Linking climate change projections for an Alaskan watershed to future coho salmon production

Developing molecular classifiers to detect environmental stressors, smolt stages and morbidity in coho salmon, Oncorhynchus kisutch

Aquatic species are increasingly confronted with environmental stressors because of climate change. Although molecular technologies have advanced our understanding of how organisms respond to stressors in laboratory settings, the ability to detect physiological responses to specific stressors under complex field conditions remains underdeveloped. This research applied multi-stressor challenge trials on coho salmon, employing the "Salmon Fit-Chips" genomic tool and a random forest-based classification model to develop classifiers predictive for chronic thermal and hypoxic stress, as well as salinity acclimation, smolt stage and morbidity status. The study also examined how smolts and de-smolts (smolts not having entered SW during the smolt window) responded transcriptionally to exposure to saltwater. Using RF classifiers optimized with 4 to 12 biomarkers, we identified transcriptional signatures that accurately predicted the presence of each stressor and physiological state, achieving prediction accuracy rates between 86.8 % and 100 %, regardless of other background stressors present. Stressor recovery time was established by placing fish back into non-stressor conditions after stress exposure, providing important context to stressor detections in field applications. Recovery from thermal and hypoxic stress requires about 3 and 2 days, respectively, with >3 days needed for re-acclimation to freshwater for seawater acclimated fish. The study also found non-additive (synergistic) effects of multiple stressors on mortality risk. Importantly, osmotic stress associated with de-smolts was the most important predictor of mortality. In saltwater, de-smolts exposed to salinity, high temperature, and hypoxia experienced a 9-fold increase in mortality compared to those only exposed to saltwater, suggesting a synergistic response to multiple stressors. These findings suggest that delays in hatchery releases to support release of larger fish need to be carefully scrutinized to ensure fish are not being released as de-smolts, which are highly susceptible to additional climate-induced stressors like rising temperatures and reduced dissolved oxygen levels in the marine environment.

Same streams in a different forest? Investigations of forest harvest legacies and future trajectories across 30 years of stream habitat monitoring on the Tongass National Forest, Alaska

The effects of timber harvest practices and climate change have altered forest ecosystems in southeast Alaska. However, quantification of patterns and trends in stream habitats associated with these forests is limited owing to a paucity of data available in remote watersheds. Here, we analyzed a 30-year dataset from southeast Alaska's Tongass National Forest to understand how these factors shape stream habitats. First, we examined differences between broad management classes (i.e., harvested and non-harvested) that have been used to guide stream channel restoration goals. Second, we assessed associations between intrinsic landscape characteristics, watershed management, and timber harvest legacies on aquatic habitat metrics. And third, we examined trends in stream habitat metrics over the duration of the dataset to anticipate future management challenges for these systems. Small effect sizes for some harvest-related predictors suggest that some stream habitat metrics, such as pool densities, are less responsive than others, and management practices such as protecting riparian buffers as well as post-harvest restoration may help conserve fish habitats. Large wood densities increased with time since harvest at sites harvested >50 years ago, indicating that multiple decades of post-harvest forest regrowth may contribute large wood to streams (possibly alder), but that it is not enough time for old-growth trees (e.g., spruce, Picea, or hemlock, Tsuga,), classified as key wood, to develop and be delivered to streams. The declining trend in key wood (i.e., the largest size class of wood) regardless of management history may reflect that pre-harvest legacy old-growth trees are declining along streams, with low replacement. The introduction of wood to maintain complex stream habitats may fill this gap until riparian stands again contribute structural key wood to streams. Trend analyses indicate an increasing spatial extent of undercut banks that may also be influenced by shifting hydrologic regimes under climate change.

Saviour A. Watershed-scale climate influences productivity of Chinook salmon populations across southcentral Alaska

The ecosystems supporting Pacific salmon (Oncorhynchus spp.) are changing rapidly as a result of climate change and habitat alteration. Understanding how-and how consistently-salmon populations respond to changes at regional and watershed scales has major implications for fisheries management and habitat conservation. Chinook salmon (O. tshawytscha) populations across Alaska have declined over the past decade, resulting in fisheries closures and prolonged impacts to local communities. These declines are associated with large-scale climate drivers, but uncertainty remains about the role of local conditions (e.g., precipitation, streamflow, and stream temperature) that vary among the watersheds where salmon spawn and rear. We estimated the effects of these and other environmental indicators on the productivity of 15 Chinook salmon populations in the Cook Inlet basin, southcentral Alaska, using a hierarchical Bayesian stock-recruitment model. Salmon spawning during 2003-2007 produced 57% fewer recruits than the previous long-term average, leading to declines in adult returns beginning in 2008. These declines were explained in part by density dependence, with reduced population productivity following years of high spawning abundance. Across all populations, productivity declined with increased precipitation during the fall spawning and early incubation period and increased with above-average precipitation during juvenile rearing. Above-average stream temperatures during spawning and rearing had variable effects, with negative relationships in many warmer streams and positive relationships in some colder streams. Productivity was also associated with regional indices of streamflow and ocean conditions, with high variability among populations. The cumulative effects of adverse conditions in freshwater, including high spawning abundance, heavy fall rains, and hot, dry summers may have contributed to the recent population declines across the region. Identifying both coherent and differential responses to environmental change underscores the importance of targeted, watershed-specific monitoring and conservation efforts for maintaining resilient salmon runs in a warming world.

The interactive effects of climate change and land use on boreal stream fish communities

Ongoing and projected climate change is likely to greatly alter co-occurring stressor mechanisms, yet these potential interactions remain poorly understood in natural freshwater systems worldwide. As the global biodiversity crisis deepens, successful conservation efforts will hinge on developing mechanistic multiple stressor frameworks that have been ground-truthed in natural systems containing complex species dynamics and ecological processes. Our study examined the combined and interacting effects of potential climate and land use stressors on boreal stream fishes using data from over 300 catchments across a broad 250,000 km² region. To characterize boreal fish community health, we examined four indicators including species richness, total catch per unit effort, the proportion of lithophilic spawners (fish sensitive to sedimentation), and the assemblage tolerance index which provides a measurement of the overall community tolerance to disturbance. Land use stressors included total anthropogenic land use area and linear disturbance at multiple watershed scales as well as two site-specific habitat degradation indicators (dissolved oxygen and the proportion of fine substrate). Overall community richness and productivity were not negatively related to land use changes indicating potential compensatory dynamics (e.g. where intolerant species are replaced with more tolerant species as habitat quality degrades). In contrast, we observed declines for sensitive species, including highly valued salmonids, that varied depending on interactions between local climate, land use, and stream type. Sensitive species declines were concentrated in regions experiencing increased land use and warming, whereas increases were observed in cooler regions consistent with a subsidy-stress response. In addition, lithophilic spawners declined in watersheds experiencing warmer and wetter conditions owing to potential indirect effects on spawning habitat quality. Results from our study provide novel insight into complex climate and land use interactions occurring across a broad, real-world landscape, and highlight the potential for amplified species declines under future warming and land use scenarios.

Modelling climate change effects on Atlantic salmon: Implications for mitigation in regulated rivers

Climate change is expected to alter future temperature and discharge regimes of rivers. These regimes have a strong influence on the life history of most aquatic river species, and are key variables controlling the growth and survival of Atlantic salmon. This study explores how the future abundance of Atlantic salmon may be influenced by climate-induced changes in water temperature and discharge in a regulated river, and investigates how negative impacts in the future can be mitigated by applying different regulated discharge regimes during critical periods for salmon survival. A spatially explicit individual-based model was used to predict juvenile Atlantic salmon population abundance in a regulated river under a range of future water temperature and discharge scenarios (derived from climate data predicted by the Hadley Centre's Global Climate Model (GCM) HadAm3H and the Max Plank Institute's GCM ECHAM4), which were then compared with populations predicted under control scenarios representing past conditions. Parr abundance decreased in all future scenarios compared to the control scenarios due to reduced wetted areas (with the effect depending on climate scenario, GCM, and GCM spatial domain). To examine the potential for mitigation of climate change-induced reductions in wetted area, simulations were run with specific minimum discharge regimes. An increase in abundance of both parr and smolt occurred with an increase in the limit of minimum permitted discharge for three of the four GCM/GCM spatial domains examined. This study shows that, in regulated rivers with upstream storage capacity, negative effects of climate change on Atlantic salmon populations can potentially be mitigated by release of water from reservoirs during critical periods for juvenile salmon.

Projecting species' vulnerability to climate change: Which uncertainty sources matter most and extrapolate best?

Species distribution models (SDMs) are commonly used to assess potential climate change impacts on biodiversity, but several critical methodological decisions are often made arbitrarily. We compare variability arising from these decisions to the uncertainty in future climate change itself. We also test whether certain choices offer improved skill for extrapolating to a changed climate and whether internal cross‐validation skill indicates extrapolative skill. We compared projected vulnerability for 29 wetland‐dependent bird species breeding in the climatically dynamic Prairie Pothole Region, USA. For each species we built 1,080 SDMs to represent a unique combination of: future climate, class of climate covariates, collinearity level, and thresholding procedure. We examined the variation in projected vulnerability attributed to each uncertainty source. To assess extrapolation skill under a changed climate, we compared model predictions with observations from historic drought years. Uncertainty in projected vulnerability was substantial, and the largest source was that of future climate change. Large uncertainty was also attributed to climate covariate class with hydrological covariates projecting half the range loss of bioclimatic covariates or other summaries of temperature and precipitation. We found that choices based on performance in cross‐validation improved skill in extrapolation. Qualitative rankings were also highly uncertain. Given uncertainty in projected vulnerability and resulting uncertainty in rankings used for conservation prioritization, a number of considerations appear critical for using bioclimatic SDMs to inform climate change mitigation strategies. Our results emphasize explicitly selecting climate summaries that most closely represent processes likely to underlie ecological response to climate change. For example, hydrological covariates projected substantially reduced vulnerability, highlighting the importance of considering whether water availability may be a more proximal driver than precipitation. However, because cross‐validation results were correlated with extrapolation results, the use of cross‐validation performance metrics to guide modeling choices where knowledge is limited was supported.

Stream network geomorphology mediates predicted vulnerability of anadromous fish habitat to hydrologic change in southeast Alaska

In rivers supporting Pacific salmon in southeast Alaska, USA, regional trends toward a warmer, wetter climate are predicted to increase mid- and late-21st-century mean annual flood size by 17% and 28%, respectively. Increased flood size could alter stream habitats used by Pacific salmon for reproduction, with negative consequences for the substantial economic, cultural, and ecosystem services these fish provide. We combined field measurements and model simulations to estimate the potential influence of future flood disturbance on geomorphic processes controlling the quality and extent of coho, chum, and pink salmon spawning habitat in over 800 southeast Alaska watersheds. Spawning habitat responses varied widely across watersheds and among salmon species. Little variation among watersheds in potential spawning habitat change was explained by predicted increases in mean annual flood size. Watershed response diversity was mediated primarily by topographic controls on stream channel confinement, reach-scale geomorphic associations with spawning habitat preferences, and complexity in the pace and mode of geomorphic channel responses to altered flood size. Potential spawning habitat loss was highest for coho salmon, which spawn over a wide range of geomorphic settings, including steeper, confined stream reaches that are more susceptible to streambed scour during high flows. We estimated that 9-10% and 13-16% of the spawning habitat for coho salmon could be lost by the 2040s and 2080s, respectively, with losses occurring primarily in confined, higher-gradient streams that provide only moderate-quality habitat. Estimated effects were lower for pink and chum salmon, which primarily spawn in unconfined floodplain streams. Our results illustrate the importance of accounting for valley and reach-scale geomorphic features in watershed assessments of climate vulnerability, especially in topographically complex regions. Failure to consider the geomorphic context of stream networks will hamper efforts to understand and mitigate the vulnerability of anadromous fish habitat to climate-induced hydrologic change.

Hydrologic Alterations from Climate Change Inform Assessment of Ecological Risk to Pacific Salmon in Bristol Bay, Alaska

We developed an integrated hydrologic model of the upper Nushagak and Kvichak watersheds in the Bristol Bay region of southwestern Alaska, a region under substantial development pressure from large-scale copper mining. We incorporated climate change scenarios into this model to evaluate how hydrologic regimes and stream temperatures might change in a future climate, and to summarize indicators of hydrologic alteration that are relevant to salmon habitat ecology and life history. Model simulations project substantial changes in mean winter flow, peak flow dates, and water temperature by 2100. In particular, we find that annual hydrographs will no longer be dominated by a single spring thaw event, but will instead be characterized by numerous high flow events throughout the winter. Stream temperatures increase in all future scenarios, although these temperature increases are moderated relative to air temperatures by cool baseflow inputs during the summer months. Projected changes to flow and stream temperature could influence salmon through alterations in the suitability of spawning gravels, changes in the duration of incubation, increased growth during juvenile stages, and increased exposure to chronic and acute temperature stress. These climate-modulated changes represent a shifting baseline in salmon habitat quality and quantity in the future, and an important consideration to adequately assess the types and magnitude of risks associated with proposed large-scale mining in the region.