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Dynamic Habitat Models for Estuary-Dependent Chinook Salmon: Informing Management in the Face of Climate Impacts

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Dynamic Habitat Models for Estuary-Dependent Chinook Salmon: Informing Management in the Face of Climate Impacts Dynamic habitat models for estuary-dependent Chinook salmon: informing management in the face of climate impacts Melanie Jeanne Davis A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2019 Reading Committee: Julian D. Olden, Co-Chair David A. Beauchamp, Co-Chair Charles A. Simenstad Program Authorized to Offer Degree: School of Aquatic and Fishery Sciences © Copyright 2019 Melanie Jeanne Davis University of Washington Abstract Dynamic habitat models for estuary-dependent Chinook salmon: informing management in the face of climate impacts Melanie Jeanne Davis Co-chairs of the Supervisory Committee: Dr. Julian D. Olden Dr. David A. Beauchamp A complex mosaic of estuarine habitats is postulated to bolster the growth and survival of juvenile Chinook salmon by diversifying the availability and configuration of prey and refugia. Consequently, efforts are underway along the North American Pacific Coast to return modified coastal ecosystems to historical or near-historical conditions, but restoring habitats are often more sensitive to anthropogenic or climate-mediated disturbance than relict (unaltered) habitats. Estuaries are expected to experience longer inundation durations as sea-levels rise, leading to reductions in intertidal emergent marshes, mudflats, and eelgrass beds. Furthermore, rising ocean temperatures may have metabolic consequences for fall-run populations of Chinook salmon, which tend to out-migrate during the spring and summer. Extensive monitoring programs have allowed managers to assess the initial benefits of management efforts (including restoration) for juvenile salmon at local and regional scales, but at present they have limited options for predicting and responding to the concurrent effects of climate change in restoring and relict coastal ecosystems. For my dissertation I addressed this gap in knowledge using a comprehensive monitoring dataset from the restoring Nisqually River Delta in southern Puget Sound, Washington. I focused on the following questions: 1) How do juvenile Chinook salmon prey consumption and dietary energy density vary throughout a mosaic of estuarine habitats, and is this variation related to differences in physiological condition? 2) How do among-habitat differences in thermal regime and prey consumption affect the bioenergetic growth potential of juvenile Chinook salmon? 3) How will shifts in the estuarine habitat mosaic vary under different sea-level rise and management scenarios? and 4) How will these climate- and management-mediated shifts in the estuarine habitat mosaic impact habitat quality for juvenile Chinook salmon? To address the first question, I used stomach content and stable isotope analyses to analyze the diets of wild and hatchery Chinook salmon captured in different estuarine habitats during the out-migration season (March–July of 2014 and 2015). I also linked measures of stomach fullness and dietary energy density to body condition. To address the second question, I used a bioenergetics model to determine how among-habitat differences in water temperature and diet might affect juvenile Chinook salmon growth. To address the third question, I designed and calibrated a marsh accretion model and decision support tool using post-restoration monitoring data sets and spatial coverages. Finally, to address the fourth question, I combined output from the marsh accretion model, a hydrological model, and measurements of prey availability into a spatially explicit version of the bioenergetics model to assess the habitat quality and growth rate potential of the entire estuarine habitat mosaic under different sea-level rise and management scenarios. When considered in tandem, these chapters represent a novel approach to habitat management. Assessments of juvenile salmon diet and physiology, marsh accretion models, and bioenergetics models have been independently implemented along the Pacific Coast, but the amalgamation of all three approaches into a single, spatially explicit analysis represents a novel and significant contribution to the scientific literature. In conducting these analyses for the Nisqually River Delta, some major themes emerged regarding the importance and vulnerability of specific habitats. An integrative diet analysis using stomach contents and stable isotopes found distinct dietary niches between wild and hatchery Chinook salmon. Wild fish were more likely to utilize the freshwater tidal forested and transitional brackish marsh habitats along the main stem river, where energy-rich insect drift made up most of their dietary biomass. The availability and consumption of insect prey resulted in distinct benefits to body condition and growth, as determined by direct physiological measurements and output from the habitat-specific bioenergetics model. These findings highlight the importance of freshwater and brackish emergent marsh habitats with overhanging vegetation, which can regulate water temperatures and supply insect drift. Unfortunately, freshwater tidal forests, brackish marshes, and low and high elevation emergent salt marshes are highly vulnerable to sea-level rise, especially when geological and anthropogenic features limit sediment accretion or lateral expansion. When spatial layers from the marsh accretion model were incorporated into the spatially explicit version of the bioenergetics model, output indicated that loss of low and high salt marsh reduced the amount of prey available for juvenile salmon, thus decreasing modeled growth rate potential. In all, these findings highlight the importance of preserving the estuarine habitat mosaic for out- migrating juvenile salmon, especially as tidal regimes and ocean temperatures continue to shift through time. TABLE OF CONTENTS List of Figures .......................................................................................................................iv List of Tables ........................................................................................................................vi Chapter 1. Coastal habitat loss and its effect on salmon in the Pacific Northwest ........1 Introduction ............................................................................................................................1 References ..............................................................................................................................5 Chapter 2. Integrated diet analyses reveal contrasting trophic niches for wild and hatchery juvenile Chinook salmon in a large river delta .................................................................9 Abstract ..................................................................................................................................9 Introduction ............................................................................................................................10 Methods..................................................................................................................................13 Study area...........................................................................................................................13 Field sampling ....................................................................................................................15 Stomach content analysis ...................................................................................................17 Stable isotope analysis .......................................................................................................18 Juvenile salmon migration patterns, body condition, and habitat use ...............................22 Results ....................................................................................................................................24 Stomach content analysis ...................................................................................................24 Stable isotope analysis .......................................................................................................25 Juvenile salmon migration patterns, body condition, and habitat use ...............................27 Discussion ..............................................................................................................................28 Acknowledgments..................................................................................................................34 References ..............................................................................................................................35 Tables .....................................................................................................................................43 Figures....................................................................................................................................48 Appendix: Additional tables and figures ...............................................................................55 Chapter 3. Freshwater tidal forests and estuarine wetlands may confer early-life growth advantages for delta-rearing Chinook Salmon .................................................................60 Abstract ..................................................................................................................................60 Introduction ............................................................................................................................61 Methods..................................................................................................................................64
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