SUMMARY1. In this review, we first summarize how hydrologic connectivity has been studied for riverine fish capable of moving long distances, and then identify research opportunities that have clear conservation significance. Migratory species, such as anadromous salmonids, are good model organisms for understanding ecological connectivity in rivers because the spatial scale over which movements occur among freshwater habitats is large enough to be easily observed with available techniques; they are often economically or culturally valuable with habitats that can be easily fragmented by human activities; and they integrate landscape conditions from multiple surrounding catchment(s) with in-river conditions. Studies have focussed on three themes: (i) relatively stable connections (connections controlled by processes that act over broad spatio-temporal scales >1000 km 2 and >100 years); (ii) dynamic connections (connections controlled by processes acting over fine to moderate spatio-temporal scales 1-1000 km 2 and <1-100 years); and (iii) anthropogenic influences on hydrologic connectivity, including actions that disrupt or enhance natural connections experienced by fish. 2. We outline eight challenges to understanding the role of connectivity in riverine fish ecology, organized under three foci: (i) addressing the constraints of river structure; (ii) embracing temporal complexity in hydrologic connectivity; and (iii) managing connectivity for riverine fishes. Challenges include the spatial structure of stream networks, the force and direction of flow, scale-dependence of connectivity, shifting boundaries, complexity of behaviour and life histories and quantifying anthropogenic influence on connectivity and aligning management goals. As we discuss each challenge, we summarize relevant approaches in the literature and provide additional suggestions for improving research and management of connectivity for riverine fishes. 3. Specifically, we suggest that rapid advances are possible in the following arenas: (i) incorporating network structure and river discharge into analyses; (ii) increasing explicit consideration of temporal complexity and fish behaviour in the scope of analyses; and (iii) parsing degrees of human and natural influences on connectivity and defining acceptable alterations. Multiscale analyses are most likely to identify dominant patterns of connections and disconnections, and the appropriate scale at which to focus conservation activities.

The term “invader” is typically paired with adjectives such as “non‐native” and “alien”, yet native species can also cause ecological and economic impacts that rival those of well‐known invasive species. By spreading within their historical range, attaining extreme abundances, and exerting severe per‐capita effects as a result of predation or competition, native invaders can create an unusual set of challenges for science, management, policy, and society. Identifying when, where, and why species become invaders in their native ranges requires additional scientific inquiry, outside the current focus of invasion biology. Management strategies often mitigate the symptoms rather than address the causes of problematic native species invasions. Convincing stakeholders to comply with management actions aimed at controlling native invaders creates societal challenges and policy makers must prioritize goals from varied and often conflicting human interests. We illustrate these challenges by highlighting native species that adversely affect threatened and endangered Pacific salmon (Oncorhynchus spp).

Twelve salmonid evolutionarily significant units (ESUs) throughout the Columbia River Basin are currently listed as threatened or endangered under the Endangered Species Act; these ESUs are affected differentially by a variety of human activities. We present a standardized quantitative status and risk assessment for 152 listed salmonid stocks in these ESUs and 24 nonlisted stocks. Using data from 1980-2000, which represents a time of stable conditions in the Columbia River hydropower system and a period of ocean conditions generally regarded as poor for Columbia Basin salmonids, we estimated the status of these stocks under two different assumptions: that hatchery-reared spawners were not reproducing during the period of the censuses, or that hatchery-reared spawners were reproducing and thus that reproduction from hatchery inputs was masking population trends. We repeated the analyses using a longer time period containing both ''good' ' and ''bad'' ocean conditions (1965-2000) as a first step toward determining whether recent apparent declines are a result of sampling a period of poor ocean conditions.All the listed ESUs except Columbia River chum showed declining trends with estimated long-term population growth rates ('s) ranging from 0.85 to 1.0, under the assumption that hatchery fish were not reproducing and not masking the true . If hatchery fish were reproducing, the estimated 's ranged from 0.62 to 0.89, indicating extremely low natural reproduction and survival. For most ESUs, there was no significant decline in population growth rates calculated for the 1980-2000 vs. 1965-2000 time periods, suggesting that the current population status for most ESUs is not solely a result of changes in ocean conditions, and that without other changes, risks will persist even during upturns in ocean conditions. However, estimated population growth rates for the Snake River spring-summer chinook salmon and steelhead ESUs were significantly lower during the longer time period. This difference may be due to a period of dam building on the Snake River during the 1960s and 1970s. For 33 stocks and seven ESUs, the probability of extinction could be estimated. The estimates were generally low for all ESUs with the exception of Upper Columbia River spring chinook and Upper Willamette River steelhead. The probability of 90% decline could be estimated for all stocks. The mean probability of 90% decline in 50 years was highest for Upper Columbia River spring chinook (95% mean probability across all stocks within the ESU) and Lower Columbia River steelhead (80% mean probability).We estimated the effects of two different management actions on long-term growth rates for the ESUs. Harvest reductions offer a means to mitigate risks for ESUs that bear substantial harvest pressure, but they are unlikely to increase population growth rates enough to produce stable or increasing trends for all ESUs. Similarly, anticipated improvements to passage survival through the Snake and mainstem Columbia hydropower systems may be important, but add...

Fin clipping is gaining momentum for stable isotope analysis in fish as a nonlethal alternative to lethally collecting dorsal white muscle tissue. The main advantage of fin clipping is the elimination of lethal collection, which thus increases the potential for stable isotope research involving threatened or endangered species. To make comparisons across studies using different methods, the degree to which fin clips and dorsal muscle are correlated for both d 15 N and d 13 C across time and space must be quantified. We evaluated the efficacy of using caudal fin clips by comparing tissues collected across time (2003)(2004)(2005), space (21 streams), and body size (fork length, 40-140 mm) for juvenile Chinook salmon Oncorhynchus tshawytscha and O. mykiss (rainbow trout and steelhead [anadromous rainbow trout]). We also addressed several analytical and sampling issues to assess the potential benefits and limitations of using fin clips for d 15 N and d 13 C determination. We found that the relationship between fin and muscle tissue was consistent across years and streams. On average, d 15 N was lower in fin tissue than in muscle tissue, whereas d 13 C was greater in fin tissue. Although the magnitude of the difference between fin and muscle tissue is lower than the thresholds typically used to define trophic level increases, the biological significance of these differences is context dependent. Power analyses indicated that fin and muscle tissue were equal in their ability to detect differences in d 15 N and d 13 C in juvenile fish and that larger sample sizes are needed to statistically quantify these differences. Finally, the use of fin clips is not a viable option for smaller fish (,50 mm) because the majority of the caudal fin is necessary for analysis. Nonetheless, fin clipping does represent a promising nonlethal sampling technique for quantifying d 15 N and d 13 C in juvenile salmonids.

The human footprint is now large in all the Earth's ecosystems, and construction of large dams in major river basins is among the anthropogenic changes that have had the most profound ecological consequences, particularly for migratory fishes. In the Columbia River basin of the western USA, considerable effort has been directed toward evaluating demographic effects of dams, yet little attention has been paid to evolutionary responses of migratory salmon to altered selective regimes. Here we make a first attempt to address this information gap. Transformation of the free-flowing Columbia River into a series of slackwater reservoirs has relaxed selection for adults capable of migrating long distances upstream against strong flows; conditions now favour fish capable of migrating through lakes and finding and navigating fish ladders. Juveniles must now be capable of surviving passage through multiple dams or collection and transportation around the dams. River flow patterns deliver some groups of juvenile salmon to the estuary later than is optimal for ocean survival, but countervailing selective pressures might constrain an evolutionary response toward earlier migration timing. Dams have increased the cost of migration, which reduces energy available for sexual selection and favours a nonmigratory life history. Reservoirs are a benign environment for many non-native species that are competitors with or predators on salmon, and evolutionary responses are likely (but undocumented). More research is needed to tease apart the relative importance of evolutionary vs. plastic responses of salmon to these environmental changes; this research is logistically challenging for species with life histories like Pacific salmon, but results should substantially improve our understanding of key processes. If the Columbia River is ever returned to a quasinatural, free-flowing state, remaining populations might face a Darwinian debt (and temporarily reduced fitness) as they struggle to re-evolve historical adaptations.

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As a popular sportfish, smallmouth bass (Micropterus dolomieu) generates considerable angling opportunities with benefits to local economies even outside of their native range. Smallmouth bass was first introduced to the Pacific Northwest region of North America as a sportfish over 80 years ago, and this species is now widely distributed. More recently, smallmouth bass have become a large component of the fish community in many streams, rivers, and lakes. Smallmouth bass thrive in the Pacific Northwest largely due to the habitat created by human modifications of the landscape. While a desired sportfish, smallmouth bass may also negatively affect native fishes. Of greatest concern is predation on threatened and endangered Pacific salmon; however, the current level of knowledge is inadequate to make informed management decisions for smallmouth bass. Management options for smallmouth bass are complicated further because fisheries agencies are simultaneously charged with enhancing fishing opportunities and controlling predators of threatened and endangered salmon. To advance conservation science, there is a need to determine the utility of different management approaches, and testing options in key areas of overlap between smallmouth bass and salmon is suggested.

Large portions of anadromous salmonid habitat in the western United States has been lost because of dams and other blockages. This loss has the potential to affect salmonid evolution through natural selection if the loss is biased, affecting certain types of habitat differentially, and if phenotypic traits correlated with those habitat types are heritable. Habitat loss can also affect salmonid evolution indirectly, by reducing genetic variation and changing its distribution within and among populations. In this paper, we compare the characteristics of lost habitats with currently accessible habitats and review the heritability of traits which show correlations with habitat/environmental gradients. We find that although there is some regional variation, inaccessible habitats tend to be higher in elevation, wetter and both warmer in the summer and colder in the winter than habitats currently available to anadromous salmonids. We present several case studies that demonstrate either a change in phenotypic or life history expression or an apparent reduction in genetic variation associated with habitat blockages. These results suggest that loss of habitat will alter evolutionary trajectories in salmonid populations and Evolutionarily Significant Units. Changes in both selective regime and standing genetic diversity might affect the ability of these taxa to respond to subsequent environmental perturbations. Both natural and anthropogenic and should be considered seriously in developing management and conservation strategies.