In large river basins, migratory fish populations are threatened by the combination of hydropower and climate change. With river temperatures rising and hydropower development increasing globally, the longstanding monitoring programs for threatened Pacific salmon populations in the Columbia River Basin present an opportunity to study these impacts over extended time scales. We fit a statistical model to 20 years of PIT‐tagging...

Species with complex life cycles, such as anadromous fish that perform spawning migrations between freshwater and the ocean, may be particularly sensitive to global change because freshwater and marine habitats experience distinct shifts in climate and ecosystem dynamics. Abundances of wild steelhead trout ( Oncorhynchus mykiss ) have declined across most of their range over the past 40–50 years. We examined whether declines i...

Bivalves such as oysters and clams have been farmed in intertidal zones across the Puget Sound region of the Salish Sea for thousands of years. The variety of gear types used on bivalve farms creates complex vertical structure and attachment points for aquatic epiphytes and invertebrates which increases habitat structural complexity, but may alter eelgrass cover in areas where bivalve farms and eelgrass meadows overlap. Eelgra...

Long‐term research provides a unique perspective on environmental processes, dynamics of populations and communities of organisms, and emergent properties of ecosystems. Many key ecological relationships can be obscured in short term studies by common features such as time lags, natural variability, nonlinear relationships, interactive drivers, or relatively slow processes. Aquatic ecosystems have yielded major scientific disc...

Aim Spatial analysis of the distribution and density of species is of continuing interest within theoretical and applied ecology. Species distribution models (SDMs) are being increasingly used to analyse count, presence–absence and presence‐only data sets. There is a growing literature on dynamic SDMs (which incorporate temporal variation in species distribution), joint SDMs (which simultaneously analyse the correlated distrib...

Managing natural populations and communities requires detailed information regarding demographic processes at large spatial and temporal scales. This combination is challenging for both traditional scientific surveys, which often operate at localized scales, and recent citizen science designs, which often provide data with few auxiliary information (i.e., no information about individual age or condition). We therefore combine...

In recent years, returns of adult sockeye salmon O ncorhynchus nerka to the C olumbia R iver B asin have reached numbers not observed since the 1950s. To understand factors related to these increased returns, we first looked for changes in freshwater production and survival of juvenile migrants. We then evaluated productivity changes by estimating smolt‐to‐adult return rates ( SAR ) for juvenile migration years 1985–2010. We f...

Long‐term ecological data sets present opportunities for identifying drivers of community dynamics and quantifying their effects through time series analysis. Multivariate autoregressive (MAR) models are well known in many other disciplines, such as econometrics, but widespread adoption of MAR methods in ecology and natural resource management has been much slower despite some widely cited ecological examples. Here we review p...

Captive rearing and translocation are often used concurrently for species conservation, yet the effects of these practices can interact and lead to unintended outcomes that may undermine species’ recovery efforts. Controls in translocation or artificial‐propagation programs are uncommon; thus, there have been few studies on the interacting effects of these actions and environmental conditions on survival. The Columbia River ba...

Climatic effects in the ocean at the community level are poorly described, yet accurate predictions about ecosystem responses to changing environmental conditions rely on understanding biotic responses in a food‐web context to support knowledge about direct biotic responses to the physical environment. Here we conduct time‐series analyses with multivariate autoregressive ( MAR ) models of marine zooplankton abundance in the No...

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 re...

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 ( Oncorhynchu...

Effective conservation and management of natural resources requires accurate predictions of ecosystem responses to future climate change, but environmental science has largely failed to produce these reliable forecasts. The future response of Pacific salmon ( Oncorhynchus spp.) to a changing environment and continued anthropogenic disturbance is of particular interest to the public because of their high economic, social, and c...

Recent studies of lakes suggest that the relative availability of light and phosphorus in the mixed layer helps determine the quality of phytoplankton consumed by herbivorous zooplankton. In turn, increases in algal quality positively affect zooplankton growth and reproductive rates. However, these studies have concentrated on explaining variation among lakes over relatively short time periods and have not evaluated the tempor...