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Effective conservation of stream fishes and their habitats is complicated by the fact that human stressors alter the way in which natural factors such as stream size, catchment geology, and regional climate influence stream ecosystems. Consequently, efforts to assess the condition of stream fishes and their habitats must not only attempt to characterize the effects of human stressors but must account for the effects of natural influences as well. This study is an assessment of all stream fish habitats in the Mississippi River basin, USA. The basin supports over 400 stream fish species, drains a land area of 3.2 M km2, and includes a myriad of human stressors such as intensive agriculture, urbanization, nutrient loading, and habitat fragmentation by dams and road/stream crossings. To effectively characterize types and levels of human stressors specifically impacting the basin’s stream fish species, our assessment approach first accounted for the influence of natural landscape conditions on species abundances with multiple steps, including stratifying our analyses by region and stream size and quantitatively modeling the influences of natural factors on stream fishes. We next quantified individual fish species responses to explicit human stressors for different measures of land use, fragmentation, and water quality, including summaries of measures in local vs. catchment extents. Results showed that many species had negative threshold responses to human stressors and that impacts varied by species, by region, and by the spatial extents in which stressors were summarized. Our spatially explicit results indicated the degree of stream reach impairment for specific stressor categories, for individual species, and for entire assemblages, all of which are types of information that can aid decision makers in achieving specific conservation goals in the region.

AIM: To assess the effectiveness of protected areas in two catchment scales (local and network) in conserving regionally common fluvial fishes using modelled species distributions. LOCATION: Conterminous United States. METHODS: A total of 150 species were selected that were geographically widespread, abundant, non‐habitat specialists and native within nine large ecoregions. Species distribution models were developed using boosted regression trees, and modelled distributions were assessed for protection status under two alternatives: lands strictly managed for biodiversity (Highly Restricted Use) and those allowing multiple uses (Multiple Use), with protection target levels (i.e., the amount of protected area required for protection) for local and network catchments being developed from ecoregion‐based urban and agricultural land use thresholds from fish responses. RESULTS: Overall, less than 2% of fluvial catchments in the conterminous USA are meeting both local and network catchment protection target levels under the Highly Restricted Use alternative, whereas 16% of catchments met protection levels for the Multiple Use alternative, with protection largely concentrated in the western USA. For common native species distributions within ecoregions, only one species had >10% of streams meeting combined local and network catchment protection target levels under the Highly Restricted Use alternative, whereas 50 distributions (~14% of species distribution models) met this level under the Multiple Use alternative. MAIN CONCLUSIONS: Even for fishes considered widespread and abundant, protection levels are lacking, particularly when considering only lands that are actively managed for biodiversity. Given the increasing intensification of anthropogenic activities and substantial uncertainty associated with climate change, considering the conservation status for all species, including those currently considered common, is warranted.

Species conservation often faces many challenges, such as addressing threats from multiple stressor sources, representing under-studied taxa, and understanding implications of spatial extent. To overcome these challenges, we assessed contemporary anthropogenic threats from stream fragmentation and landscape disturbance as well as future habitat suitability under climate change for traditionally well-studied (fishes) and under-studied (mussels) imperiled fluvial taxa in Michigan, USA. To understand how threats to species vary spatially, predicted habitat suitability was analyzed for three hierarchically nested spatial extents: statewide, within species’ biogeographic ranges, and within river patches fragmented by barriers. Comparison of current and future habitat suitability for 27 fish and 23 mussel species indicates large potential statewide gains for many warmwater and/or large river fishes and several mussel species, however these gains are greatly diminished by biogeographic range limitations and habitat fragmentation among current and future habitats. One mussel species and several cold- and coolwater fishes are projected to have significant habitat losses under climate change irrespective of spatial extent. On average, 79% of habitats for mussels and 58% for fishes were considered moderately to severely disturbed from current human landscape activities. Habitat fragmentation was greater for fishes than mussels, with large dams playing a primary role in fragmenting habitats relative to small dams and waterfalls. Results indicate that threat assessments can vary substantially according to spatial extent and taxa, and consideration of both contemporary and future threats to habitats is needed to inform conservation of imperiled fluvial organisms.

Despite increasing efforts globally to remove dams and construct fish passage structures, broad-scale analyses balancing tradeoffs between cost and habitat gains from these mitigations infrequently consider invasive species. We present an optimization-based approach for prioritizing dam mitigations to restore habitat connectivity for native fish species, while limiting invasive species spread. Our methodology is tested with a case study involving 240 dams in the Upper Mississippi River, USA. We integrate six native migratory fish species distribution models, distributions of two invasive fishes, and estimated costs for dam removal and construction of fish passes. Varying budgets and post-mitigation fish passage rates are analyzed for two scenarios: ‘no invasives’ where non-selective mitigations (e.g., dam removal) are used irrespective of potential invasive species habitat gains and ‘invasives’ where a mixture of selective (e.g., lift-and-sort fish passage) and non-selective mitigations are deployed to limit invasive species range expansion. To achieve the same overall habitat connectivity gains, we find that prioritizations accounting for invasive species are 3 to 6 times more costly than those that do not. Habitat gains among native fish species were highly variable based on potential habitat overlap with invasive species and post-mitigation passabilities, ranging from 0.4–58.9% (‘invasives’) and 7.9–95.6% (‘no invasives’) for a $50M USD budget. Despite challenges associated with ongoing nonnative fish invasions, opportunities still exist to restore connectivity for native species as indicated by individual dams being frequently selected in both scenarios across varying passabilities and budgets, however increased restoration costs associated with invasive species control indicates the importance of limiting their further spread within the basin. Given tradeoffs in managing for native vs. invasive species in river systems worldwide, our approach demonstrates strategies for identifying a portfolio of candidate barriers that can be investigated further for their potential to enhance native fish habitat connectivity while concurrently limiting invasive species dispersal.

Stream classifications can be used to understand patterns within and across river networks and are most informative when they offer insight into patterns in stream habitat or biology. We developed a classification of Hawaiian stream reaches based on influences of natural landscape features on distributions of stream organisms to understand patterns in ecological potential across five Hawaiian Islands. Our objectives were to (1) identify natural landscape variables strongly associated with species distributions and likely to affect stream habitat; and (2) classify Hawaiian stream reaches based on relationships between landscape variables and distributions of native stream taxa. We used canonical correspondence analysis to identify natural landscape variables associated with distributions of nine native stream taxa. To classify reaches, we then used a conditional inference tree that identified significant influences of natural landscape variables on taxa distributions and showed that elevation, channel slope, hydrologic soil grouping, and rainfall were all important predictors of species distributions. Results were used to develop reach classes that describe differences in stream habitat. Our research adds to current understanding of landscape controls on the biota of tropical island streams and provides a tool for decision makers tasked with developing conservation and adaptation strategies.

Understanding patterns in freshwater mussel distributions and habitat use, particularly for imperiled species, is critical for their conservation. To aid in management of imperiled mussels, and to demonstrate the utility using both landscape-based and biotic predictors in assessing species habitat suitability, we modeled 11 imperiled mussels in rivers of Michigan, USA. Models were developed with MaxEnt using a combination of host fish richness, natural abiotic reach variables, and landscape-based natural and anthropogenic variables. Because potential host fishes are important biological determinants of mussel distributions, fluvial host fish distributions (n = 37) were modeled and integrated as a predictor in mussel models. Key predictors determining habitat suitability for mussels included host fish richness, a strong positive predictor for 8 of 11 mussel species, stream discharge, urban land use, and upstream dam density. Models predicted 853 to 10,138 stream km of suitable habitat (1.1 to 13.6% of the state’s stream length) for the 11 mussel species, with 54 to 1,382 km (0.1 to 1.8%) being considered highly suitable habitat. Mapping of suitable habitats identified streams with available habitat for multiple listed species, allowing for more informed decisions in conservation planning and management of Michigan’s listed freshwater mussels and their fish hosts.

Despite the prevalence of damming as a global disturbance to river habitats, detailed reach-based assessments of the ecological effects of dams are lacking, particularly across large spatial extents. Using data from nearly 50,000 large dams, we assessed stream network fragmentation and flow alteration by large dams for streams of the conterminous USA. We developed 21 dam metrics characterizing a diversity of dam influences operating at both localized (e.g., distances-to-dams) and landscape scales (e.g., cumulative reservoir storage throughout stream networks) for every stream reach in the study region. We further evaluated how dams have affected stream fish assemblages within large ecoregions using more than 37,000 stream fish samples. Streams have been severely fragmented by large dams, with the number of stream segments increasing by 801% compared to free-flowing streams in the absence of dams and a staggering 79% of stream length is disconnected from their outlet (i.e., oceans and Great Lakes). Flow alteration metrics demonstrate a landscape-scale disturbance of dams, resulting in total upstream reservoir storage volumes exceeding estimated annual discharge volumes of many of the nation's largest rivers. Further, we show large-scale changes in fish assemblages with dams. Species adapted to lentic habitats increase with dams across the conterminous USA, while rheophils, lithophils, and intolerant fishes decrease with dams. Overall, fragmentation and flow alteration by dams have affected fish assemblages as much or more than other anthropogenic stressors, with dam effects generally increasing with stream size. Dam-induced stream fragmentation and flow alteration are critical natural resource issues. This study emphasizes the importance of considering dams as a landscape-scale disturbance to river habitats along with the need to assess differential effects that dams may have on river habitats and the fishes they support. Together, these insights are essential for more effective conservation of stream resources and biotic communities globally.

Improving quality and better availability of continuous stream temperature data allow natural resource managers, particularly in fisheries, to understand associations between different characteristics of stream thermal regimes and stream fishes. However, there is no convenient tool to efficiently characterize multiple metrics reflecting stream thermal regimes with the increasing amount of data from continuously recording data loggers. This article describes a software program packaged as a library in R to facilitate this process. With this freely available package, users will be able to quickly summarize metrics that describe five categories of stream thermal regimes: magnitude, variability, frequency, timing, and rate of change. The installation and usage instruction of this package, the definition of calculated thermal metrics, as well as the output format from the package are described, along with an application showing the utility for multiple metrics. We believe that this package can be widely utiliz...

Water resources and transportation infrastructure such as dams and culverts provide countless socio-economic benefits; however, this infrastructure can also disconnect the movement of organisms, sediment, and water through river ecosystems. Trade-offs associated with these competing costs and benefits occur globally, with applications in barrier addition (e.g. dam and road construction), reengineering (e.g. culvert repair), and removal (e.g. dam removal and aging infrastructure). Barrier prioritization provides a unique opportunity to: (i) restore and reconnect potentially large habitat patches quickly and effectively and (ii) avoid impacts prior to occurrence in line with the mitigation hierarchy (i.e. avoid then minimize then mitigate). This paper synthesizes 46 watershed-scale barrier planning studies and presents a procedure to guide barrier prioritization associated with connectivity for aquatic organisms. We focus on practical issues informing prioritization studies such as available data sets, methods, techniques, and tools. We conclude with a discussion of emerging trends and issues in barrier prioritization and key opportunities for enhancing the body of knowledge. Copyright © 2016 John Wiley & Sons, Ltd.

Although localized effects of individual dams on stream fish assemblages have been relatively well-studied, less is known about the effects of multiple dams within a stream network on fishes and the patterns that emerge when the combined effects of individual and multiple dams are viewed across entire river basins, ecoregions, and states. This study evaluated multiple stream network fragmentation metrics representing localized (e.g., distance-to-dams) and cumulative (e.g., total upstream reservoir storage) dam influences on streams in Michigan, Wisconsin, and Minnesota, developing an approach for identifying suitable fish indicators of dam effects. We used change point and correlation analyses to determine associations of stream fish catch per unit effort and various stream network fragmentation metrics with data from more than 2000 fish survey sites stratified by stream size, thermal regime, and ecoregion. Of the identified indicator species, predominantly warmwater, large river, and/or lentic species were positively associated with stream network fragmentation, whereas cold and coolwater lotic species were negatively associated with fragmentation. These results suggest a combination of downstream thermal effects and upstream influences from impoundments generated by dams. Variance partitioning analyses based on identified indicator species revealed greater upstream-dominated dam influences in headwaters than mid-sized streams, and a greater relative influence of dams vs. other non-dam anthropogenic influences in cold streams than warm streams. Overall, a combination of localized and cumulative fragmentation metrics, as well as upstream and downstream-oriented measures, were influential in indicator species responses, emphasizing the importance of selecting a diversity of fragmentation metrics when assessing effects of dams on stream fishes. Understanding multiple dam influences on stream fishes, including localized effects from individual dams and cumulative effects from all dams within a river basin, would provide useful information for a variety of management activities, including dam operation and dam removal prioritization. Dams significantly affect conservation and management options for stream fishes, with identification of multi-scale dam influences on fishes being critical to restoration and maintenance of aquatic biodiversity throughout the world.

A B S T R A C T Mining impacts on stream systems have historically been studied over small spatial scales, yet investigations over large areas may be useful for characterizing mining as a regional source of stress to stream fishes. The associations between co-occurring stream fish assemblages and densities of various “classes” of mining occurring in the same catchments were tested using threshold analysis. Threshold analysis identifies the point at which fish assemblages change substantially from best available habitat conditions with increasing disturbance. As this occurred over large regions, species comprising fish assemblages were represented by various functional traits as well as other measures of interest to management (characterizing reproductive ecology and life history, habitat preferences, trophic ecology, assemblage diversity and evenness, tolerance to anthropogenic disturbance and state-recognized game species). We used two threshold detection methods: change-point analysis with indicator analysis and piecewise linear regression. We accepted only those thresholds that were highly statistically significant (p � 0.01) for both techniques and overlapped within � 5% error. We found consistent, wedge-shaped declines in multiple fish metrics with increasing levels of mining in catchments, suggesting mines are a regional source of disturbance. Threshold responses were consistent across the three ecoregions occurring at low mine densities. For 47.2% of the significant thresholds, a density of only � 0.01 mines/km 2 caused a threshold response. In fact, at least 25% of streams in each of our three study ecoregions have mine densities in their catchments with the potential to affect fish assemblages. Compared to other anthropogenic impacts assessed over large areas (agriculture, impervious surface or urban land use), mining had a more pronounced and consistent impact on fish assemblages.

Biodiversity in stream networks is threatened globally by interactions between habitat fragmentation and altered hydrologic regimes. In the Great Plains of North America, stream networks are fragmented by >19 000 anthropogenic barriers, and flow regimes are altered by surface water retention and groundwater extraction. We documented the distribution of anthropogenic barriers and dry stream segments in five basins covering the central Great Plains to assess effects of broad-scale environmental change on stream fish community structure and distribution of reproductive guilds. We used an information-theoretic approach to rank competing models in which fragmentation, discharge magnitude, and percentage of time streams had zero flow (a measure of desiccation) were included to predict effects of environmental alterations on the distribution of fishes belonging to different reproductive guilds. Fragmentation caused by anthropogenic barriers was most common in the eastern Great Plains, but stream desiccation beca...

Biological assessments of river conditions are increasingly conducted at regional and continental scales that match the extent of large-scale river management efforts. Multimetric indices composed of biological community indicators are commonly used to assess ecological condition and indices have recently been applied in large regions. Methods for large-scale multimetric index creation emphasize repeatability, comparability across regions, and objective selection of candidate metrics. Here we used an extensive fish dataset to create a large pool of fish community metrics which were screened to create multimetric indices (MMIs) in eight ecoregions covering the conterminous U.S. Candidate metrics were tested for metric range, corrected for natural gradients using boosted regression trees, and then tested for repeatability and sensitivity to landscape disturbance. Temporally stable and repeatable metrics were then evaluated for redundancy and used to compose MMIs for each region. Our MMIs were significantly correlated to independently developed MMIs, accurately reproducing prior index values with moderate to high precision and little bias. Our study demonstrates the utility of boosted regression tree models for correcting metric values for natural abiotic gradients and shows that the order of screening tests has a potentially important influence on metric selection. The resultant regional indices and component metrics provide a basis for assessing condition and testing hypotheses about landscape influences on aquatic ecosystems at a national scale in the US.

Fisheries management programs, such as the National Fish Habitat Action Plan (NFHAP), urgently need a nationwide spatial framework and database for health assessment and policy development to protect and improve riverine systems. To meet this need, we developed a spatial framework and database using National Hydrography Dataset Plus (I-.100,000-scale); http://www.horizon-systems.com/nhdplus). This framework uses interconfluence river reaches and their local and network catchments as fundamental spatial river units and a series of ecological and political spatial descriptors as hierarchy structures to allow users to extract or analyze information at spatial scales that they define. This database consists of variables describing channel characteristics, network position/connectivity, climate, elevation, gradient, and size. It contains a series of catchment-natural and human-induced factors that are known to influence river characteristics. Our framework and database assembles au river reaches and t...

Regional assessment of cumulative impacts of dams on riverine fish assemblages provides resource managers essential information for dam operation, potential dam removal, river health assessment and overall ecosystem management. Such an assessment is challenging because characteristics of fish assemblages are not only affected by dams, but also influenced by natural variation and human-induced modification (in addition to dams) in thermal and flow regimes, physicochemical habitats and biological assemblages. This study evaluated the impacts of dams on river fish assemblages in the non-impoundment sections of rivers in the states of Michigan and Wisconsin using multiple fish assemblage indicators and multiple approaches to distinguish the influences of dams from those of other natural and human-induced factors. We found that environmental factors that influence fish assemblages in addition to dams should be incorporated when evaluating regional effects of dams on fish assemblages. Without considering such co-influential factors, the evaluation is inadequate and potentially misleading. The role of dams alone in determining fish assemblages at a regional spatial scale is relatively small (explained less than 20% of variance) compared with the other environmental factors, such as river size, flow and thermal regimes and land uses jointly. However, our results do demonstrate that downstream and upstream dams can substantially modify fish assemblages in the non-impoundment sections of rivers. After excluding river size and land-use influences, our results clearly demonstrate that dams have significant impacts on fish biotic-integrity and habitat-and-social-preference indicators. The influences of the upstream dams, downstream dams, distance to dams, and dam density differ among the fish indicators, which have different implications for maintaining river biotic integrity, protecting biodiversity and managing fisheries. Copyright © 2010 John Wiley & Sons, Ltd.

Reversal of widespread fish habitat degradation in the conterminous United States will require effective spatial planning, which begins with spatial assessment of current habitat conditions. We present an assessment of cumulative anthropogenic disturbance to fish habitats in approximately 2.23 million U.S. river reaches under the assumption that downstream local habitat conditions will reflect conditions in the catchment upstream. We used geographic information systems data to attribute 15 disturbance variables to the catchments of mapped river reaches to calibrate an index of cumulative disturbance that considered effects originating from both local and upstream catchments. The influence of each variable was adjusted in the index based on the results of multiple linear regression analyses of all variables against percent intolerant fishes at a site—a commonly used biological indicator of habitat condition. Urban landscape indicators were weighted most heavily, followed by point-source pollution, pasture lands, and dam densities. Local factors were found to be less influential on fishes than those originating from the upstream river network. Skewed cumulative disturbance scores indicated that disturbance levels of some reaches far exceeded the national median. Future assessments should include stratification of analyses within regions, expanded use of response metrics and datasets, and alternative analytical approaches to help tease apart the influences of interacting landscape disturbance types. We demonstrate how our results can be visualized and used to make regional comparisons among large-scale planning units and also show how reach-level information about upstream versus local disturbance levels can be used to identify potential habitat management strategies that are suitable to different landscape contexts.

The growing quality and availability of spatial map layers (e.g., climate, geology, and land use) allow stream studies, which historically have occurred over small areas like a single watershed or stream reach, to increasingly explore questions from a landscape perspective. This large-scale perspective for fluvial studies depends on the ability to characterize influences on streams resulting from throughout entire upstream networks or catchments. While acquiring upstream information for a single reach is relatively straight-forward, this process becomes demanding when attempting to obtain summaries for all streams throughout a stream network and across large basins. Additionally, the complex nature of stream networks, including braided streams, adds to the challenge of accurately generating upstream summaries. This paper outlines an approach to solve these challenges by building a database and applying an algorithm to gather upstream landscape information for digitized stream networks. This approach avoids the need to directly use spatial data files in computation, and efficiently and accurately acquires various types of upstream summaries of landscape information across large regions using tabular processing. In particular, this approach is not limited to the use of any specific database software or programming language, and its flexibility allows it to be adapted to any digitized stream network as long as it meets a few minimum requirements. This efficient approach facilitates the growing demand of acquiring upstream summaries at large geographic scales and helps to support the use of landscape information in assisting management and decision-making across large regions. Electronic supplementary material The online version of this article (doi:10.1186/2193-1801-3-589) contains supplementary material, which is available to authorized users.