Freshwater ecosystems respond rapidly to perturbations in climate, geomorphology, and population abundances. For migratory species in interconnected habitat networks, local habitat conditions can control the productivity of individual populations. Asynchronous variation in habitat quality can simultaneously stabilize ecological processes at broad scales but also complicate understanding of ecosystem dynamics. We investigated habitat-specific trends in indicators of the rearing capacity for juvenile sockeye salmon in a remote watershed in Alaska over the last ~60 years. The motivation of this effort was to understand if the collapse of the local salmon fishery in 2018 could be traced to changes in habitat quality within the nursery watershed. Our analyses describe high variability in the habitat conditions across both spatial and temporal scales, yet do not suggest a decline in the overall sockeye salmon rearing capacity of the watershed. We observed increasing maximum water temperatures in a shallow lake but more stable conditions in a deep lake, an improvement in zooplankton prey resources in the deep lake, and increased juvenile sockeye salmon growth rates throughout the watershed. Although we detected no long-term decline in rearing habitat quality, there was a decrease in juvenile sockeye salmon abundance from 2013-2016, suggesting high early life stage mortality prior to the period of juvenile rearing leading up to the fishery collapse.

A key challenge in ecosystem-based fisheries management is sustainably harvesting co-occurring species and populations that differ in their vulnerability to fishing. This challenge is exemplified in western Alaska Chinook salmon, where recent population declines have led to closures of in-river subsistence fisheries, but identifying the cause of these declines is limited by an inability to identify the river of origin for marine-caught fish in offshore fisheries that target more abundant species and populations. This problem is particularly acute for estimating the impacts of bycatch on individual salmon populations which have demographic independence but no genetic differentiation from which stock assignments can be made. Here we use machine learning approaches to assess the efficacy of using the microchemical history preserved in fish otoliths to assign individuals to their river of origin in western Alaska. We tested the classification ability of three machine learning algorithms (Random Forest, K-Nearest Neighbors, and Support Vector Machines) combined with two time series smoothing techniques (Moving Average and Generalized Additive Models) to classify Chinook salmon to their river of origin using otolith time series data. Model accuracy ranged from 71.9% to 92.5%, with optimal performance achieved by Random Forest applied to GAM-smoothed data. Watershed-specific performance ranged from 86.8% to 93.7%, with most misclassifications occurring between spatially proximate Kuskokwim and Nushagak rivers. Raw predicted probabilities from classification algorithms were calibrated to reflect true class probabilities, enabling the incorporation of model results into decision analyses with explicit consideration of misclassification risk tolerance. The success of these models offers immediate utility for estimating marine mortality impacts across the region’s three major river systems as well as an opportunity to understand commercial fisheries impacts on individual populations at substantially finer spatial scales than had been previously possible.

Objective Numerous populations of Pacific salmon have experienced decreased abundance and body size in the past 50 years. Ni'iinlii Njik (Fishing Branch River) in northern Yukon is the natal stream to the largest population of Chum Salmon Oncorhynchus keta in northern Canada. For over 50 years, total spawner abundance, age, sex and fork length data were collected from thousands of spawning Chum Salmon. We asked whether there were systematic changes in the body length, age, and sex ratio of spawning Chum Salmon from this population over this time frame.Methods Age, sex, and fork length were sampled from 23,906 spawning Chum Salmon, and total spawner abundance was counted over 50 years (1972-2022) from the Fishing Branch River, a tributary of the Yukon River and natal stream to the largest Chum Salmon population in northern Canada.Results Total spawner abundance has decreased significantly since the 1970s, and the average fork length of females and males declined 3.1% and 3.6%, respectively. This statistically significant decline in average length was associated with significant reductions in length at age of 4- and 5-year-old fish. Age-3 females and 6-year-old fish did not have significant declines, though they are much smaller components of the age structure. There is some indication that Chum Salmon are also maturing to spawn at earlier ages in this population, with age-4 fish increasing in relative abundance. The average age of spawners decreased from 4.6 to 4.3 years for male fish and from 4.5 to 4.2 years for female fish. These declines parallel other documented declines in body length and age of salmon in the North Pacific Ocean.Conclusions Causes for body size and abundance declines may include changing marine conditions and increased competition from hatchery and wild Pink Salmon Oncorhynchus gorbuscha and Chum Salmon across the North Pacific Ocean. Decreased body length translates into lower per-capita reproductive output, and management strategies that do not incorporate these shifting demographic characteristics may have detrimental consequences on future abundance and productivity of Chum Salmon in this and other ecosystems. Body length of Chum Salmon from the largest spawning population in northern Canada has declined since 1972. The associated decline in per-capita reproductive output has implications for understanding density-dependent population dynamics and for establishing escapement goals currently informed only by spawner abundance.

Bristol Bay supports the world’s largest fishery for sockeye salmon which are harvested during an extremely condensed time period as fish return to their natal rivers. Uncertainties in preseason forecasts of run size challenge managers and the fishing community because of limited time to adapt strategies within a season. Preseason forecast errors from 2000 to 2023 were as large as 29%, with a mean absolute % error (MAPE) of 15%. We used autoregressive models including mean size-at-age of returning sockeye salmon, along with other environmental covariates, and weighted these models by the inverse of their MAPE to produce an ensemble in-season model that was subsequently weighted with preseason forecasts. This methodology improved forecasts of run size substantially earlier in the fishing season than currently possible and had an average MAPE of 12% (∼6 million fish), approximately 1 week into the fishing season. This level of error is not met by current in-season methods until approximately 2 weeks later after the season has peaked, and is better than current preseason methods in most years.

Changes in population demographic structure can have tangible but unknown effects on management effectiveness. Fishery management of Pacific salmon is often informed by estimates of the number of spawners expected to produce maximum sustainable yield (SMSY), implicitly assuming that reproductive output per spawner does not change over time. However, many salmon populations have experienced long-term trends in age, sex and length compositions that have resulted in smaller body sizes of mature fish. We present an empirically based simulation approach for evaluating management implications of declining reproductive output resulting from shifting demographics. We simulated populations with or without demographic trends, selective or unselective harvests, and harvest policies based on assessment methods that did or did not account explicitly for demographic trends when estimating SMSY. A management strategy evaluation showed reduced expected harvests and run sizes when populations exhibited negative demographic trends. Reduced abundances and increased conservation risks (higher probability of falling below an abundance threshold) could be partially mitigated by using stock-recruitment analyses based on total egg mass instead of spawner abundance, or via precautionary management where target escapements were higher than SMSY, especially in fisheries that selectively removed large fish. Explicit accounting of demographic trends in stock-recruit analyses resulted in up to 25% higher run sizes and up to 20% lower conservation risks compared to traditional methods when trends toward smaller, younger and male-biased runs were present in the population. Conservation of population demographic structure may be critical for sustaining productive fish populations and their benefits to ecosystems and people.

Understanding the spatial ecology of migratory species is uniquely challenging using conventional approaches. In fisheries such as for Pacific salmon, genetic stock identification (GSI) and isotope‐based methods have emerged as strategies for reconstructing spatial ecology but are limited by the spatial resolution of genetic differentiation and isotopic heterogeneity. We show that integrating these complementary datasets improve the spatial resolution of provenance assignments. To do so, we reconstructed basin‐wide estimates of natal origin locations for Chinook salmon in the Yukon River using samples ( n = 247) from an experimental fishery designed to assess in‐season run timing. A combined framework improved precision of likely provenance assignments (stream km > 0.7 posterior probability) by 92% over genetic assignments and 52% over strontium isotope methods. In doing so, we illustrate watershed scale estimates of natal origin distributions with a greater resolution available from GSI or isotope data alone.

Reef-building corals are declining globally, putting important ecosystem services at risk. Here we discuss the potential risks and benefits of coral ecological replacement, in which new species are introduced to replace the functional roles of species that have declined or disappeared.

Ocean warming interacts with local stressors to negatively affect coral reefs. The adaptive capacity of reefs to survive these stressors is driven by ecological and evolutionary processes occurring at multiple spatial scales. Marine protected area (MPA) networks are one solution that can address both local and regional threats, yet the impacts of MPA network design on adaptive processes remains unclear. In this paper, we used an eco-evolutionary model to simulate hypothetical MPA configurations in the Caribbean, Southwest Pacific and Coral Triangle under projected warming. We found that protecting thermal refugia (i.e., cooler reefs) largely benefited corals inside the refugia while other reefs declined. In contrast, protecting a diverse habitat portfolio led to increased coral cover both inside and outside of the MPA network. We then quantified the thermal habitat and connectivity representations of reefs both inside and outside existing MPA networks across each region. Most strikingly, reefs in current MPA networks in the Southwest Pacific and Coral Triangle are approximately 2 degrees Celsius cooler than reefs outside the MPA networks, while the Caribbean's MPA network is approximately 1 degree Celsius warmer than reefs outside the network, based on mean temperatures from 2008-2018. These results suggest that the Caribbean MPA network is poised to protect sources of warm-adapted larvae but not destinations, and the opposite is true of the Southwest Pacific and Coral Triangle. Our results suggest that 1) by protecting sites with particular temperature and connectivity characteristics, marine spatial planning may alter eco-evolutionary processes to enhance or inhibit the adaptive capacity of a reef network and 2) the distribution, extent, and effectiveness of local interventions have the potential to affect regional distributions of coral cover beyond what would be expected from local benefits alone, due to the potentially wide-reaching effects of larval dispersal and gene flow. ### Competing Interest Statement The authors have declared no competing interest.

Freshwater mercury (Hg) contamination is a widespread environmental concern but how proximate sources and downstream transport shape Hg spatial patterns in riverine food webs is poorly understood. We measured total Hg (THg) in slimy sculpin (Cottus cognatus) across the Kuskokwim River, a large boreal river in western Alaska and home to subsistence fishing communities which rely on fish for primary nutrition. We used spatial stream network models (SSNMs) to quantify watershed and instream conditions influencing sculpin THg. Spatial covariates for local watershed geology and slope accounted for 55 % of observed variation in sculpin THg and evidence for downstream transport of Hg in sculpins was weak. Empirical semivariograms indicated these spatial covariates accounted for most spatial autocorrelation in observed THg. Watershed geology and slope explained up to 70 % of sculpin THg variation when SSNMs accounted for instream spatial dependence. Our results provide network-wide predictions for fish tissue THg based largely on publicly available geospatial data and open-source software for SSNMs, and demonstrate how these emerging models can be used to understand contaminant behavior in spatially complex aquatic ecosystems.

Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA. The targeted 16S rRNA gene (V3-V4 region) was sequenced on the Illumina NovaSeq 6000 platform. After quality control, demultiplexing and adapter trimming reads were analyzed using the DADA2 pipeline to obtain Amplicon Sequencing Variants (ASVs) which were subsequently taxonomically assigned. We found two phyla dominating the gut ecosystem present in every sample, Firmicutes and Fusobacteria, followed by lower abundances of Cyanobacteria, Proteobacteria and Bacteroidetes. At the genus level, we found high relative abundances of Cetobacterium and Clostridium sensu stricto 1. Interestingly, we did not identify often dominant genera Mycoplasma, Pseudomonas or Weisella which were prevalent in numerous studies previously, in cultured rainbow trout. Wild fish are exposed to a plethora of unpredictable environmental challenges, ranging from fluctuating water temperatures to variable food availability, as opposed to controlled conditions in production facilities. Examining and comparing the gut ecosystem of wild and reared individuals holds great potential in optimizing management practices for commercially important species. Microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention and increase sustainability in aquaculture production.

Indirect ecological effects-in which interactions of two species are modified by another species or abiotic factor-are generally considered equal to or greater in magnitude than direct effects. The ecological literature describing indirect effects suffers from redundancy and confusion regarding terminology and quantification, limiting its utility to regulators working to estimate indirect relative to direct effects in assessing environmental risks of development. To evaluate consideration for indirect ecological effects in regulatory practice, we reviewed 24 National Environmental Policy Act (NEPA) documents for proposed US mining projects to compare the treatment of indirect effects in the regulatory versus ecological literature. A clear dichotomy between regulatory and academic definitions of indirect effects suggests that NEPA documents overlook scientifically defined ecological impacts of development. Consequently, for scientific inquiry to be useful to regulators and for regulation of development to comprehensively assess risks, multidisciplinary efforts are urgently needed to bridge the gap between ecological science and environmental management.

Many lakes around the world have plankton communities that are structured by an ecological phenomenon known as size selective predation. Size selective predation is a form of predation that selects for prey of a specific desired size by the predator. Size selective predation can have an effect on both size distribution of the prey population as well as the composition of zooplankton taxa in a lake ecosystem. The overarching question being asked in this experiment is how the different zooplankton populations are affected under conditions where they are subjected to size selective predation. Within our study, we assessed the effects of size selective predation in two lakes in British Columbia, and reproduced the natural phenomenon in the lab using live zooplankton and their predators to simulate interactions in the natural world.

Declining body sizes have been documented for several species of Pacific salmon; however, whether size declines are caused mainly by ocean warming or other ecological factors, and whether they result primarily from trends in age at maturation or changing growth rates remain poorly understood. We quantified changes in mean body size and contributions from shifting size-at-age and age structure of mature sockeye salmon returning to Bristol Bay, Alaska, over the past 60 years. Mean length declined by 3%, corresponding to a 10% decline in mean body mass, since the early 1960s, though much of this decline occurred since the early 2000s. Changes in size-at-age were the dominant cause of body size declines and were more consistent than trends in age structure among the major rivers that flow into Bristol Bay. Annual variation in size-at-age was largely explained by competition among Bristol Bay sockeye salmon and interspecific competition with other salmon in the North Pacific Ocean. Warm winters were associated with better growth of sockeye salmon, whereas warm summers were associated with reduced growth. Our findings point to competition at sea as the main driver of sockeye salmon size declines, and emphasize the trade-off between fish abundance and body size.

Large wood (LW) is a critical habitat-forming feature in rivers, but our understanding of its spatial and temporal dynamics remains incomplete due to its historical removal from waterways. Few studies have the necessary spatial and temporal extent and resolution to assess wood dynamics over long time periods or in response to flood disturbance. We used an exceptional dataset from 65 km of a free-flowing coastal river in Oregon, USA, to characterize LW dynamics over a 12-year period (1989–2000). Our objectives were to assess the spatial dynamics of LW over multiple spatial scales and characterize changes in these patterns in response to a major flood in November 1996. Higher LW densities were found in the tributaries, and higher temporal variation of density existed in the main stem. Within years and among reaches, LW density varied by 2 to 3 orders of magnitude across the river. Patterns of LW accumulation across the river were not comparably different when considered at spatial resolutions < 6 km. A large flood in 1996 homogenized the wood distribution across the system, particularly at fine spatial scales (that is, 1.5–0.1 km scales), but considerable heterogeneity was reestablished within 2–3 years post disturbance. At the habitat unit scale, LW tended to accumulate in locations with narrow channel widths, and to a lesser extent, in shallow reaches. These data highlight the dynamic nature of the natural wood regime in coastal rivers that is produced by continuous recruitment and transport through the system.

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

To facilitate evolutionary adaptation to climate change, we must protect networks of coral reefs that span a range of environmental conditions - not just apparent 'refugia'.

Changing the course of Earth's climate is increasingly urgent, but there is also a concurrent need for proactive stewardship of the adaptive capacity of the rapidly changing biosphere. Adaptation ultimately underpins the resilience of Earth's complex systems; species, communities, and ecosystems shift and evolve over time. Yet oncoming changes will seriously challenge current natural resource management and conservation efforts. We review forward-looking conservation approaches to enable adaptation and resilience. Key opportunities include expanding beyond preservationist approaches by including those that enable and facilitate ecological change. Conservation should not just focus on climate change losers but also on proactive management of emerging opportunities. Local efforts to conserve biodiversity and generate habitat complexity will also help to maintain a diversity of future options for an unpredictable future.

In many watersheds, nitrogen (N)-fixing alder (Alnus spp.) provides key nutrient subsidies to terrestrial and aquatic ecosystems. The importance of these subsidies may increase as alder cover expands under climate warming at high latitudes. We assessed how landscape features and meteorological conditions affect aquatic N and phosphorus (P) availability and stoichiometry in 26 streams across natural gradients of alder cover in southwestern Alaska over the spring and summer, covering 4 years. Analyses of resin lysimeter samples from select watersheds showed that annually, soils under alder leached almost three times more N, and two times more P than under non-alder vegetation. Stream NO3− concentrations displayed a non-linear relationship with alder cover; NO3− was low where alder cover was < 30%, but increased markedly where alder cover was > 30%. Watershed elevation was inversely related to alder cover, stream NO3− concentrations, and stream NO3− yields. Dissolved and particulate stream P were unrelated to alder cover, watershed elevation or discharge, highlighting decoupling of controls on P between terrestrial and aquatic ecosystems. Snowmelt-associated nutrient pulses and hydrology likely resulted in greater stream N and P in the spring, compared to the summer. However, weather parameters only impacted stream N via their interaction with alder. Stream DIN:TP increased with alder cover and decreased with elevation, suggesting that alder intensified P-limitation. Hence, aquatic P-limitation may become increasingly pronounced as climate-induced alder expansion continues. These results demonstrate that the elevational gradient in watershed alder cover determined spatial patterns in stream N availability and nutrient limitation.

Fishery managers often rely on forecasts of future population abundance to set allowable harvest quotas or exploitation rates. While there has been substantial research devoted to identifying environmental factors that can predict recruitment for individual populations, such correlations often degrade over time, thereby limiting their utility for management. Conversely, examining multiple populations at once to detect shared, spatially structured patterns can offer insights into their recruitment dynamics that are advantageous for forecasting. Here, we develop a population dynamics model for natural origin coho salmon (Oncorhynchus kisutch) stocks in Washington State that leverages spatial and temporal autocorrelation in marine survival to improve one-year-ahead forecasts of adult returns. Executed in a Bayesian hierarchical integrated modelling framework, our spatiotemporal approach incorporates multiple data types and shares information among stocks to estimate key biological parameters that are informative for forecasting. Retrospective evaluation of one-year-ahead forecast skill indicated that the spatiotemporal integrated population model (ST-IPM) outperformed existing forecasts of Washington State coho salmon returns by 25–38 % on average. Moreover, the ST-IPM estimates parameters that were previously non-identifiable for many stocks, and propagates uncertainty from multiple contributing data sources into model forecasts. Our results add to a growing body of work demonstrating the utility of spatiotemporal and integrated approaches for modelling population dynamics, and the framework developed here has broad applications to the assessment and management of coho salmon in Washington State and elsewhere throughout their range.

Emerging evidence suggests that zooplankton production is affected by physiological and nutritional constraints due to climate change and eutrophication, which in turn could have broad implications for food-web dynamics and fish-eries production. In this study, we developed a resource-based zooplankton production dynamics model that causally links freshwater cladoceran and copepod daily production-to-biomass (P/B) ratios with water temperature, phytoplankton bio-mass and community composition, and zooplankton feeding selectivity. This model was used to evaluate constraints on zooplankton growth under four hypothetical scenarios: involving natural plankton community seasonal succession; lake fertilization to enhance fisheries production; eutrophication; and climatic warming. Our novel modeling approach predicts zooplankton production is strongly dependent on seasonal variation in resource availability and quality, which results in more complex zooplankton dynamics than predicted by simpler temperature-dependent models. For mesotrophic and hypereutrophic lakes, our study suggests that the ultimate control over zooplankton P/B ratios shifts from physiological control during colder periods to strong resource control during warmer periods. Our resource-based model provides impor-tant insights into the nature of biophysical control of zooplankton under a changing climate that has crucial implications for food web energy transfer and fisheries production.