Jeffrey C. Jorgensen

Stream temperature is a key performance driver for aquatic species and a direct metric of climate impacts. We adapted a stream temperature model to predict daily temperatures across the Pacific Northwest USA through 2100. Our results suggested that stream temperatures may rise by ~1°C by the 2050's and 2°C by the 2080's, with seasonal and geographic nuances. Snowmelt‐fed streams were especially likely to experience seasonal shifts in temperature patterns. We built local models for two watersheds to show how predictions can guide Pacific salmon conservation planning. In the North Santiam River, a Willamette River tributary in Oregon, we found that Chinook salmon and Steelhead spawners and eggs may face increasingly stressful conditions below large dams. Whereas above‐dam thermal habitat will remain or become suitable, suggesting the importance of maintaining dam passage. In the Wenatchee River, an upper Columbia River tributary in Washington, future temperatures may contribute to higher pre‐spawn mortality of Chinook salmon. Cooler thermal refuges may persist in glacial and snow‐influenced parts of the landscape, but reaching high‐elevation refuges will require migrating through warming rivers. It is essential to consider temperature patterns alongside other cumulative impacts throughout the salmon life cycle. Future stream temperature estimates can help anticipate climate‐driven habitat changes and support proactive conservation strategies for lotic species.

Life history diversity can significantly affect population dynamics and effects of management actions. For instance, variation in individual responses to environmental variability can reduce extirpation risk to populations, as the portfolio effect dampens temporal variability in abundance. Moreover, differences in habitat use may cause individuals to respond differently to habitat management and climate variability. To explore the role of life history diversity in population trajectories, population models need to incorporate within-population variation. Integrated population modeling (IPM) is a population modeling approach that offers several advantages for sharing information and propagating uncertainty across datasets. In this study, we developed an IPM for an endangered population of Chinook salmon ( Oncorhynchus tshawytscha) in the Wenatchee River, Washington, USA, that accounts for diversity in juvenile life histories, spawning location, and return age. Our analysis revealed that diversity in the age of juvenile emigration from natal streams had a portfolio effect, resulting in a 20% reduction in year-to-year variability in adult abundance in population projections. Our population viability analysis suggests that management interventions may be necessary to meet recovery goals, and our model should be useful for simulating the outcomes of proposed actions.

Differences in the life history pathways (LHPs) of juvenile animals are often associated with differences in demographic rates in later life stages. For migratory animals, different LHPs often result in animals from the same population occupying distinct habitats subjected to different environmental drivers. Understanding how demographic rates differ among animals expressing different LHPs may reveal fitness trade‐offs that drive the expression of alternative LHPs and enable better prediction of population dynamics in a changing environment. To understand how demographic outcomes and their relationships with environmental variables differ among animals with different LHPs, we analyzed a long‐term (2006–2021) mark–recapture dataset for Chinook salmon (Oncorhynchus tshawytscha) from the Wenatchee River, Washington, USA. Distinct LHPs represented in this population include either remaining in the natal stream until emigrating to the ocean as a 1‐year‐old (natal‐reach rearing) or emigrating from the natal stream and rearing in downstream habitats for several months before completing the emigration to the ocean as a 1‐year‐old (downstream rearing). We found that downstream‐rearing fish emigrated to the ocean 19 days earlier on average and returned as adults from the ocean at higher rates. We detected a positive correlation between rate of return from the ocean by downstream‐rearing fish and coastal upwelling in their spring of outmigration, whereas for natal‐reach‐rearing fish we detected a positive correlation with sea surface temperature during their first marine summer. Different responses to environmental variability should lead to asynchrony in adult abundance among juvenile LHPs. A higher proportion of downstream‐rearing fish returned at younger ages compared with natal‐reach‐rearing fish, which contributed to variability in age at reproduction and greater mixing across generations. Our results demonstrate how diversity in juvenile LHPs is associated with heterogeneity in demographic rates during subsequent life stages, which can in turn affect variance in aggregate population abundance and response to environmental change. Our findings underscore the importance of considering life history diversity in demographic analyses and provide insights into the effects of life history diversity on population dynamics and trade‐offs that contribute to the maintenance of life history diversity.

Stream temperatures in the Pacific Northwest are projected to increase with climate change, placing additional stress on cold-water salmonids. We modeled the potential impact of increased stream temperatures on four anadromous salmonid populations in the Chehalis River Basin (spring-run and fall-run Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss), as well as the potential for floodplain reconnection and stream shade restoration to offset the effects of future temperature increases. In the Chehalis River Basin, peak summer stream temperatures are predicted to increase by as much as 3°C by late-century, but restoration actions can locally decrease temperatures by as much as 6°C. On average, however, basin-wide average stream temperatures are expected to increase because most reaches have low temperature reduction potential for either restoration action relative to climate change. Results from the life cycle models indicated that, without restoration actions, increased summer temperatures are likely to produce significant declines in spawner abundance by late-century for coho (-29%), steelhead (-34%), and spring-run Chinook salmon (-95%), and smaller decreases for fall-run Chinook salmon (-17%). Restoration actions reduced these declines in all cases, although model results suggest that temperature restoration alone may not fully mitigate effects of future temperature increases. Notably, floodplain reconnection provided a greater benefit than riparian restoration for steelhead and both Chinook salmon populations, but riparian restoration provided a greater benefit for coho. This pattern emerged because coho salmon tend to spawn and rear in smaller streams where shade restoration has a larger effect on stream temperature, whereas Chinook and steelhead tend to occupy larger rivers where temperatures are more influenced by floodplain connectivity. Spring-run Chinook salmon are the only population for which peak temperatures affect adult prespawn survival in addition to rearing survival, making them the most sensitive species to increasing stream temperatures.

In the Pacific Northwest, USA, climate change is expected to result in a shift in average hydrologic conditions and increase variability. The relative vulnerabilities to peak flow changes among salmonid species within the same basin have not been widely evaluated. We assessed the impacts of predicted increases in peak flows on four salmonid populations in the Chehalis River basin. Coupling observations of peak flows, emissions projections, and multi-stage Beverton–Holt matrix-type life cycle models, we ran 100-year simulations of spawner abundance under baseline, mid-century, and late-century climate change scenarios. Coho (Oncorhynchus kisutch) and spring Chinook salmon (Oncorhynchus tshawytscha) shared the highest projected increase in interannual variability (SD = ±15%). Spring Chinook salmon had the greatest reduction in median spawner abundance (–13% to –15%), followed by coho and fall Chinook salmon (–7% to –9%), then steelhead (Oncorhynchus mykiss) (–4%). Our results show that interspecies and life history variability within a single basin is important to consider. Species with diverse age structures are partially buffered from population variability, which may increase population resilience to climate change.

An investigation into the causes of species decline should include examination of habitats important for multiple life stages. Integrating habitat impacts across life stages with life-cycle models (LCMs) can reveal habitat impairments inhibiting recovery and help guide restoration efforts. As part of the final elements of the Habitat Restoration Planning model (HARP; Beechie et al. this volume), we developed LCMs for four populations of three species of anadromous salmonids (Oncorhynchus kisutch, O. tshawytscha, and O. mykiss), and ran diagnostic scenarios to examine effects of barrier removal, fine sediment reduction, wood augmentation, riparian shade, restoration of the main channel and bank conditions, beaver pond restoration, and floodplain reconnection. In the wood scenario, spawner abundance for all populations increased moderately (29–48%). In the shade scenario, spring-run Chinook salmon abundance increased the most (48%) and fall-run Chinook salmon and steelhead were much less responsive. Coho responded strongly to the beaver pond and floodplain scenarios (76% and 54%, respectively). The fine sediment scenario most benefitted fall- and spring-run Chinook salmon (32–63%), whereas steelhead and coho were less responsive (11–21% increase). More observations are needed to understand high fine sediment and its impacts. Our LCMs were region-specific, identifying places where habitat actions had the highest potential effects. For example, the increase in spring-run Chinook salmon in the wood scenario was driven by the Cascade Mountains Ecological Region. And, although the overall response of coho salmon was small in the barrier removal scenario (6% increase at the scale of the entire basin), barrier removals had important sub-regional impacts. The HARP analysis revealed basin-wide and regional population-specific potential benefits by action types, and this habitat-based approach could be used to develop restoration strategies and guide population rebuilding. An important next step will be to ground-truth our findings with robust empirically-based estimates of life stage-specific survivals and abundances.

In the western United States, the long-term recovery of many Pacific salmon populations is inextricably linked to freshwater habitat quality. Industrial activities from the past century have left a legacy of pollutants that persist, particularly near working waterfronts. The adverse impacts of these contaminants on salmon health have been studied for decades, but the population-scale consequences of chemical exposure for salmonids are still poorly understood. We estimated acute and delayed mortality rates for seaward migrating juvenile Chinook salmon that feed and grow in a Superfund-designated area in the Lower Willamette River in Portland, Oregon. We combined previous, field-collected exposure data for juvenile Chinook salmon together with reduced growth and disease resistance data from earlier field and laboratory studies. Estimates of mortality were then incorporated into a life cycle model to explore chemical habitat-related fish loss. We found that 54% improved juvenile survival—potentially as a result of future remediation activities—could increase adult Chinook salmon population abundance by more than 20%. This study provides a framework for evaluating pollution remediation as a positive driver for species recovery.

For species of conservation concern, an essential part of the recovery planning process is identifying discrete population units and their location with respect to one another. A common feature among geographically proximate populations is that the number of organisms tends to covary through time as a consequence of similar responses to exogenous influences. In turn, high covariation among populations can threaten the persistence of the larger metapopulation. Historically, explorations of the covariance in population size of species with many (>10) time series have been computationally difficult. Here, we illustrate how dynamic factor analysis (DFA) can be used to characterize diversity among time series of population abundances and the degree to which all populations can be represented by a few common signals. Our application focuses on anadromous Chinook salmon (Oncorhynchus tshawytscha), a species listed under the US Endangered Species Act, that is impacted by a variety of natural and anthropogenic factors. Specifically, we fit DFA models to 24 time series of population abundance and used model selection to identify the minimum number of latent variables that explained the most temporal variation after accounting for the effects of environmental covariates. We found support for grouping the time series according to 5 common latent variables. The top model included two covariates: the Pacific Decadal Oscillation in spring and summer. The assignment of populations to the latent variables matched the currently established population structure at a broad spatial scale. At a finer scale, there was more population grouping complexity. Some relatively distant populations were grouped together, and some relatively close populations – considered to be more aligned with each other – were more associated with populations further away. These coarse‐ and fine‐grained examinations of spatial structure are important because they reveal different structural patterns not evident in other analyses.