The ongoing biodiversity crisis is especially severe in freshwater habitats. Anthropized watersheds, such as the Seine-Normandie basin in France, are particularly affected by human interference. The study of fish species distribution in watersheds often relies on environmental drivers such as land use or climate. Yet, fish are also exposed to river connectivity constraints, such as dams, that are understudied despite their potential impact on fish dispersal. For this study, we investigated the role of local and whole-basin longitudinal connectivity in fish distribution. We designed connectivity indices based on river network characteristics and specific mobility for 33 species and included these indices in species distribution models, taking into account habitat suitability, to quantify their role in species distribution. Keeping the best index for each species, an average of 29 % - and up to 57 % - of explained fish distribution, depending on species, was tied to connectivity. We found that high connectivity often had a significant and positive linear effect on species presence probability. Using a scoring system across multiple indices, we found connectivity indices that took local context into account (e.g. the ecological zonation of the river) performed consistently better than others. Indices that took only dispersal limitation into account scored higher for 12 species, while barriers, alone, were the most important constraint for 10 species, the remaining 11 being associated with both. This work points to fragmentation as a cause for lower likelihood of presence for many non-diadromous river fish species. It highlights the importance of considering both physical and functional connectivity constraints in fish distribution and provides additional insights for river management and restoration.

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.

Inland navigation in Europe is proposed to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this would impact biodiversity at large scales and interact with existing stressors. Here we addressed this knowledge gap by analysing fish and macroinvertebrate community time series across large European rivers comprising 19,592 observations from 4,049 sampling sites spanning the past 32 years. We found ship traffic to be associated with biodiversity declines, that is, loss of fish and macroinvertebrate taxonomic richness, diversity and trait richness. Ship traffic was also associated with increases in taxonomic evenness, which, in concert with richness decreases, was attributed to losses in rare taxa. Ship traffic was especially harmful for benthic taxa and those preferring slow flows. These effects often depended on local land use and riparian degradation. In fish, negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was evident only when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian habitats and landscape characteristics could help to mitigate these impacts. An analysis of fish and macroinvertebrate communities in European rivers over 32 years shows that inland ship traffic is associated with declining taxonomic richness, diversity and trait richness and with increased taxonomic evenness.

Freshwater navigation is expected to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this will impact biodiversity at large scales and interact with existing stressors. We addressed this knowledge gap by analyzing fish and macroinvertebrate community time series spanning the last 30 years across large European rivers comprising 19,592 observations from 4,049 sampling sites. We found ship traffic to be associated with biodiversity declines, i.e. decreases in fish and macroinvertebrate taxonomic richness and diversity, and trait richness. Shipping was also associated with increases in taxonomic evenness, which, in concert with richness decreases, can likely be attributed to losses in rare/smaller populations. In particular, shipping was especially harmful for benthic taxa and those preferring slow flows. These effects were often dependent on local land use and degradation. In fish, the negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was only evident when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian and landscape characteristics could help to mitigate these impacts.

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S'il ne fait aucun doute que la biodiversité décline à l'échelle mondiale, il est surprenant de constater que les dynamiques locales peuvent être contrastées. Nous possédons une compréhension encore incomplète de la façon dont les écosystèmes évoluent sous l'effet du changement global. Ici, nous avons cherché à caractériser la dynamique temporelle récente de la biodiversité des rivières en France, d'un point de vue taxonomique et fonctionnel, concernant différents organismes clés (diatomées, macro-invertébrés et poissons), à partir d’un large panel de mesures de la biodiversité et sur une période multi-décennale. Les résultats convergent vers la mise en évidence d'un retour significatif des taxons sensibles à l'eutrophisation, signe d'amélioration de la qualité des cours d’eau au cours de la période d’étude du point de vue de l’enrichissement trophique. D'autre part, la richesse en diatomées et, dans une moindre mesure, en poissons, a diminué au fil du temps, tandis que la richesse taxonomique des macro-invertébrés a augmenté. Enfin, l'étude a révélé des réarrangements cohérents au sein des communautés des cours d'eau, avec le passage d’une production primaire planctonique à une production primaire benthique, entraînant des modifications fonctionnelles des communautés de macro-invertébrés et de poissons.

While it is recognized that biodiversity currently declines at a global scale, we still have an incomplete understanding of local biodiversity trends under global change. To address this deficiency, we examined the recent decadal trends in water quality and biodiversity (taxonomic and functional) of key river organisms (diatoms, macroinvertebrates and fish) in France. We implemented regression, RLQ and fourth-corner analyses. Our results showed that nutrient loads tended to decrease, diatom richness tended to decline and macoinvertebrate richness tended to increase. The recovery of sensitive taxa in all three groups suggested a successful outcome of water quality management in France over the past decades. Our study further revealed consistent rearrangements within river communities, with a decrease in the ratio of planktonic to benthic diatoms, and corresponding functional changes in macroinvertebrate and fish trait composition, indicative of a trophic cascade in response to changes in environmental conditions.

Landscape perspectives in riverine ecology have been undertaken increasingly in the last 30 years, leading aquatic ecologists to develop a diverse set of approaches for conceptualizing, mapping and understanding 'riverscapes'. Spatiotemporally explicit perspectives of rivers and their biota nested within the socio-ecological landscape now provide guiding principles and approaches in inland fisheries and watershed management. During the last two decades, scientific literature on riverscapes has increased rapidly, indicating that the term and associated approaches are serving an important purpose in freshwater science and management. We trace the origins and theoretical foundations of riverscape perspectives and approaches and examine trends in the published literature to assess the state of the science and demonstrate how they are being applied to address recent challenges in the management of riverine ecosystems. We focus on approaches for studying and visualizing rivers and streams with remote sensing, modelling and sampling designs that enable pattern detection as seen from above (e.g. river channel, floodplain, and riparian areas) but also into the water itself (e.g. aquatic organisms and the aqueous environment). Key concepts from landscape ecology that are central to riverscape approaches are heterogeneity, scale (resolution, extent and scope) and connectivity (structural and functional), which underpin spatial and temporal aspects of study design, data collection and analysis. Mapping of physical and biological characteristics of rivers and floodplains with high-resolution, spatially intensive techniques improves understanding of the causes and ecological consequences of spatial patterns at multiple scales. This information is crucial for managing river ecosystems, especially for the successful implementation of conservation, restoration and monitoring programs. Recent advances in remote sensing, field-sampling approaches and geospatial technology are making it increasingly feasible to collect high-resolution data over larger scales in space and time. We highlight challenges and opportunities and discuss future avenues of research with emerging tools that can potentially help to overcome obstacles to collecting, analysing and displaying these data. This synthesis is intended to help researchers and resource managers understand and apply these concepts and approaches to address real-world problems in freshwater management.

The spread of non-native species is nowadays recognized as a major threat to the biodiversity of freshwater ecosystems. However, for a very long time the introduction and acclimatization of new species has been perceived mainly as a source of wealth for human societies. Here, we examined the establishment of non-native fish species in the Seine River basin from a historical perspective by adopting a twofold approach. In a first step, at the whole basin scale, considering various written and archeological sources, we traced the chronology, over the last millennium, of the establishments of non-native species. In a second step, by analyzing fish monitoring from several hundred sites covering the diversity of rivers and streams, we examined the changes in numbers and abundance of non-native species in local fish communities over the last three decades. The first documented species introduction dates back to the 13th century but it is from the middle of the 19th century that the introduction attempts accelerated. Today, these introductions have reached an unprecedented level and 46% of the species recorded in the basin are non-native. During the last three decades, non-native species have continued to increase within fish communities both in terms of number of species and abundance of individuals. The most pronounced increases are noted on large rivers and sites where anthropic pressures are strong. Waterways connecting European basins, globalization of trade, and ongoing climate change provide a general background suggesting that the increase in the proportion of non-native species in the fish communities of the Seine River basin is likely to continue for several decades.

To understand the long-term fate of fish assemblages in the context of global change and to design efficient restoration measures in river management, it is essential to consider the historical component of these ecosystems. The human-impacted Seine River Basin is a relevant case that has experienced the extinction of diadromous fishes over the last two centuries and has recently witnessed the recolonization of some species. One key issue is to understand the historical evolution of habitat accessibility for these migratory species. Thanks to the unique availability of historical, mainly hand-written sources of multiple types (river engineering projects, navigation maps, paper-based databases on oxygen, etc.), we documented and integrated, in a geographic information system-based database, the changes to physical and chemical barriers in the Seine River from the sea to Paris for three time periods (1900s, 1970s, and 2010s). The potential impact of these changes on the runs of three migratory species that have different migratory behaviors—Atlantic salmon, allis shad, and sea lamprey—was evaluated by ecological connectivity modeling, using a least-cost approach that integrates distance, costs, and risks related to barriers. We found that accessibility was contrasted between species, emphasizing the crucial role of the migration type, period, and level of tolerance to low dissolved oxygen values. The highest disruption of ecological connectivity was visible in the 1970s, when the effects of large hypoxic areas were compounded by those of impassable navigation weirs (i.e., without fish passes). As the approach was able to reveal the relative contribution of physical and chemical barriers on overall functional connectivity, it may constitute a model work in assessing the functioning of large river ecosystems.

AbstractUsing both historical and current data, we retrace the long-term evolution of fish assemblages in the Seine River basin since 1880, from headwaters to upstream of the Seine River estuary. Successive phases are observed, related to anthropogenic impacts on habitat conditions and river water quality. Temporal trajectories were thus reconstructed on several reaches based on the change of the proportion of species’ ecological traits, in order to detect the main drivers of alteration. Contrasted trends occur between large rivers and small streams of the basin. In this context, migratory fish declined, whereas the proportion of non-native species increased in the fish community of the Seine River.

In the context of increasing pressure on water bodies, many fish-based indices have been developed to evaluate the ecological status of rivers. However, most of these indices suffer from several limitations, which hamper the capacity of water managers to select the most appropriate measures of restoration. Those limitations include: (i) being dependent on reference conditions, (ii) not satisfactorily handling complex and non-linear biological responses to pressure gradients, and (iii) being unable to identify specific risks of stream degradation in a multi-pressure context. To tackle those issues, we developed a diagnosis-based approach using Random Forest models to predict the impairment probabilities of river fish communities by 28 pressure categories (chemical, hydromorphological and biological). In addition, the database includes the abundances of 72 fish species collected from 1527 sites in France, sampled between 2005 and 2015; and fish taxonomic and biological information. Twenty random forest models provided at least good performances when evaluating impairment probabilities of fish communities by those pressures. The best performing models indicated that fish communities were impacted, on average, by 7.34 ± 0.03 abiotic pressure categories (mean ± SE), and that hydromorphological alterations (5.27 ± 0.02) were more often detected than chemical ones (2.06 ± 0.02). These models showed that alterations in longitudinal continuity, and contaminations by Polycyclic Aromatic Hydrocarbons were respectively the most frequent hydromorphological and chemical pressure categories in French rivers. This approach has also efficiently detected the functional impact of invasive alien species. Identifying and ranking the impacts of multiple anthropogenic pressures that trigger functional shifts in river biological communities is essential for managers to prioritize actions and to implement appropriate restoration programmes. Actually implemented in an R package, this approach has the capacity to detect a variety of impairments, resulting in an efficient assessment of ecological risks across various spatial and temporal scales.

Diadromous fishes have drastically declined over the last century, especially in Europe. Several authors have highlighted the role of large dams in this decline, but in fact, its causes are potentially multiple and cumulative, including degradation of local environmental conditions and widespread fragmentation of hydrographic networks associated with the pervasive establishment of smaller barriers. Consequently, there is a need to improve the identification and prioritization of the drivers of diadromous species loss in order to identify and apply the most appropriate conservation and restoration measures. In this study, we used both historical sources (from mid-18th to early 20th century) and current data to quantify the long-term loss of diadromous taxa over 555 sites throughout the French river network. Then, we modeled the effects of several anthropogenic pressures (e.g. barriers, water quality, hydrological and river morphological alterations) on diadromous taxon loss. Lastly, we assessed the potential consequences of four different scenarios of anthropogenic pressure reduction. Due to uncertainties in historical sources, some species were grouped into taxa leading to a potential underestimation of actual species extinctions. Despite this limitation, our results showed that the decline in diadromous assemblages is widespread but with contrasting magnitudes depending on site locations. The maximum height and density of barriers appeared as the major factors of taxon loss. Over the scenarios tested, we observed that exclusively improving local conditions have much more limited effects than restoring river continuity. Focusing actions on large dam removal did not show the strongest responses compared to removing medium and small-sized barriers. For effective and sustainable restoration of diadromous fish assemblage, (1) historical occurrences of diadromous fishes should be used as an indicator for assessing recovery, and (2) undertaken measures must be adapted to each basin to target and limit the number of barriers to remove while allowing diadromous fish recovery.