The contribution of estuary-resident life histories to the return of adult Oncorhynchus kisutch

Physiological condition infers habitat choice in juvenile sockeye salmon

The amount of time that juvenile salmon remain in an estuary varies among and within populations, with some individuals passing through their estuary in hours while others remain in the estuary for several months. Underlying differences in individual physiological condition, such as body size, stored energy and osmoregulatory function, could drive individual variation in the selection of estuary habitat. Here we investigated the role of variation in physiological condition on the selection of estuarine and ocean habitat by sockeye salmon (Oncorhynchus nerka) smolts intercepted at the initiation of their 650-km downstream migration from Chilko Lake, Fraser River, British Columbia (BC). Behavioural salinity preference experiments were conducted on unfed smolts held in fresh water at three time intervals during their downstream migration period, representing the stage of migration at lake-exit, and the expected timing for estuary-entry and ocean-entry (0, 1 and 3 weeks after lake-exit, respectively). In general, salinity preference behaviour varied across the three time periods consistent with expected transition from river to estuary to ocean. Further, individual physiological condition did influence habitat choice. Smolt condition factor (K) and energy density were positively correlated with salinity preference behaviour in the estuary and ocean outmigration stages, but not at lake-exit. Our results suggest that smolt physiological condition upon reaching the estuary could influence migratory behaviour and habitat selection. This provides evidence on the temporally dependent interplay of physiology, behaviour and migration in wild juvenile Pacific salmon, with juvenile rearing conditions influencing smolt energetic status, which in turn influences habitat choice during downstream migration. The implication for the conservation of migratory species is that the relative importance of stopover habitats may vary as a function of initial condition.

An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories"

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., "PST"), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life-history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life-history traits. Life history is generally used in organismal- and ecology-based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic- and evolution-based journals. "Satellite species" is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life-history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

Applying cumulative effects to strategically advance large-scale ecosystem restoration

International efforts to restore degraded ecosystems will continue to expand over the coming decades, yet the factors contributing to the effectiveness of long-term restoration across large areas remain largely unexplored. At large scales, outcomes are more complex and synergistic than the additive impacts of individual restoration projects. Here, we propose a cumulative-effects conceptual framework to inform restoration design and implementation and to comprehensively measure ecological outcomes. To evaluate and illustrate this approach, we reviewed long-term restoration in several large coastal and riverine areas across the US: the greater Florida Everglades; Gulf of Mexico coast; lower Columbia River and estuary; Puget Sound; San Francisco Bay and Sacramento-San Joaquin Delta; Missouri River; and northeastern coastal states. Evidence supported eight modes of cumulative effects of interacting restoration projects, which improved outcomes for species and ecosystems at landscape and regional scales. We conclude that cumulative effects, usually measured for ecosystem degradation, are also measurable for ecosystem restoration. The consideration of evidence-based cumulative effects will help managers of large-scale restoration capitalize on positive feedback and reduce countervailing effects.

Impact of multiple stressors on juvenile fish in estuaries of the northeast Pacific

A key step in identifying global change impacts on species and ecosystems is to quantify effects of multiple stressors. To date, the science of global change has been dominated by regional field studies, experimental manipulation, meta-analyses, conceptual models, reviews, and studies focusing on a single stressor or species over broad spatial and temporal scales. Here, we provide one of the first studies for coastal systems examining multiple stressor effects across broad scales, focused on the nursery function of 20 estuaries spanning 1,600 km of coastline, 25 years of monitoring, and seven fish and invertebrate species along the northeast Pacific coast. We hypothesized those species most estuarine dependent and negatively impacted by human activities would have lower presence and abundances in estuaries with greater anthropogenic land cover, pollution, and water flow stress. We found significant negative relationships between juveniles of two of seven species (Chinook salmon and English sole) and estuarine stressors. Chinook salmon were less likely to occur and were less abundant in estuaries with greater pollution stress. They were also less abundant in estuaries with greater flow stress, although this relationship was marginally insignificant. English sole were less abundant in estuaries with greater land cover stress. Together, we provide new empirical evidence that effects of stressors on two fish species culminate in detectable trends along the northeast Pacific coast, elevating the need for protection from pollution, land cover, and flow stressors to their habitats. Lack of response among the other five species could be related to differing resistance to specific stressors, type and precision of the stressor metrics, and limitations in catch data across estuaries and habitats. Acquiring improved measurements of impacts to species will guide future management actions, and help predict how estuarine nursery functions can be optimized given anthropogenic stressors and climate change scenarios.

An expert panel process to evaluate habitat restoration actions in the Columbia River estuary

We describe a process for evaluating proposed ecosystem restoration projects intended to improve survival of juvenile salmon in the Columbia River estuary (CRE). Changes in the Columbia River basin (northwestern USA), including hydropower development, have contributed to the listing of 13 salmon stocks as endangered or threatened under the U.S. Endangered Species Act. Habitat restoration in the CRE, from Bonneville Dam to the ocean, is part of a basin-wide, legally mandated effort to mitigate federal hydropower impacts on salmon survival. An Expert Regional Technical Group (ERTG) was established in 2009 to improve and implement a process for assessing and assigning "survival benefit units" (SBUs) to restoration actions. The SBU concept assumes site-specific restoration projects will increase juvenile salmon survival during migration through the 234 km CRE. Assigned SBUs are used to inform selection of restoration projects and gauge mitigation progress. The ERTG standardized the SBU assessment process to improve its scientific integrity, repeatability, and transparency. In lieu of experimental data to quantify the survival benefits of individual restoration actions, the ERTG adopted a conceptual model composed of three assessment criteria-certainty of success, fish opportunity improvements, and habitat capacity improvements-to evaluate restoration projects. Based on these criteria, an algorithm assigned SBUs by integrating potential fish density as an indicator of salmon performance. Between 2009 and 2014, the ERTG assessed SBUs for 55 proposed projects involving a total of 181 restoration actions located across 8 of 9 reaches of the CRE, largely relying on information provided in a project template based on the conceptual model, presentations, discussions with project sponsors, and site visits. Most projects restored tidal inundation to emergent wetlands, improved riparian function, and removed invasive vegetation. The scientific relationship of geomorphic and salmonid responses to restoration actions remains the foremost concern. Although not designed to establish a broad strategy for estuary restoration, the scoring process has adaptively influenced the types, designs, and locations of restoration proposals. The ERTG process may be a useful model for others who have unique ecosystem restoration goals and share some of our common challenges.

Linking Hydroclimate to Fish Phenology and Habitat Use with Ichthyographs

Streamflow and water temperature (hydroclimate) influence the life histories of aquatic biota. The relationship between streamflow and temperature varies with climate, hydrogeomorphic setting, and season. Life histories of native fishes reflect, in part, their adaptation to regional hydroclimate (flow and water temperature), local habitats, and natural disturbance regimes, all of which may be affected by water management. Alterations to natural hydroclimates, such as those caused by river regulation or climate change, can modify the suitability and variety of in-stream habitat for fishes throughout the year. Here, we present the ichthyograph, a new empirically-based graphical tool to help visualize relationships between hydroclimate and fish phenology. Generally, this graphical tool can be used to display a variety of phenotypic traits. We used long-term data sets of daily fish passage to examine linkages between hydroclimate and the expression of life-history phenology by native fishes. The ichthyograph may be used to characterize the environmental phenology for fishes across multiple spatio-temporal domains. We illustrate the ichthyograph in two applications to visualize: 1) river use for the community of fishes at a specific location; and 2) stream conditions at multiple locations within the river network for one species at different life-history stages. The novel, yet simple, ichthyograph offers a flexible framework to enable transformations in thinking regarding relationships between hydroclimate and aquatic species across space and time. The potential broad application of this innovative tool promotes synergism between assessments of physical characteristics and the biological needs of aquatic species.

Adaptive management of large aquatic ecosystem recovery programs in the United States

Adaptive management (AM) is being employed in a number of programs in the United States to guide actions to restore aquatic ecosystems because these programs are both expensive and are faced with significant uncertainties. Many of these uncertainties are associated with prioritizing when, where, and what kind of actions are needed to meet the objectives of enhancing ecosystem services and recovering threatened and endangered species. We interviewed nine large-scale aquatic ecosystem restoration programs across the United States to document the lessons learned from implementing AM. In addition, we recorded information on ecological drivers (e.g., endangered fish species) for the program, and inferred how these drivers reflected more generic ecosystem services. Ecosystem services (e.g., genetic diversity, cultural heritage), albeit not explicit drivers, were either important to the recovery or enhancement of the drivers, or were additional benefits associated with actions to recover or enhance the program drivers. Implementing programs using AM lessons learned has apparently helped achieve better results regarding enhancing ecosystem services and restoring target species populations. The interviews yielded several recommendations. The science and AM program must be integrated into how the overall restoration program operates in order to gain understanding and support, and effectively inform management decision-making. Governance and decision-making varied based on its particular circumstances. Open communication within and among agency and stakeholder groups and extensive vetting lead up to decisions. It was important to have an internal agency staff member to implement the AM plan, and a clear designation of roles and responsibilities, and long-term commitment of other involved parties. The most important management questions and information needs must be identified up front. It was imperative to clearly identify, link and continually reinforce the essential components of an AM plan, including objectives, constraints, uncertainties, hypotheses, management actions, decision criteria and triggers, monitoring, and research. Some employed predictive models and the results of research on uncertainties to vet options for actions. Many relied on best available science and professional judgment to decide if adjustments to actions were needed. All programs emphasized the need to be nimble enough to be responsive to new information and make necessary adjustments to management action implementation. We recommend that ecosystem services be explicit drivers of restoration programs to facilitate needed funding and communicate to the general public and with the global efforts on restoring and conserving ecosystems.

Food Shortage Causes Differential Effects on Body Composition and Tissue-Specific Gene Expression in Salmon Modified for Increased Growth Hormone Production

Growth hormone (GH) transgenic salmon possesses markedly increased metabolic rate, appetite, and feed conversion efficiency, as well as an increased ability to compete for food resources. Thus, the ability of GH-transgenic fish to withstand periods of food deprivation as occurs in nature is potentially different than that of nontransgenic fish. However, the physiological and genetic effects of transgenic GH production over long periods of food deprivation remain largely unknown. Here, GH-transgenic coho salmon (Oncorhynchus kisutch) and nontransgenic, wild-type coho salmon were subjected to a 3-month food deprivation trial, during which time performance characteristics related to growth were measured along with proximate compositions. To examine potential genetic effects of GH-transgenesis on long-term food deprivation, a group of genes related to muscle development and liver metabolism was selected for quantitative PCR analysis. Results showed that GH-transgenic fish lose weight at an increased rate compared to wild-type even though proximate compositions remained relatively similar between the groups. A total of nine genes related to muscle physiology (cathepsin, cee, insulin-like growth factor, myostatin, murf-1, myosin, myogenin, proteasome delta, tumor necrosis factor) and five genes related to liver metabolism (carnitine palmitoyltransferase, fatty acid synthase, glucose-6-phosphatase, glucose-6-phosphate dehydrogenase, glucokinase) were shown to be differentially regulated between GH-transgenic and wild-type coho salmon over time. These genetic and physiological responses assist in identifying differences between GH-transgenic and wild-type salmon in relation to fitness effects arising from elevated growth hormone during periods of long-term food shortage.

Rearing in natural and recovering tidal wetlands enhances growth and life-history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch population

This study provides evidence of the importance of tributary tidal wetlands to local coho salmon Oncorhynchus kisutch populations and life-history diversity. Subyearling and, to a lesser extent, yearling O. kisutch life histories utilized various estuary habitats within the Grays River, a tidal freshwater tributary of the Columbia River estuary, including restoring emergent wetlands and natural forested wetlands. Migration timing data, size distributions, estuary residence and scale patterns suggest a predominance of subyearling migrant life histories, including several that involve extended periods of estuary rearing. Estuarine-rearing subyearling O. kisutch exhibited the greatest overall growth rates; the highest growth rates were seen in fish that utilized restoring emergent wetlands. These results contrast with studies conducted in the main-stem Columbia River estuary, which captured few O. kisutch, of which nearly all were hatchery-origin yearling smolts. Restoration and preservation of peripheral and tributary wetland habitats, such as those in the Grays River, could play an important role in the recovery of natural O. kisutch populations in the Columbia River and elsewhere.