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Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site‐associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F‐statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome‐level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.

Habitat restoration is a key strategy for recovering imperiled species, and planning habitat restoration activities cost effectively can help advance recovery objectives. Habitat restoration planning involves decisions about where and when to undertake restoration, and what type of restoration to undertake. This article focuses on decisions about the amount of restoration to undertake for a given type, location, and time, termed intervention intensity. A return on investment framework is developed for incorporating intervention intensity into habitat restoration planning. The framework is then applied in the context of planning habitat restoration for Pacific salmon recovery as a case study. Results showed that no single intervention type or location dominated, and several returns to scale relationships emerged across the candidate interventions. Scenarios that considered interventions across multiple intensities outperformed single-intensity scenarios in terms of total benefits and cost effectiveness. These findings highlight the usefulness of exploratory return on investment analysis for prioritizing habitat restoration interventions, and underscore the importance of systematically considering how much restoration to undertake, in addition to what to do and where.

International audience; Changes to our climate and oceans are already affecting living marine resources (LMRs) and the people, businesses, and economies that depend on them. As a result, the U.S. National Marine Fisheries Service (NMFS) has developed a Climate Science Strategy (CSS) to increase the production and use of the climate-related information necessary to fulfill its LMR stewardship mission for fisheries management and protected species conservation. The CSS establishes seven objectives: (1) determine appropriate, climate-informed reference points; (2) identify robust strategies for managing LMRs under changing climate conditions; (3) design decision processes that are robust to climate-change scenarios; (4) predict future states of ecosystems, LMRs, and LMR-dependent human communities; (5) determine the mechanisms of climate-change related effects on ecosystems, LMRs, and LMR-dependent human communities; (6) track trends in ecosystems, LMRs, and LMR-dependent human communities and provide early warning of change; and (7) build and maintain the science infrastructure required to fulfill NMFS mandates under changing climate conditions. These objectives provide a nationally consistent approach to addressing climate-LMR science needs that supports informed decision-making and effective implementation of the NMFS legislative mandates in each region. Near term actions that will address all objectives include: (1) conducting climate vulnerability analyses in each region for all LMRs; (2) establishing and strengthening ecosystem indicators and status reports in all regions; and (3) developing a capacity to conduct management strategy evaluations of climate-related impacts on management targets, priorities, and goals. Implementation of the Strategy over the next few years and beyond is critical for effective fulfillment of the NMFS mission and mandates in a changing climate.

Spatial and temporal management measures to reduce nontarget catch are important strategies for rebuilding overfished rockfish (Sebastes spp.) populations in the Northeast Pacific. We describe efforts to support reducing rockfish bycatch in central California trawl fisheries by testing the efficacy of move-on rules on catch data from 2002 to 2010. Move-on rules are regulations or guidelines that trigger the temporary closure of a fishery in a targeted area when a bycatch threshold is reached, without the closure of the entire fishery. Move-on rules based on spatiotemporal autocorrelation (clustering) were effective in reducing bycatch with modest impact on target catch, removing between 35% and 77% of future hauls with bycatch within a specified distance and time of a bycatch-containing haul, while foregoing target catch by an average of 12%. The spatial and temporal peak clustering scales show correlation with the level of schooling behavior by each species; however, the efficiency of the rules measured either in reduction in bycatch hauls or diminished target catch was not strongly affected by those aggregation behaviors. Our analysis provides information for fishers, such as those in the California Risk Pool, in the continuing development of responses that are more refined in both scale and impact.

Although climate-induced shifts in fish distribution have been widely reported at the population level, studies that account for ontogenetic shifts and subregional differences when assessing responses are rare.In this study, groundfish distributional changes in depth, latitude, and longitude were assessed at different size classes by species within nine subregions. We examined large, quality-controlled datasets of depth-stratified-random bottom trawl surveys conducted during summer in three large regions-the Gulf of Alaska and the west coasts of Canada and the United States-over the period 1996-2015, a time period punctuated by a marine "heat wave." Temporal biases in bottom temperature were minimized by subdividing each region into three subregions, each with short-duration surveys. Near-bottom temperatures, weighted by stratum area, were unsynchronized across subregions and exhibited varying subregional interannual variability. The weighted mean bottom depths in the subregions also vary largely among subregions. The centroids (centers of gravity) of groundfish distribution were weighted with catch per unit effort and stratum area for 10 commercially important groundfish species by size class and subregion. Our multivariate analyses showed that there were significant differences in aggregate fish movement responses to warm temperatures across subregions but not among species or sizes. Groundfish demonstrated poleward responses to warming temperatures only in a few subregions and moved shallower or deeper to seek colder waters. The temperature responses of groundfish depended on where they were. Under global warming, groundfish may form geographically distinct thermal ecoregions along the northeast Pacific shelf. Shallow-depth species exhibited greatly different distributional responses to temperature changes across subregions while deep-depth species of different subregions tend to have relatively similar temperature responses. Future climate studies would benefit by considering fish distributions on small subregional scales.

Author(s): Herbold, Bruce; Carlson, Stephanie M.; Henery, Rene; Johnson, Rachel C.; Mantua, Nate; McClure, Michelle; Moyle, Peter B.; Sommer, Ted | Abstract: California’s salmonids are at the southern limits of their individual species’ ranges, and display a wide diversity of strategies to survive in California’s highly variable climate. Land use changes after statehood in 1850 eliminated important habitats, or blocked access to them, and reduced the abundance, productivity, and distribution of California’s salmon. Habitat simplification, fishing, hatchery impacts, and other stressors led to the loss of genetic and phenotypic (life history, morphological, behavioral, and physiological) diversity in salmonids. Limited diversity and habitat loss left California salmon with reduced capacity to cope with a variable and changing climate. Since 1976, California has experienced frequent droughts, as were common in the paleo-climatological record, but rare in the peak dam-building era of 1936–1976. Increasing temperatures and decreasing snowpacks have produced harsher conditions for California’s salmon in their current habitats than they experienced historically. The most likely way to promote salmon productivity and persistence in California is to restore habitat diversity, reconnect migratory corridors to spawning and rearing habitats, and refocus management to replenish the genetic and phenotypic diversity of these southernmost populations.

Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations’ anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research.

Declining abundance of Chinook Salmon Oncorhynchus tshawytscha across the Pacific Northwest is an issue of great concern ecologically, culturally, and economically. Growth during the first summer is vitally important for juvenile Chinook Salmon, as it influences not only life history decisions (to smolt or not to smolt) but also subsequent river and ocean survival. Using Ecopath with Ecosim, we developed a food web model for a representative stream in the Salmon River basin, Idaho, to evaluate potential species-specific and food web effects of three management strategies: (1) adding salmon carcasses or carcass analogs to promote primary production and detrital availability that were lost due to declining salmon returns; (2) removal of nonnative Brook Trout Salvelinus fontinalis, which are competitors with and predators on juvenile Chinook Salmon; and (3) stocking hatchery Chinook Salmon into streams to supplement wild production. Overall, juvenile Chinook Salmon responded strongly to increases in ...

Local extirpations of Pacific salmon Oncorhynchus spp. and steelhead O. mykiss, often due to dams and other stream barriers, are common throughout the western United States. Reestablishing salmonid populations in areas they historically occupied has substantial potential to assist conservation efforts, but best practices for reintroduction are not well established. In this paper, we present a framework for planning reintroductions designed to promote the recovery of salmonids listed under the Endangered Species Act. Before implementing a plan, managers should first describe the benefits, risks, and constraints of a proposed reintroduction. We define benefits as specific biological improvements towards recovery objectives. Risks are the potential negative outcomes of reintroductions that could worsen conservation status rather than improve it. Constraints are biological factors that will determine whether the reintroduction successfully establishes a self-sustaining population. We provide guidance ...

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Increased concern over climate change is demonstrated by the many efforts to assess climate effects and develop adaptation strategies. Scientists, resource managers, and decision makers are increasingly expected to use climate information, but they struggle with its uncertainty. With the current proliferation of climate simulations and downscaling methods, scientifically credible strategies for selecting a subset for analysis and decision making are needed. Drawing on a rich literature in climate science and impact assessment and on experience working with natural resource scientists and decision makers, we devised guidelines for choosing climate-change scenarios for ecological impact assessment that recognize irreducible uncertainty in climate projections and address common misconceptions about this uncertainty. This approach involves identifying primary local climate drivers by climate sensitivity of the biological system of interest; determining appropriate sources of information for future changes in those drivers; considering how well processes controlling local climate are spatially resolved; and selecting scenarios based on considering observed emission trends, relative importance of natural climate variability, and risk tolerance and time horizon of the associated decision. The most appropriate scenarios for a particular analysis will not necessarily be the most appropriate for another due to differences in local climate drivers, biophysical linkages to climate, decision characteristics, and how well a model simulates the climate parameters and processes of interest. Given these complexities, we recommend interaction among climate scientists, natural and physical scientists, and decision makers throughout the process of choosing and using climate-change scenarios for ecological impact assessment. Seleccion y Uso de Escenarios de Cambio Climatico para Estudios de Impacto Ecologico y Decisiones de Conservacion.

Significant challenges remain in the ability to estimate habitat change under the combined effects of natural variability, climate change, and human activity. We examined anticipated effects on shallow water over low-sloped beaches to these combined effects in the lower Willamette River, Oregon, an area highly altered by development. A proposal to stabilize some shoreline with large rocks (riprap) would alter shallow water areas, an important habitat for threatened Chinook salmon (Oncorhynchus tshawytscha), and would be subject to U.S. Endangered Species Act-mandated oversight. In the mainstem, subyearling Chinook salmon appear to preferentially occupy these areas, which fluctuate with river stages. We estimated effects with a geospatial model and projections of future river flows. Recent (1999-2009) median river stages during peak subyearling occupancy (April-June) maximized beach shallow water area in the lower mainstem. Upstream shallow water area was maximized at lower river stages than have occurred recently. Higher river stages in April-June, resulting from increased flows predicted for the 2080s, decreased beach shallow water area 17-32%. On the basis of projected 2080s flows, more than 15% of beach shallow water area was displaced by the riprap. Beach shallow water area lost to riprap represented up to 1.6% of the total from the mouth to 12.9 km upstream. Reductions in shallow water area could restrict salmon feeding, resting, and refuge from predators and potentially reduce opportunities for the expression of the full range of life-history strategies. Although climate change analyses provided useful information, detailed analyses are prohibitive at the project scale for the multitude of small projects reviewed annually. The benefits of our approach to resource managers include a wider geographic context for reviewing similar small projects in concert with climate change, an approach to analyze cumulative effects of similar actions, and estimation of the actions' long-term effects.

Aquatic species are threatened by climate change but have received comparatively less attention thanterrestrial species.Wegleanedkey strategiesforscientistsandmanagers seekingtoaddressclimatechange in aquatic conservation planning from the literature and existing knowledge. We address 3 categories of conservation effort that rely on scientific analysis and have particular application under the U.S. Endangered Species Act (ESA): assessment of overall risk to a species; long-term recovery planning; and evaluation of effects of specific actions or perturbations. Fewer data are available for aquatic species to support these analyses, and climate effects on aquatic systems are poorly characterized. Thus, we recommend scientists conducting analyses supporting ESA decisions develop a conceptual model that links climate, habitat, ecosystem, and species response to changing conditions and use this model to organize analyses and future research. We recommend that current climate conditions are not appropriate for projections used in ESA analyses and that long-term projections of climate-change effects provide temporal context as a species-wide assessment provides spatial context. In these projections, climate change should not be discounted solely because the magnitude of projected change at a particular time is uncertain when directionality of climate change is clear. Identifying likely future habitat at the species scale will indicate key refuges and potential range shifts. However, the risks and benefits associated with errors in modeling future habitat are not equivalent. The ESA offers mechanisms for increasing the overall resilience and resistance of species to climate changes, including establishing recovery goals requiring increased genetic and phenotypic diversity, specifying critical habitat in areas not currently occupied but likely to become important, and using adaptive management.

This study considered whether different population viability analyses give similar estimates of extinction risk across management contexts. We compared the performance of population viability analyses developed by numerous scientific teams to estimate extinction risk of anadromous Pacific salmonids listed under the U.S. Endangered Species Act and challenged each analysis with data from 34 populations. We found variation in estimated extinction risk among analytical techniques, which was driven by varying model assumptions and the inherent uncertainty of risk forecasts. This result indicates that the scientific teams developed techniques that perform differently. We recommend that managers minimize uncertainty in risk estimates by using multiple models tailored to the local ecology. Assessment of relative extinction risk was less sensitive to model assumptions than was assessment of absolute extinction risk. Thus, the former method is better for comparing population status and raises caution about...

The combined effects of water diversion and climate change are a major conservation challenge for freshwater ecosystems. In the Lemhi Basin, Idaho (U.S.A.), water diversion causes changes in streamflow, and climate change will further affect streamflow and temperature. Shifts in streamflow and temperature regimes can affect juvenile salmon growth, movement, and survival. We examined the potential effects of water diversion and climate change on juvenile Chinook salmon (Oncorhynchus tshawytscha), a species listed as threatened under the U.S. Endangered Species Act (ESA). To examine the effects for juvenile survival, we created a model relating 19 years of juvenile survival data to streamflow and temperature and found spring streamflow and summer temperature were good predictors of juvenile survival. We used these models to project juvenile survival for 15 diversion and climate-change scenarios. Projected survival was 42-58% lower when streamflows were diverted than when streamflows were undiverted. For diverted streamflows, 2040 climate-change scenarios (ECHO-G and CGCM3.1 T47) resulted in an additional 11-39% decrease in survival. We also created models relating habitat carrying capacity to streamflow and made projections for diversion and climate-change scenarios. Habitat carrying capacity estimated for diverted streamflows was 17-58% lower than for undiverted streamflows. Climate-change scenarios resulted in additional decreases in carrying capacity for the dry (ECHO-G) climate model. Our results indicate climate change will likely pose an additional stressor that should be considered when evaluating the effects of anthropogenic actions on salmon population status. Thus, this type of analysis will be especially important for evaluating effects of specific actions on a particular species. Efectos Interactivos de la Desviacion del Agua y el Cambio Climatico en Individuos Juveniles de Salmon Chinook en la Cuenca del Rio Lemhi (E.U.A.).

Climate change is expected to be a top driver of global biodiversity loss in the 21st century. It poses new challenges to conserving and managing imperiled species, particularly in marine and estuarine ecosystems. The use of climate-related science in statutorily driven species management, such as under the U.S. Endangered Species Act (ESA), is in its early stages. This article provides an overview of ESA processes, with emphasis on the mandate to the National Marine Fisheries Service (NMFS) to manage listed marine, estuarine, and anadromous species. Although the ESA is specific to the United States, its requirements are broadly relevant to conservation planning. Under the ESA, species, subspecies, and "distinct population segments" may be listed as either endangered or threatened, and taking of most listed species (harassing, harming, pursuing, wounding, killing, or capturing) is prohibited unless specifically authorized via a case-by-case permit process. Government agencies, in addition to avoiding take, must ensure that actions they fund, authorize, or conduct are not likely to jeopardize a listed species' continued existence or adversely affect designated critical habitat. Decisions for which climate change is likely to be a key factor include: determining whether a species should be listed under the ESA, designating critical habitat areas, developing species recovery plans, and predicting whether effects of proposed human activities will be compatible with ESA-listed species' survival and recovery. Scientific analyses that underlie these critical conservation decisions include risk assessment, long-term recovery planning, defining environmental baselines, predicting distribution, and defining appropriate temporal and spatial scales. Although specific guidance is still evolving, it is clear that the unprecedented changes in global ecosystems brought about by climate change necessitate new information and approaches to conservation of imperiled species. El Cambio Climatico, los Ecosistemas Marinos y el Acta Estadunidense de Especies en Peligro.

Hatchery supplementation of anadromous salmon is extensive across the Pacific Northwest region with millions of juvenile salmon stocked annually. The influence of hatchery-origin fish as prey items in recipient ecosystems has been explored, but influences of these fish on broader stream nutrient dynamics has not been well-studied. Salmon-derived nutrients (SDN) associated with the mortality of adult anadromous salmon provide key subsidies to freshwater habitats. While a number of studies have estimated current and historic SDN loading from returning wild salmon, SDN contributions from the mortality of hatchery-origin juveniles (many of which die in the stream prior to emigration) remains largely unknown. We conducted a mass balance analysis of SDN input and export via hatchery activities (stocking and broodstock collection) in the Snake River watershed. Using Chinook salmon Oncorhynchus tshawytscha as a model species, we accounted for yearly SDN input (via hatchery-origin juvenile fish mortality)...

Pacific salmon Oncorhynchus spp. experience multiple small-scale disturbances throughout their freshwater habitat, but the cumulative effect of these disturbances is often not known or not easily quantifiable. One such disturbance is water diversions, which can entrain fish and alter streamflow regimes. Threatened Lemhi River (Idaho) Chinook salmon O. tshawytscha smolts encounter 41–71 water diversions during their out-migration. We used passive integrated transponder tag data to model the entrainment rate of Chinook salmon smolts as a function of the proportion of water removed by an irrigation diversion. Under median-streamflow conditions with unscreened diversions, the estimated cumulative effect of the diversions was a loss of 71.1% of out-migrating smolts due to entrainment. This is a large potential source of mortality, but screening is an effective mitigation strategy, as estimated mortality was reduced to 1.9% when all diversions were screened. If resources are limited, targeting the dive...

Rivers and their associated floodplains are among the world's most highly altered ecosystems, resulting in billions of dollars in restoration expenditures. Successful restoration of these systems requires information at multiple spatial scales (from localized reaches to broader-scale watersheds), as well as information spanning long time frames. Here, we develop a suite of historical landscape indicators of riverine status, primarily from the perspective of salmonid management, using a case study in the Interior Columbia Basin, Washington, USA. We use a combination of historical and modern aerial photography to quantify changes in land cover and reach type, as well as potential fish habitat within channel and off-channel floodplain areas. As of 1949, 55% of the Wenatchee River floodplain had been converted to agriculture. By 2006, 62% had been modified by anthropogenic development, of which 20% was due to urban expansion. The historical percentage of agricultural land in the watershed and the contemporary percentage of urban area surpass thresholds in land cover associated with deleterious impacts on river systems. In addition, the abundance of reach types associated with the highest quality salmonid habitat (island braided and meandering reaches) has declined due to conversion to straight reach types. The area occupied by fish habitats associated with channel migration (slow/stagnant channels and dry channels) has declined approximately 25-30%. Along highly modified rivers, these habitats have also become increasingly fragmented. Caveats related to visual quality and seasonal timing of historical photographs were important considerations in the interpretation of changes witnessed for headwater island braided systems, as well as for floodplain ponds. Development of rigorous, long-term, multi-scale monitoring techniques is necessary to guide the management and restoration of river-floodplain systems for the diversity of ecosystem services they provide.

Interpopulation variation in dynamics can buffer species against environmental change. We compared population synchrony in a group of threatened Chinook salmon in the highly impacted Snake River basin (Oregon, Washington, Idaho) to that in the sockeye salmon stock complex of less impact Bristol Bay (Alaska). Over the last 40 years, >90% of populations in the Snake River basin became more synchronized with one another. However, over that period, sockeye populations from Alaska did not exhibit systemic changes in synchrony. Coincident with increasing Snake River population synchrony, there was an increase in hatchery propagation and the number of large dams, potentially homogenizing habitats and populations. A simulation using economic portfolio theory revealed that synchronization of Snake River salmon decreased risk-adjusted portfolio performance (the ratio of portfolio productivity to variance) and decreased benefits of population richness. Improving portfolio performance for exploited species, especially given future environmental change, requires protecting a diverse range of populations and the varied habitats upon which they depend.

We empirically assess the relationship between population growth rate (lambda, a parameter central to ecology) and effective population size (N(e), a key parameter in evolutionary biology). Recent theoretical and numerical studies indicate that in semelparous species with variable age at maturity (such as Pacific salmon, many monocarpic plants, and various other species), differences in mean reproductive success among individuals reproducing in different years leads to variation in lambda, and this in turn can reduce N(e). However, this phenomenon has received little empirical evaluation. We examined time series of abundance data for 56 populations of chinook salmon (Onchorhynchus tshawytscha) from the northwestern United States and compared N(e) (calculated from demographic data) with the total number of spawners each generation (NT). Important results include: (1) The mean multigenerational ratio N(e)/N(T) was 0.64 (median = 0.67), indicating that annual variation in lambda reduces effective population size in chinook salmon by an average of approximately 35%. These reductions are independent of, and in addition to, factors that reduce N(e) within individual cohorts (uneven sex ratio and greater-than-random variance in reproductive success). (2) The coefficient of variation of lambda was the most important factor associated with reductions in N(e), explaining up to two-thirds of the variance in N(e)/N(T). (3) Within individual generations, N(e) was lower when there was a negative correlation between annual N(i) and lambda, i.e., when relatively few breeders produced relatively high numbers of offspring. Our results thus highlight an important and little-studied eco-evolutionary trade-off: density-dependent compensation has generally favorable ecological consequences (promoting stability and long-term viability) but incurs an evolutionary cost (reducing N(e) because a few individuals make a disproportionate genetic contribution). (4) For chinook salmon, N(eH) (an estimator based on the harmonic mean number of breeders per year) is generally a good proxy for true N(e) and requires much less data to calculate.

SUMMARY 1. A key element of conservation planning is the extremely challenging task of estimating the likely effect of restoration actions on population status. To compare the relative benefits of typical habitat restoration actions on Pacific salmon (Oncorhynchus spp.), we modelled the response of an endangered Columbia River Chinook salmon (O. tshawytscha) population to changes in habitat characteristics either targeted for restoration or with the potential to be degraded. 2. We applied a spatially explicit, multiple life stage, Beverton-Holt model to evaluate how a set of habitat variables with an empirical influence on spring-run Chinook salmon survivorship influenced fish population abundance, productivity, spatial structure and diversity. Using habitat condition scenarios – historical conditions and future conditions with restoration, no restoration, and degradation – we asked the following questions: (i) how is population status affected by alternative scenarios of habitat change, (ii) which individual habitat characteristics have the potential to substantially influence population status and (iii) which life stages have the largest impact on population status? 3. The difference in population abundance and productivities resulting from changes in modelled habitat variables from the ‘historical’ to ‘current’ scenarios suggests that there is substantial potential for improving population status. Planned restoration actions directed toward modelled variables, however, produced only modest improvements. 4. The model predicted that population status could be improved by additional restoration efforts directed toward further reductions in the percentage of fine sediments in the streambed, a factor that has a large influence on egg survival. Actions reducing fines were predicted to be especially effective outside the national forest that covers most of the basin. Scenarios that increased capacity by opening access to habitat in good condition also had a positive but smaller effect on spawner numbers. 5. Degradation in habitat quality, particularly in percent fine sediments, within stream reaches located in the national forest had great potential to further reduce this population’s viability. This finding supports current forest planning efforts to minimise road density and clear-cut harvests and to return forest stand structure in dry regions to the historical condition that promoted frequent low-intensity fires rather than catastrophic standreplacing fires, as these landscape factors have been shown to influence percent fine sediment in streams.

Summary 1. Conservation planning is often hampered by the lack of causal quantitative links between landscape characteristics, restoration actions and habitat conditions that impact the status of imperilled species. Here we present a first step toward linking actions on the landscape to the population status of endangered stream-type Chinook salmon (Oncorhynchus tshawytscha). 2. We developed relationships between land use, landscape characteristics and freshwater habitat of spring Chinook salmon in the Wenatchee River basin. Available data allowed us to find relationships that described water temperatures at several life stages (prespawning, egg incubation and summer rearing) and substratum characteristics, including fine sediments, cobble and embeddedness. Predictors included altitude, gradient, mean annual precipitation, total and riparian forest cover, road density, impervious surface and alluvium. We used a model averaging approach to account for parameter and model selection uncertainty. Key predictors were total forest cover and impervious surface area for prespawning and summer rearing temperatures; precipitation and stream gradients were important predictors of the percent of fine sediments in stream substrata. 3. We estimated habitat conditions using these relationships in three alternative landscape scenarios: historical, no restoration and one that included a set of restoration actions from local conservation planning. We found that prespawning and summer temperatures were estimated to be slightly higher historically relative to current conditions in dry sparsely forested areas, but lower in some important Chinook salmon spawning and rearing areas and lower in those locations under the restoration scenario. Fine sediments were lower in the historical scenario and were reduced as a consequence of restoration actions in two areas currently unoccupied by Chinook salmon that contain reaches with some potential for high quality spawning and rearing. Cobble and embeddedness in general were predicted to be higher historically and changed little as a result of restoration actions relative to current conditions. 4. This modelling framework converts suites of restoration actions into changes in habitat condition, thereby enabling restoration planners to evaluate alternative combinations of proposed actions. It also provides inputs to models linking habitat conditions to population status. This approach represents a first step in estimating impacts of restoration strategies, and can provide key information for conservation managers and planners.

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.

Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning.

Endangered and threatened populations of Pacific salmon (Oncorhynchus spp.) in the United States span major freshwater and marine ecosystems from southern California to northern Washington, Their wide-ranging habits and anadromous life history exposes them to a variety of risk factors and influences, including hydropower operations, ocean and freshwater harvest, habitat degradation, releases of hatchery-reared salmon, variable ocean productivity, toxic contaminants, density-dependent effects, and a suite of native and non-native predators and competitors. We review the range of analyses that form the scientific backbone of recovery plans being developed for Pacific salmon listed under the U.S. Endangered Species Act. This process involves: identifying the appropriate conservation units (demographically independent Evolutionarily Significant Units [ESUs] and their populations), developing viability criteria for Pacific salmon populations and overall ESUs, and using coarse-resolution habitat analys...

Caspian terns Sterna caspia breeding in the Columbia River estuary exploit Pacific salmon Oncorhynchus spp. as prey, consuming millions of outmigrating juvenile salmonids annually. We analyzed recoveries of salmonid passive integrated transponder (PIT) tags from the East Sand Island tern colony to calculate predation rates (% of available fish taken) on 4 Columbia and Snake River steelhead O. mykiss Evolutionarily Significant Units (ESUs). A life cycle modeling approach was used to estimate potential increases in ESU population growth rate (λ) given potential reductions in Caspian tern numbers on East Sand Island. Reducing tern predation on steelhead ESUs by 50 - 100% increased λ from 0.8 to 2.5%, depending on the ESU and the reproductive contribution of hatchery fish, and assuming no compensatory mortality. This is comparable to survival improvements modeled for hydropower improvements in the basin but less than those modeled for harvest reduc- tions. Reducing avian predation as part of an effort to reduce all sources of mortality may assist in ESU recovery. A thorough understanding of such predator-prey relationships is needed to manage conflicts between predators and their threatened and endangered Pacific salmonid prey.

Climate change is likely to lead to increasing population variability and extinction risk. Theoretically, greater population diversity should buffer against rising climate variability, and this theory is often invoked as a reason for greater conservation. However, this has rarely been quantified. Here we show how a portfolio approach to managing population diversity can inform metapopulation conservation priorities in a changing world. We develop a salmon metapopulation model in which productivity is driven by spatially distributed thermal tolerance and patterns of short- and long-term climate change. We then implement spatial conservation scenarios that control population carrying capacities and evaluate the metapopulation portfolios as a financial manager might: along axes of conservation risk and return. We show that preserving a diversity of thermal tolerances minimizes risk, given environmental stochasticity, and ensures persistence, given long-term environmental change. When the thermal tolerances of populations are unknown, doubling the number of populations conserved may nearly halve expected metapopulation variability. However, this reduction in variability can come at the expense of long-term persistence if climate change increasingly restricts available habitat, forcing ecological managers to balance society's desire for short-term stability and long-term viability. Our findings suggest the importance of conserving the processes that promote thermal-tolerance diversity, such as genetic diversity, habitat heterogeneity, and natural disturbance regimes, and demonstrate that diverse natural portfolios may be critical for metapopulation conservation in the face of increasing climate variability and change.

The viability of populations is influenced by driving forces such as density dependence and climate variability, but most population viability analyses (PVAs) ignore these factors because of data limitations. Additionally, simplified PVAs produce limited measures of population viability such as annual population growth rate (λ) or extinction risk. Here we developed a "mechanistic" PVA of threatened Chinook salmon (Oncorhynchus tshawytscha) in which, based on 40 years of detailed data, we related freshwater recruitment of juveniles to density of spawners, and third-year survival in the ocean to monthly indices of broad-scale ocean and climate conditions. Including climate variability in the model produced important effects: estimated population viability was very sensitive to assumptions of future climate conditions and the autocorrelation contained in the climate signal increased mean population abundance while increasing probability of quasi extinction. Because of the presence of density dependence in the model, however, we could not distinguish among alternative climate scenarios through mean λ values, emphasizing the importance of considering multiple measures to elucidate population viability. Our sensitivity analyses demonstrated that the importance of particular parameters varied across models and depended on which viability measure was the response variable. The density-dependent parameter associated with freshwater recruitment was consistently the most important, regardless of viability measure, suggesting that increasing juvenile carrying capacity is important for recovery.

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 determini...

Increased concern over climate change is demonstrated by the many efforts to assess climate effects and develop adaptation strategies. Scientists, resource managers, and decision makers are increasingly expected to use climate information, but they struggle with its uncertainty. With the current proliferation of climate simulations and downscaling methods, scientifically credible strategies for selecting a subset for analysis and decision making are needed. Drawing on a rich literature in climate science and impact assessment and on experience working with natural resource scientists and decision makers, we devised guidelines for choosing climate-change scenarios for ecological impact assessment that recognize irreducible uncertainty in climate projections and address common misconceptions about this uncertainty. This approach involves identifying primary local climate drivers by climate sensitivity of the biological system of interest; determining appropriate sources of information for future changes in those drivers; considering how well processes controlling local climate are spatially resolved; and selecting scenarios based on considering observed emission trends, relative importance of natural climate variability, and risk tolerance and time horizon of the associated decision. The most appropriate scenarios for a particular analysis will not necessarily be the most appropriate for another due to differences in local climate drivers, biophysical linkages to climate, decision characteristics, and how well a model simulates the climate parameters and processes of interest. Given these complexities, we recommend interaction among climate scientists, natural and physical scientists, and decision makers throughout the process of choosing and using climate-change scenarios for ecological impact assessment. Selección y Uso de Escenarios de Cambio Climático para Estudios de Impacto Ecológico y Decisiones de Conservación.

Aquatic species are threatened by climate change but have received comparatively less attention than terrestrial species. We gleaned key strategies for scientists and managers seeking to address climate change in aquatic conservation planning from the literature and existing knowledge. We address 3 categories of conservation effort that rely on scientific analysis and have particular application under the U.S. Endangered Species Act (ESA): assessment of overall risk to a species; long-term recovery planning; and evaluation of effects of specific actions or perturbations. Fewer data are available for aquatic species to support these analyses, and climate effects on aquatic systems are poorly characterized. Thus, we recommend scientists conducting analyses supporting ESA decisions develop a conceptual model that links climate, habitat, ecosystem, and species response to changing conditions and use this model to organize analyses and future research. We recommend that current climate conditions are not appropriate for projections used in ESA analyses and that long-term projections of climate-change effects provide temporal context as a species-wide assessment provides spatial context. In these projections, climate change should not be discounted solely because the magnitude of projected change at a particular time is uncertain when directionality of climate change is clear. Identifying likely future habitat at the species scale will indicate key refuges and potential range shifts. However, the risks and benefits associated with errors in modeling future habitat are not equivalent. The ESA offers mechanisms for increasing the overall resilience and resistance of species to climate changes, including establishing recovery goals requiring increased genetic and phenotypic diversity, specifying critical habitat in areas not currently occupied but likely to become important, and using adaptive management. Incorporación de las Ciencias Climáticas en las Aplicaciones del Acta Estadunidense de Especies en Peligro para Especies Acuáticas.

Climate change is expected to be a top driver of global biodiversity loss in the 21st century. It poses new challenges to conserving and managing imperiled species, particularly in marine and estuarine ecosystems. The use of climate-related science in statutorily driven species management, such as under the U.S. Endangered Species Act (ESA), is in its early stages. This article provides an overview of ESA processes, with emphasis on the mandate to the National Marine Fisheries Service (NMFS) to manage listed marine, estuarine, and anadromous species. Although the ESA is specific to the United States, its requirements are broadly relevant to conservation planning. Under the ESA, species, subspecies, and "distinct population segments" may be listed as either endangered or threatened, and taking of most listed species (harassing, harming, pursuing, wounding, killing, or capturing) is prohibited unless specifically authorized via a case-by-case permit process. Government agencies, in addition to avoiding take, must ensure that actions they fund, authorize, or conduct are not likely to jeopardize a listed species' continued existence or adversely affect designated critical habitat. Decisions for which climate change is likely to be a key factor include: determining whether a species should be listed under the ESA, designating critical habitat areas, developing species recovery plans, and predicting whether effects of proposed human activities will be compatible with ESA-listed species' survival and recovery. Scientific analyses that underlie these critical conservation decisions include risk assessment, long-term recovery planning, defining environmental baselines, predicting distribution, and defining appropriate temporal and spatial scales. Although specific guidance is still evolving, it is clear that the unprecedented changes in global ecosystems brought about by climate change necessitate new information and approaches to conservation of imperiled species. El Cambio Climático, los Ecosistemas Marinos y el Acta Estadunidense de Especies en Peligro.

Significant challenges remain in the ability to estimate habitat change under the combined effects of natural variability, climate change, and human activity. We examined anticipated effects on shallow water over low-sloped beaches to these combined effects in the lower Willamette River, Oregon, an area highly altered by development. A proposal to stabilize some shoreline with large rocks (riprap) would alter shallow water areas, an important habitat for threatened Chinook salmon (Oncorhynchus tshawytscha), and would be subject to U.S. Endangered Species Act-mandated oversight. In the mainstem, subyearling Chinook salmon appear to preferentially occupy these areas, which fluctuate with river stages. We estimated effects with a geospatial model and projections of future river flows. Recent (1999-2009) median river stages during peak subyearling occupancy (April-June) maximized beach shallow water area in the lower mainstem. Upstream shallow water area was maximized at lower river stages than have occurred recently. Higher river stages in April-June, resulting from increased flows predicted for the 2080s, decreased beach shallow water area 17-32%. On the basis of projected 2080s flows, more than 15% of beach shallow water area was displaced by the riprap. Beach shallow water area lost to riprap represented up to 1.6% of the total from the mouth to 12.9 km upstream. Reductions in shallow water area could restrict salmon feeding, resting, and refuge from predators and potentially reduce opportunities for the expression of the full range of life-history strategies. Although climate change analyses provided useful information, detailed analyses are prohibitive at the project scale for the multitude of small projects reviewed annually. The benefits of our approach to resource managers include a wider geographic context for reviewing similar small projects in concert with climate change, an approach to analyze cumulative effects of similar actions, and estimation of the actions' long-term effects. Efectos Combinados del Cambio Climático y la Estabilización de Bordes de Ríos Hábitats de Aguas Poco Profundas del Salmón Chinook.

The combined effects of water diversion and climate change are a major conservation challenge for freshwater ecosystems. In the Lemhi Basin, Idaho (U.S.A.), water diversion causes changes in streamflow, and climate change will further affect streamflow and temperature. Shifts in streamflow and temperature regimes can affect juvenile salmon growth, movement, and survival. We examined the potential effects of water diversion and climate change on juvenile Chinook salmon (Oncorhynchus tshawytscha), a species listed as threatened under the U.S. Endangered Species Act (ESA). To examine the effects for juvenile survival, we created a model relating 19 years of juvenile survival data to streamflow and temperature and found spring streamflow and summer temperature were good predictors of juvenile survival. We used these models to project juvenile survival for 15 diversion and climate-change scenarios. Projected survival was 42-58% lower when streamflows were diverted than when streamflows were undiverted. For diverted streamflows, 2040 climate-change scenarios (ECHO-G and CGCM3.1 T47) resulted in an additional 11-39% decrease in survival. We also created models relating habitat carrying capacity to streamflow and made projections for diversion and climate-change scenarios. Habitat carrying capacity estimated for diverted streamflows was 17-58% lower than for undiverted streamflows. Climate-change scenarios resulted in additional decreases in carrying capacity for the dry (ECHO-G) climate model. Our results indicate climate change will likely pose an additional stressor that should be considered when evaluating the effects of anthropogenic actions on salmon population status. Thus, this type of analysis will be especially important for evaluating effects of specific actions on a particular species. Efectos Interactivos de la Desviación del Agua y el Cambio Climático en Individuos Juveniles de Salmón Chinook en la Cuenca del Río Lemhi (E.U.A.).

Construction of four dams on the lower Snake River (in northwestern United States) between 1961 and 1975 altered salmon spawning habitat, elevated smolt and adult migration mortality, and contributed to severe declines of Snake River salmon populations. By applying a matrix model to long-term population data, we found that (i) dam passage improvements have dramatically mitigated direct mortality associated with dams; (ii) even if main stem survival were elevated to 100%, Snake River spring/summer chinook salmon ( Oncorhynchus tshawytscha) would probably continue to decline toward extinction; and (iii) modest reductions in first-year mortality or estuarine mortality would reverse current population declines.

Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning.

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.

The viability of populations is influenced by driving forces such as density dependence and climate variability, but most population viability analyses (PVAs) ignore these factors because of data limitations. Additionally, simplified PVAs produce limited measures of population viability such as annual population growth rate (lamda) or extinction risk. Here we developed a "mechanistic" PVA of threatened Chinook salmon (Oncorhynchus tshawytscha) in which, based on 40 years of detailed data, we related freshwater recruitment of juveniles to density of spawners, and third-year survival in the ocean to monthly indices of broad-scale ocean and climate conditions. Including climate variability in the model produced important effects: estimated population viability was very sensitive to assumptions of future climate conditions and the autocorrelation contained in the climate signal increased mean population abundance while increasing probability of quasi extinction. Because of the presence of density dependence in the model, however we could not distinguish among alternative climate scenarios through mean lamda values, emphasizing the importance of considering multiple measures to elucidate population viability. Our sensitivity analyses demonstrated that the importance of particular parameters varied across models and depended on which viability measure was the response variable. The density-dependent parameter associated with freshwater recruitment was consistently the most important, regardless of viability measure, suggesting that increasing juvenile carrying capacity is important for recovery.

The News Focus article “Can science rescue salmon?” by Charles C. Mann and Mark L. Plummer (4 Aug., p. [716][1]) is an admirable attempt to condense one of the nation's most complicated resource management debates into a concise, readable article. However, in its brevity the article is potentially misleading regarding several critical points. The authors give the impression that the National Marine Fisheries Service (NMFS) simply preferred the analysis performed by its own scientists over that of the general scientific community (“the fisheries agency listened to its own scientists”). In conducting the Cumulative Risk Initiative (CRI) analysis, NMFS scientists adopted a different approach than that used by the Plan for Analyzing and Testing Hypotheses (PATH) for a number of reasons. First, CRI scientists (as well as independent reviewers) were troubled by the overly optimistic results of PATH analyses. For example, PATH showed that every management option considered, including no action (that is, continuing current hydropower operations), achieves the 100-year survival standard used by PATH: no populations would go extinct. Second, whereas PATH focused on two evolutionary significant units (ESUs) in the Snake River, the CRI examined 11 ESUs across the entire Columbia Basin. By comparing the status of salmonid populations in the entire Columbia Basin, the CRI sets the stage for establishing conservation priorities. Third, the CRI is analyzing the feasibility of reversing salmon decline through a broad range of actions, which were only cursorily discussed by PATH. These feasibility studies will best be accomplished by adaptive management, which, in turn, will provide the empirical foundation for CRI. The work of the CRI has been extensively peer reviewed by the Independent Scientific Advisory Board (a panel of well-known scientists with expertise in salmon) and the editorial process of peer-reviewed journals. Finally, although Mann and Plummer include the sidebar piece about “the other H's” (harvesting, habitat degradation, and hatchery misuse) (p. [718][2]), those few words in comparison with the much longer discussion of dam breaching reinforces a pattern of Columbia Basin salmon science, which attempts to determine whether management to mitigate one isolated risk factor can eliminate the peril faced by salmon. There are too many culprits responsible for the threatened status of salmon to look for single-factor solutions. Although science may not resolve political wars and deliver the “Holy Grail,” the testing of multiple hypotheses with carefully collected data will provide a basis of what actions can rescue salmon from the brink. # {#article-title-2} Mann and Plummer portray the debate over dam removal on the Snake River as one that has divided the scientific community; however, I think that portrayal is inaccurate. As the scientist who organized a letter from more than 200 scientists in the Northwest that was sent to President Clinton in March 1999 (mentioned in Science , 23 Apr. 1999, p. [574][3]), I am convinced that the majority of scientists who are most familiar with this issue support the idea that the salmon cannot be recovered with the lower Snake River dams in place. The Idaho chapter of the American Fisheries Society (AFS) approved by a margin of 92 to 8% a resolution stating that dam removal was a necessary action if Snake River salmon are to be restored. The Oregon chapter of AFS unanimously approved a similar resolution. Perhaps George Frampton, acting chair of the White House Council on Environmental Quality, summarized the scientific debate best when he said recently, “We know that dam breaching is the single most effective thing we can do for these runs and that it may be necessary” ([1][4]). 1. [↵][5]1. E. Barker , “Breaching is last card in feds' deck,” Lewiston Morning Tribune A1 (28 Jul. 2000). # {#article-title-4} Mann and Plummer's article contains several errors and misrepresents the motivations and actions of American Rivers, a nonprofit river conservation organization that advocates bypassing four federal dams on the lower Snake River in Washington State to save imperiled salmon and steelhead runs. First, American Rivers did not and does not “scoff” at the CRI analysis. We have been working with CRI scientists to bring clarity to the scientific debate and ensure that salmon recovery efforts are grounded in the best available science. An example of such efforts was a public scientific workshop we co-sponsored with the CRI scientists to discuss areas of agreement and disagreement. Second, with Trout Unlimited, we hired Gretchen Oosterhout to critique the CRI analysis to ensure that the science informing the ultimate decision was sound, not because we saw the CRI as politically motivated. The CRI analysis was modified in response to several of her criticisms. And third, is not an American Rivers Web page, contrary to the statement in the article. This page is maintained by the Save Our Wild Salmon Coalition, of which American Rivers is one of many members. We do have our own Web site at , which contains many references to the CRI. As for the authors' statement that harvest reductions and “protecting habitat in other ways” is as likely to be effective for Snake River fall Chinook salmon leaves unanswered the critical question—effective at what? Harvest reduction may stave off extinction, but it will not result in healthy, self-sustaining fall Chinook populations. A recent study by the U.S. Geological Survey and Battelle Pacific Northwest Laboratories found that recovery of Snake River fall Chinook will require restoration of their spawning habitat in the mainstem of the Snake River, and that bypassing the four lower Snake River dams is the best way to accomplish that objective ([1][4]). The Clinton administration's draft salmon recovery plan will not result in any significant improvement in mainstem spawning habitat. There is no doubt that CRI is a positive contribution to the body of scientific information available to decision-makers developing a comprehensive recovery plan for Columbia Basin salmon. But the CRI analysis does not change the strong scientific evidence that recovering all four ESUs of imperiled Snake River salmon requires bypassing the four lower Snake River dams. In fact, it is consistent with that conclusion. 1. [↵][6]“Assessment of the impacts of development and operation of the Columbia River hydroelectric system on mainstem riverine processes and salmon habitats” (prepared by Battelle's Pacific Northwest Division, Richland, WA, and U.S. Geological Survey, Biological Resources Division, Cook, WA, for Bonneville Power Administration, Division of Fish and Wildlife, Portland, OR, June 2000). # Response {#article-title-5} Because the letter cited by Bosse was released months before either the PATH or CRI groups—the two biggest research efforts—wrote their final reports, it cannot be treated as convincing evidence of a well-informed scientific consensus. The same applies to the Idaho Fisheries Society vote in June 1999. And Frampton, also cited by Bosse, has failed to reach consensus with himself: on 12 September he told Congress that “breaching the Snake River dams may not be essential to recovering these runs, and probably would not be sufficient” ([1][4]). Regarding the letter from Hayes and Masonis, we regret attributing the remove-the-dams Web page to American Rivers. Hayes and Masonis contend that American Rivers does not “scoff” at CRI's arguments. However, the American Rivers Web site erroneously declares that the CRI concluded “dam removal alone would save endangered fall chinook and steelhead, and must also be part of any strategy designed to save endangered runs of spring/summer chinook” ([2][7]). The CRI's actual argument—that methods other than dam removal may be the best way to preserve Columbia Basin salmon—is described on the Web site as “without merit” ([3][8]). 1. [↵][9]Available at . 2. Available at . 3. Available at . [1]: /lookup/doi/10.1126/science.289.5480.716 [2]: /lookup/doi/10.1126/science.289.5480.718 [3]: /lookup/doi/10.1126/science.284.5414.574 [4]: #ref-1 [5]: #xref-ref-1-1 "View reference 1 in text" [6]: #xref-ref-2-1 "View reference 1 in text" [7]: #ref-2 [8]: #ref-3 [9]: #xref-ref-3-1 "View reference 1 in text"