Restoring stream habitat connectivity: a proposed method for prioritizing the removal of resident fish passage barriers

Disentangling effects of dispersal, environment and anthropogenic barriers on functional connectivity in aquatic systems

Disentangling the roles of structural landscape factors and animal movement behaviour can present challenges for practitioners managing landscapes to maintain functional connectivity and achieve conservation goals. We used a landscape genetics approach to combine robust demographic, behavioural and genetic datasets with spatially explicit simulations to evaluate the effects of anthropogenic barriers (dams, culverts) and natural landscape resistance (gradient, elevation) affecting dispersal behaviour, genetic connectivity and genetic structure in a resident population of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi). Analyses based on 10 years of sampling effort revealed a pattern of restricted dispersal, and population genetics identified discrete population clusters between distal tributaries and the mainstem stream and no structure within the mainstem stream. Demogenetic simulations demonstrated that, for this population, the effects of existing anthropogenic barriers on population structure are redundant with effects of restricted dispersal associated with the underlying environmental resistance. Our approach provides an example of how extensive field sampling combined with landscape genetics can be incorporated into spatially explicit simulation modelling to explore how, together, movement ecology and landscape resistance can be used to inform decisions around restoration and connectivity.

Integrating fish swimming abilities into rapid road crossing barrier assessment: Case studies in the southeastern United States

Many aquatic networks are fragmented by road crossing structures; remediating these barriers to allow fish passage is critical to restoring connectivity. Maximizing connectivity requires effective barrier identification and prioritization, but many barrier prioritization efforts do not consider swimming capabilities of target species. Given the many potential barriers within watersheds, inventory efforts integrating species-specific swimming speeds into rapid assessment protocols may allow for more accurate barrier removal prioritization. In this study, we demonstrate an approach for integrating fish swimming speeds into rapid barrier assessment and illustrate its utility via two case studies. We measured critical swimming speeds (Ucrit) of two stream-resident fish species with very different swimming modes: Yoknapatawpha Darter (Etheostoma faulkneri), an at-risk species whose current distribution is restricted to highly degraded habitat, and Bluehead Chub (Nocomis leptocephalus), an important host species for the federally endangered Carolina Heelsplitter mussel (Lasmigona decorata). We assessed potential barriers for Yoknapatawpha Darters in the Mississippi-Yocona River watershed, and Bluehead Chubs in the Stevens Creek watershed, South Carolina, USA. We integrated Ucrit into the Southeast Aquatic Resources Partnership (SARP) barrier assessment protocol by estimating the proportion of individuals per species swimming at least as fast as the current through the assessed structures. Integrating Ucrit estimates into the SARP protocol considerably increased barrier severity estimates and rankings only for Yoknapatawpha Darters in the Yocona River watershed. These results indicate the importance of including species-specific swimming abilities in rapid barrier assessments and the importance of species-watershed contexts in estimating where swimming speed information might be most important. Our method has broad application for those working to identify barriers more realistically to improve species-specific fish passage. This work represents a next step in improving rapid barrier assessments and could be improved by investigating how results change with different measurements of swimming abilities and structure characteristics.

Boosting large-scale river connectivity restoration by planning for the presence of unrecorded barriers

Conservation decisions are invariably made with incomplete data on species' distributions, habitats, and threats, but frameworks for allocating conservation investments rarely account for missing data. We examined how explicit consideration of missing data can boost return on investment in ecosystem restoration, focusing on the challenge of restoring aquatic ecosystem connectivity by removing dams and road crossings from rivers. A novel way of integrating the presence of unmapped barriers into a barrier optimization model was developed and applied to the U.S. state of Maine to maximize expected habitat gain for migratory fish. Failing to account for unmapped barriers during prioritization led to nearly 50% lower habitat gain than was anticipated using a conventional barrier optimization approach. Explicitly acknowledging that data are incomplete during project selection, however, boosted expected habitat gains by 20-273% on average, depending on the true number of unmapped barriers. Importantly, these gains occurred without additional data. Simply acknowledging that some barriers were unmapped, regardless of their precise number and location, improved conservation outcomes. Given incomplete data on ecosystems worldwide, our results demonstrate the value of accounting for data shortcomings during project selection.

Species distributions and the recognition of risk in restoration planning: A case study of salmonid fishes

One of the risks faced by habitat restoration practitioners is whether habitats included in restoration planning will be used by the target species or, conversely, whether habitats excluded from restoration planning would have benefited the target species. With the goal of providing a quantitative decision-making approach that represented varying levels of risk tolerance, we used multiple probability decision thresholds (PDT) to predict the range of occurrence for three anadromous fishes (Oncorhynchus spp.) in a watershed in southwestern Washington, USA. For each species, we compared the predicted range of occurrence to the distribution used for restoration planning and quantified the amount of habitat blocked by anthropogenic barriers. Coho salmon (O. kisutch) had the broadest predicted range of occurrence (3061.6-6357.9 km; 0.75-0.25 PDT), followed by steelhead trout (O. mykiss; 1828.8-2836.8 km) and chum salmon (O. keta; 1373.9-1629.1 km). For each species, the predicted range of occurrence was similar or greater than the distribution used for restoration planning, suggesting that the current plan may exclude habitats that would benefit each species. Coho salmon had the greatest percentage of habitat blocked by anthropogenic barriers, followed by steelhead trout and chum salmon, respectively. Modeling species distributions at multiple risk-tolerance scenarios acknowledges uncertainty in restoration planning and allows practitioners to weigh the ecological benefits and budgetary constraints when considering locations for restoration. To effectively communicate restoration science to support practitioners in decision-making, we developed an R Shiny application online user interface available at: https://shiny.wdfw-fish.us/ChehalisRiverBasinSalmonidRangeOfOccurence/.

Operational methods for prioritizing the removal of river barriers: Synthesis and guidance

Barrier removal can be an efficient method to restore river continuity but resources available for defragmenting rivers are limited and a prioritization strategy is needed. We review methods for prioritizing barriers for removal and report on a survey asking practitioners which barrier prioritization methods they use. Opportunities for barrier removal depend to a large extent on barrier typology, as this dictates where barriers are normally located, their size, age, condition, and likely impacts. Crucially, river fragmentation depends chiefly on the number and location of barriers, not on barrier size, while the costs of barrier removal typically increase with barrier height. Acting on many small barriers will often be more cost-efficient than acting on fewer larger structures. Barriers are not randomly distributed and a small proportion of barriers have a disproportionately high impact on fragmentation, therefore targeting these 'fragmentizers' can result in substantial gains in connectivity. Barrier prioritization methods can be grouped into six main types depending on whether they are reactive or proactive, whether they are applied at local or larger spatial scales, and whether they employ an informal or a formal approach. While mathematical optimization sets the gold standard for barrier prioritization, a hybrid approach that explicitly considers uncertainties and opportunities is likely to be the most effective. The effectiveness of barrier removal can be compromised by inaccurate stream networks, erroneous barrier coordinates, and underestimation of barrier numbers. Such uncertainties can be overcome by ground truthing via river walkovers and predictive modelling, but the cost of collecting additional information must be weighed against the cost of inaction. To increase the success of barrier removal projects, we recommend that barriers considered for removal fulfill four conditions: (1) their removal will bring about a meaningful gain in connectivity; (2) they are cost-effective to remove; (3) they will not cause significant or lasting environmental damage, and (4) they are obsolete structures. Mapping barrier removal projects according to the three axes of opportunities, costs, and gains can help locate any 'low hanging fruit.'

Multispecies fishways in a Mediterranean river: Contributions as migration corridors and compensatory habitat for fish

River connectivity is essential for the resilience of fish assemblages and populations and is a priority goal to reach good ecological status for river systems. Increasing knowledge on the functionality of restoration tools such as fishways is relevant for future management strategies. The present two-year assessment showed clear ecological contributions of different types of multispecies fishways in the fish assemblage of a strongly modified Mediterranean-type river. Just after their implementation, early and extended use by dominant river-resident fish of both naturelike and technical fishways were observed. All fishways were used in different seasons, especially during the migratory periods by potamodromous cyprinids, suggesting a possible use as migration corridors. Fishways also may provide compensatory habitats for small and juvenile individuals throughout the annual cycles, mostly for rheophilic fish inside nature-like bypasses and for limnophilics inside technical types. Fluvial habitat characteristics and lower flow variability inside the fishways could favour their role as a fish refuge, mainly to juveniles of cyprinids, in heavily regulated rivers where large flow fluctuations occurred. Nature-like fishways could be a better option to function as a compensatory habitat for rheophilic cyprinids in Mediterranean-type Rivers, even more because their use by large nonnative limnophilics seems to be very scarce. However, technical fishways could offer the opportunity to establish control traps of some nonnative fish, which could be of interest to reduce the risk of spreading invasive fish. Therefore, fish ecology and local hydrology should drive the decision between the types to implement. The obtained information on the ecological functionality of multispecies fishways should be considered for applying successful river restorations that are demanded by water and wildlife management schemes (e.g., the European Water Framework Directive).

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

Barrier removal and dynamics of intermittent stream habitat regulate persistence and structure of fish community

Barrier effects observed in the presence of weirs are exacerbated by low water levels. We conducted a 10-year study to assess the ecological effects of stream restoration while analysing the possibility of a seasonal lack of hydrological continuity, with multiple measurements before and after restoring stream structural continuity. The research hypothesis assumes that in intermittent streams, there would be little or no change in the fish community downstream the barrier before vs. after barrier removal, and a significant change upstream the barrier before vs. after. Our results indicate, that by removing small barriers, their detrimental effects on the longitudinal passage of riverine fishes and fish assemblages can be rehabilitated. In the wet season, fish migrants from the mainstem river appeared in the downstream section of the stream. Stream intermittency, however, placed a habitat filter over the assemblage. Thus, after barrier removal, only two small-bodied fish species that tolerate periodic oxygen deficiencies and rising water temperatures gradually shifted upstream and formed stable populations. We emphasize, that we should not refrain from restoring the longitudinal continuity of intermittent streams, because they periodically provide fish valuable refugia and can also be a source of new generations and strengthen fish populations in mainstem river.

A machine learning approach to identify barriers in stream networks demonstrates high prevalence of unmapped riverine dams

Restoring stream ecosystem integrity by removing unused or derelict dams has become a priority for watershed conservation globally. However, efforts to restore connectivity are constrained by the availability of accurate dam inventories which often overlook smaller unmapped riverine dams. Here we develop and test a machine learning approach to identify unmapped dams using a combination of publicly available topographic and geospatial habitat data. Specifically, we trained a random forest classification algorithm to identify unmapped dams using digitally engineered predictor variables and known dam sites for validation. We applied our algorithm to two subbasins in the Hudson River watershed, USA, and quantified connectivity impacts, as well as evaluated a range of predictor sets to examine tradeoffs between classification accuracy and model parameterization effort. The random forest classifier achieved high accuracy in predicting dam sites (true positive rate = 89%, false positive rate = 1.2%) using a subset of variables related to stream slope and presence of upstream lentic habitats. Unmapped dams were prevalent throughout the two test watersheds. In fact, existing dam inventories underestimated the true number of dams by ∼80-94%. Accounting for previously unmapped dams resulted in a 62-90% decrease in dendritic connectivity indices for migratory fishes. Unmapped dams may be pervasive and can dramatically bias stream connectivity information. However, we find that machine learning approaches can provide an accurate and scalable means of identifying unmapped dams that can guide efforts to develop accurate dam inventories, thereby informing and empowering efforts to better manage them.

Riverscape approaches in practice: perspectives and applications

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.

Damn those damn dams: Fluvial longitudinal connectivity impairment for European diadromous fish throughout the 20th century

River longitudinal connectivity is crucial for diadromous fish species to reproduce and grow, its fragmentation by large dams may prevent these species to complete their life cycle. This work aims to evaluate the impact of large dams on the structural longitudinal connectivity at the European scale, from a Diadromous fish species perspective, since the beginning of the 20^th century until the early 21^st century. Based on large dam locations and completion year, a multitude of river impairment metrics were calculated at three spatial scales for six European oceanic regions and 12 time periods. The number of basins affected by large dams is overall low (0.4%), but for large river basins, that cover 78% of Europe's area, 69.5% of all basins, 55.4% of the sub-basins and 68.4% of river length are impaired. River network connectivity impairment became increasingly significant during the second half of the 20^th century and is nowadays spatially widespread across Europe. Except for the North Atlantic, all oceanic regions have over 50% of impacted river length. Considering large river basins, the Mediterranean (95.2%) and West Atlantic (84.6%) regions are the most affected, while the Black (92.1%) and Caspian (96.0%) regions stand out as those with most compromised river length. In 60 years, Europe has gone from reduced impairment to over two-thirds of its large rivers with structural connectivity problems due to large dams. The number of such barriers increased significantly in the second half of the 20^th century, especially main stem dams with decreasing distance to the river mouth. Currently, the structural longitudinal connectivity of European river networks is severely impacted. This concerns all regions considered, and those in southern Europe will face even higher challenges, given that this will be a future hot spot for hydropower development and predictably more affected by climate change.

An accessible optimisation method for barrier removal planning in stream networks

Barriers associated to human infrastructure are a widespread impact in freshwater ecosystems worldwide, disrupting connectivity along river networks and key processes. Restoration of connectivity has risen in the last decade, with thousands of dams, weirs and culverts removed. Spatial optimisation methods can help inform decision on what barriers to remove to maximise gain in connectivity under limited budgets. However, current optimisation approaches rely on programming skills that are not easily accessible to stakeholders, which restrict the use of these methods. We demonstrate how Marxan, a publicly available tool, can be used to prioritise the allocation of barrier removal projects. We mapped the distribution of >900 barriers in the Tagus River (Iberian Peninsula) and 29 freshwater fish species with different movement abilities and needs. We assessed the passability of each barrier by all species and relative removal cost. We then identified priority barriers for removal to increase connectivity of populations of all species simultaneously. We tested two alternative scenarios: i) locking out barriers assesses as non-removable for their high strategic value or removal cost and ii) making all barriers available for removal. We found that connectivity recovery targets could be achieved by removing a small proportion of barriers, and avoiding large infrastructure. However, for some species, large recovery targets could only be achieved by removing some of these large infrastructures at high increases in cost. We also found some spatial differences in the recovery value of particular barriers for improving upstream and downstream connectivity. Our study demonstrates how to use a robust optimisation approach in an accessible tool, to address the complexity of prioritisation exercises commonly faced by stakeholders when deciding where to invest in barrier removal projects. This will improve decision-making for river connectivity restoration through a transparent, reproducible, and better-informed approach than traditional opportunistic or ranking-based approaches.

Undamming the Douro River Catchment: A Stepwise Approach for Prioritizing Dam Removal

Dams provide water supply, flood protection, and hydropower generation benefits, but also harm native species by altering the natural flow regime, and degrading the aquatic and riparian habitats. In the present study, which comprised the Douro River basin located in the North of Portugal, the cost-benefit assessment of dams was based upon a balance between the touristic benefits of a dammed Douro, and the ecological benefits of less fragmented Douro sub-catchments. Focused on four sub-catchments (Sabor, Tâmega, Côa and Corgo), a probabilistic stream connectivity model was developed and implemented to recommend priorities for dam removal, where this action could significantly improve the movement of potadromous fish species along the local streams. The proposed model accounts for fish movement across the dam or weir (permeability), which is a novel issue in connectivity models. However, before any final recommendation on the fate of a dam or weir, the connectivity results will be balanced with other important socio-economic interests. While implementing the connectivity model, an inventory of barriers (dams and weirs) was accomplished through an observation of satellite images. Besides identification and location of any obstacles, the inventory comprised the compilation of data on surrounding land use, reservoir water use, characteristics of the riparian gallery, and permeability conditions for fish, among others. All this information was stored in a geospatial dataset that also included geographical information on the sub-catchment drainage network. The linear (drainage network) and point (barriers) source data were processed in a computer program that provided or returned numbers for inter-barrier stream lengths (habitat), and the barrier permeability. These numbers were finally used in the same computer program to calculate a habitat connector index, and a link improvement index, used to prioritize dam removal based upon structural connectivity criteria. The results showed that habitat patch connectivity in the Sabor, Tâmega and Côa sub-catchments is not dramatically affected by the installed obstacles, because most link improvement values were generally low. For the opposite reason, in the Corgo sub-catchment, obstacles may constitute a relatively higher limitation to connectivity, and in this case the removal of eight obstacles could significantly improve this connectivity. Using the probabilistic model of structural connectivity, it was possible to elaborate a preliminary selection of dams/weirs that critically limit stream connectivity, and that will be the focus of field hydraulic characterization to precisely determine fish movement along the associated river stretches. Future work will also include the implementation of a multi-criteria decision support system for dam removal or mitigation of the critical structures, as well to define exclusion areas for additional obstacles.

Altered thermoregulation as a driver of host behaviour in glochidia-parasitised fish

Parasites alter their host behaviour and vice versa as a result of mutual adaptations in the evolutionary arms race. One of these adaptations involves changes in host thermoregulation, which has the potential to harm the parasite and thereby act as a defence mechanism. We used a model of the brown trout Salmo trutta experimentally parasitised with ectoparasitic larvae called glochidia from the endangered freshwater pearl mussel Margaritifera margaritifera to reveal whether parasitation alters fish behavioural thermoregulation. A study based on radio telemetry temperature sensors was performed during almost one year M. margaritifera parasitic stage. Glochidia infested S. trutta altered its thermoregulation through active searching for habitats with different thermal regimes. General preference for lower temperature of infested fish varied, being sometimes above, sometimes below the temperature preferred by uninfested individuals. Infested fish also preferred different temperatures across localities, while uninfested fish maintained their thermal preference no matter which stream they inhabited. Glochidia further induced the expression of a behavioural syndrome among S. trutta personality traits, suggesting that it might increase the probability that the fish host would occur in the glochidia temperature optimum. Our findings present the first evidence that thermoregulation plays a fundamental role in the relationship of affiliated mussels and their fish hosts. Incorporating thermoregulation issue in the study of this relationship can help to interpret results from previous behavioural studies as well as to optimise management measures related to endangered mussels.

Untangling the effects of multiple human stressors and their impacts on fish assemblages in European running waters

This work addresses human stressors and their impacts on fish assemblages at pan-European scale by analysing single and multiple stressors and their interactions. Based on an extensive dataset with 3105 fish sampling sites, patterns of stressors, their combination and nature of interactions, i.e. synergistic, antagonistic and additive were investigated. Geographical distribution and patterns of seven human stressor variables, belonging to four stressor groups (hydrological-, morphological-, water quality- and connectivity stressors), were examined, considering both single and multiple stressor combinations. To quantify the stressors' ecological impact, a set of 22 fish metrics for various fish assemblage types (headwaters, medium gradient rivers, lowland rivers and Mediterranean streams) was analysed by comparing their observed and expected response to different stressors, both acting individually and in combination. Overall, investigated fish sampling sites are affected by 15 different stressor combinations, including 4 stressors acting individually and 11 combinations of two or more stressors; up to 4 stressor groups per fish sampling site occur. Stressor-response analysis shows divergent results among different stressor categories, even though a general trend of decreasing ecological integrity with increasing stressor quantity can be observed. Fish metrics based on density of species 'intolerant to water quality degradation' and 'intolerant to oxygen depletion" responded best to single and multiple stressors and their interactions. Interactions of stressors were additive (40%), synergistic (30%) or antagonistic (30%), emphasizing the importance to consider interactions in multi-stressor analyses. While antagonistic effects are only observed in headwaters and medium-gradient rivers, synergistic effects increase from headwaters over medium gradient rivers and Mediterranean streams to large lowland rivers. The knowledge gained in this work provides a basis for advanced investigations in European river basins and helps prioritizing further restoration and management actions.

Supporting decision-making for improving longitudinal connectivity for diadromous and potamodromous fishes in complex catchments

Preservation and restoration of Europe's endangered migratory fish species and habitats are high on the international river basin policy agenda. Improvement through restoration of longitudinal connectivity is seen as an important measure, but although prioritization of in-stream barriers has been addressed at local and regional levels the process still lacks adequate priority on the international level. This paper introduces a well-tested method, designed to help decision makers achieve the rehabilitation of targeted ichthyofauna more successfully. This method assesses artificial barriers within waters designated under the Water Framework Directive (WFD), Europe's main legislative driver for ecological improvement of river basins. The method aggregates migratory fish communities (both diadromous and potamodromous) into functional biological units (ecological fish guilds) and defines their most pressing habitat requirements. Using GIS mapping and spatial analysis of the potential ranges (fish zonation) we pin-point the most important barriers, per guild. This method was developed and deployed over a 12 year period as a practical case study, fitting data derived from the 36 regional water management organisations in the Netherlands. We delivered national advice on the prioritization of a total of 2924 barriers located within WFD water bodies, facilitating migration for all 18 indigenous migratory fish species. Scaling up to larger geographical areas can be achieved using datasets from other countries to link water body typologies to distribution ranges of migratory fish species.