rapidly in the long term. D. villosus population change was associated with decreased taxa richness, community turnover and Shannon diversity. Main Conclusion Our results show that D. villosus is well‐established in European waters and its abundance significantly alters ecological communities. However, the multidecadal lag phase prior to observed spatial expansion suggests that initial introductions by D. villosus are cryptic, thus signalling the need for more effective early detection methods.

Protected areas are a principal conservation tool for addressing biodiversity loss. Such protection is especially needed in freshwaters, given their greater biodiversity losses compared to terrestrial and marine ecosystems. However, broad-scale evaluations of protected area effectiveness for freshwater biodiversity are lacking. Here, we provide a continental-scale analysis of the relationship between protected areas and freshwater biodiversity using 1,754 river invertebrate community time series sampled between 1986 and 2022 across ten European countries. Protected areas primarily benefited poor-quality communities (indicative of higher human impacts) that were protected, or that gained protection, across a substantial proportion of their upstream catchment. Protection had little to no influence on moderate- and high-quality communities, although high-quality communities potentially provide less scope for effect. Our results reveal the overall limited effectiveness of current protected areas for freshwater biodiversity, likely because they are typically designed and managed to achieve terrestrial conservation goals. Broadly improving effectiveness for freshwater biodiversity requires catchment-scale management approaches involving larger and more continuous upstream protection, and efforts to address remaining stressors. These approaches would also benefit connected terrestrial and coastal ecosystems, thus generally helping bend the curve of global biodiversity loss.

Riverbank erosion is linked to increasing risks in piedmont areas due to urbanization and hydromorphological alterations of rivers. Changes in riparian vegetation and in sediment dynamics modify aquatic macroinvertebrate communities. In this context, riverbank stabilization is a major issue in the conservation of stream ecosystem functioning. In this study, we aimed at assessing the impacts of riverbank stabilization techniques on the taxonomic and functional properties of benthic macroinvertebrate communities living in alpine mountain streams. For this purpose, the effects of four riverbank stabilization techniques (riprap, mixed, cribwall, and fascine) on the taxonomic richness and biological traits involved in the main ecological processes were tested and compared with natural bank conditions. Overall, the macroinvertebrate richness was lower in stabilized banks than in natural conditions, and communities welcomed on natural banks were significantly different from those found on managed banks. The biological trait composition such as “maximum potential size,” “life cycle duration,” “reproduction,” “feeding habits,” and “trophic status” differed significantly among riverbanks, especially between natural banks and the riprap, mixed, and cribwall trio. In a context of macroinvertebrate biodiversity and functional restoration, we can advocate the fascine technique as the most suitable technique tested.

Aim: Estimate the current and future distribution of brown trout and identify priority areas for conservation of the species.Location: Rhône River basin and Mediterranean streams.Methods: We first developed a spatially explicit species distribution model to es- timate the current and future distribution of brown trout for three time horizons (2030, 2055 and 2080) and two climate change scenarios (RCP 4.5 and RCP 8.5). We then performed a prioritization analysis to identify priority areas for brown trout conservation, accounting for: (a) spatial dependencies along the riverine system, (b) several sources of uncertainty arising from climate-related forecasts and (c) different protected area scenarios by comparing hypothetical, optimal protected networks to an actual protected network designed by regional fish experts.Results: Future projections of brown trout densities exhibited a general trend to- wards a gradual range contraction, with a significant risk of extirpation across moun- tainous regions of low to mid-elevation. Overall, the projected current and future distributions were well-covered by the existing protected network. In addition, up to 70% of the river reaches included in this expert-based protection network were also priorities in the optimal priority set (e.g. the best set of areas to maximize biodiversity protection). Finally, a large proportion of these reaches were invariably identified re- gardless of climate change scenarios and uncertainties or spatial dependencies. Main conclusions: Our analytical approach highlighted priority areas for brown trout conservation which were robust to a set of climate and connectivity assumptions. This core priority network could be further refined by taking into account key fine- scale processes like thermal refugia. Therefore, we advocate for combining computa- tional and expert-based approaches in conservation planning of riverine ecosystems to achieve a relevant consensus between regional-scale management and fine-grain ecological knowledge.

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.