Joseph E. Merz

Spawning habitat rehabilitation ‐I. Conceptual approach and methods

Abstract Altered sediment and flow regimes in regulated rivers limit available spawning habitat for many fishes, especially salmonids. Mitigation efforts include spawning habitat rehabilitation and dam‐removal, but often neglect conceptual or predictive models of hydrogeomorphic and ecological processes. Complete restoration of processes necessary for maintaining spawning habitat is often unrealistic in regulated rivers. However, we present a framework for spawning habitat rehabilitation based on the premise that certain ecologic functions and geomorphic processes can be restored in a manner that facilitates testing of underlying scientific theories. SHIRA (Spawning Habitat Integrated Rehabilitation Approach) provides a science‐based, systematic framework for reach‐scale rehabilitation of salmonid spawning habitat in regulated rivers. This approach is driven by a mix of field data, conceptual models and numerical models to provide predictive and explanatory insight into the rehabilitation process. Conceptual models are advocated for developing multiple design scenarios and explicit hypotheses about hydrogeomorphic processes and ecologic functions provided by said designs. Hydrodynamic, habitat suitability and sediment entrainment models that test the potential validity of design hypotheses prior to construction are reviewed. It is presumed that the added insight would improve the outcome of rehabilitation projects and test underlying scientific theories against the rigors of real‐world uncertainties.

Evaluation of a Spawning Habitat Enhancement Site for Chinook Salmon in a Regulated California River

Abstract An evaluation of the effectiveness of a project to enhance spawning habitat for Chinook salmon Oncorhynchus tshawytscha was conducted in the Mokelumne River, a regulated stream in Californias Central Valley. Approximately 976 m3 of clean river gravel (25–150 mm) was placed in berm and gravel bar configurations along the 45-m enhancement site. Physical measurements taken before and after gravel placement indicate that the project significantly increased channel water velocities, intergravel permeability, and dissolved oxygen; reduced channel depths; and equilibrated intergravel and ambient river temperatures. These positive benefits remained throughout the 30-month monitoring period. Adult Chinook salmon began spawning at the previously unused site within 2 months after gravel placement and continued to use the site during the three spawning seasons encompassed by the study. Bed material movement was documented by channel bathymetry surveys over two water years. Topographical channel surveys prov...

Spawning habitat rehabilitation ‐ II. Using hypothesis development and testing in design, Mokelumne river, California, U.S.A.

Abstract Rehabilitation of salmonid spawning habitat in regulated rivers through spawning bed enhancement is commonly used to mitigate altered sediment and flow regimes and associated declines in salmonid communities. Partial design‐phase predictive results are reported from the application of SHIRA (Spawning Habitat Integrated Rehabilitation Approach) on the lower Mokelumne River, California. The primary management goal of the project was to improve habitat for spawning and incubation life stages of fall‐run chinook salmon (Oncorhynchus tshawytscha). In the summer of 2001, we conducted a pre‐project appraisal followed by development and testing of 12 design scenarios. A subsample of eight design hypotheses, used in three of the design scenarios, is presented. Hydrodynamic, habitat suitability and sediment entrainment model results were used to test five of the eight design hypotheses. Two of the three hypotheses not tested were due to inadequate data on flow boundary conditions at high discharges. In September 2001, the project was constructed in a 152 m reach of the LMR from a final design based on all eight of the design hypotheses presented. Transparent hypothesis development and testing in design is emphasized as opposed to declaring success or failure from an ongoing long‐term monitoring campaign of the case study presented.

Steelhead Life History on California's Central Coast: Insights from a State-Dependent Model

Abstract Steelhead Oncorhynchus mykiss display a dizzying array of life history variation (including the purely resident form, rainbow trout). We developed a model for female steelhead in coastal California (close to the southern boundary of their range) in small coastal streams. We combined proximate (physiological) and ultimate (expected reproductive success) considerations to generalize the notion of a threshold size for emigration or maturity through the development of a state-dependent life history theory. The model involves strategies that depend on age, size or condition, and recent rates of change in size or condition during specific periods (decision windows) in advance of the actual smolting or spawning event. This is the first study in which such a model is fully parameterized based on data collected entirely from California steelhead populations, the majority of data coming from two watersheds the mouths of whose rivers are separated by less than 8 km along the coast of Santa Cruz County. We p...

Salmon, Wildlife, And Wine: Marine-Derived Nutrients In Human-Dominated Ecosystems Of Central California

Pacific salmon transfer large quantities of marine-derived nutrients to adjacent forest ecosystems with profound effects on plant and wildlife production. We investigated this process for two highly modified California wine country rivers, one with consistent salmon runs (Mokelumne River) and one without (Calaveras River). Mokelumne River Chinook salmon transported biomass and N comparable to Pacific Northwest salmon streams. Calaveras River levels were much less. Scavenger numbers correlated with salmon carcass counts over time on the Mokelumne River but not the Calaveras River. Likewise, salmon carcasses were consumed significantly faster on the Mokelumne River. Native riparian vegetation as well as cultivated wine grapes adjacent to Mokelumne River spawning sites received 18-25% of foliar N from marine sources, significantly higher than vegetation along the Calaveras River. These data suggest that robust salmon runs continue to provide important ecological services with high economic value, even in impaired watersheds. Loss of Pacific salmon can not only negatively affect stream and riparian ecosystem function, but can also affect local economies where agriculture and salmon streams coexist.

State-dependent life history models in a changing (and regulated) environment: steelhead in the California Central Valley

We use a state dependent life history model to predict the life history strategies of female steelhead trout (Oncorhynchus mykiss) in altered environments. As a case study of a broadly applicable approach, we applied this model to the American and Mokelumne Rivers in central California, where steelhead are listed as threatened. Both rivers have been drastically altered, with highly regulated flows and translocations that may have diluted local adaptation. Nevertheless, evolutionary optimization models could successfully predict the life history displayed by fish on the American River (all anadromous, with young smolts) and on the Mokelumne River (a mix of anadromy and residency). The similar fitness of the two strategies for the Mokelumne suggested that a mixed strategy could be favored in a variable environment. We advance the management utility of this framework by explicitly modeling growth as a function of environmental conditions and using sensitivity analyses to predict likely evolutionary endpoints under changed environments. We conclude that the greatest management concern with respect to preserving anadromy is reduced survival of emigrating smolts, although large changes in freshwater survival or growth rates are potentially also important. We also demonstrate the importance of considering asymptotic size along with maximum growth rate.

Smolt Transformation in Two California Steelhead Populations: Effects of Temporal Variability in Growth

Abstract We tested the effect of temporal patterns in food supply on life history decisions in coastal steelhead Oncorhynchus mykiss irideus from a Central California coastal (CCC) population (Scott Creek) and a Northern California Central Valley (NCCV) population (upper Sacramento River basin). We manipulated growth through feeding experiments conducted from May to the following March using warm (2006 cohort) and cool (2007 cohort) temperature regimes. Survival in seawater challenges just before the time of typical juvenile emigration provided an index of steelhead smolt versus nonsmolt life history pathways. Survival varied significantly with fish size (with larger fish being more likely to survive than smaller fish) and by source population (with CCC steelhead being more likely to survive than NCCV steelhead of the same size). The timing of increased food supply (treatment group) did not significantly affect seawater survival rates in either NCCV or CCC steelhead. For both strains, the eventual survivo...

Contrasts in Habitat Characteristics and Life History Patterns of Oncorhynchus mykiss in California's Central Coast and Central Valley

Abstract Oncorhynchus mykiss exhibit high plasticity in their life history patterns. Individual life history decisions are hypothesized to result from genetic thresholds shaped by local adaptation, with variation in environmental factors influencing the trajectories of growth and condition (e.g., Fultons K, lipid content). We compared growth rates and life history patterns in two coastal creeks (Scott and Soquel) and two Central Valley (CV) rivers (American and Mokelumne) in California. The two regions differed markedly in habitat and physical factors, including hydrograph timing and amplitude, temperature regime, and food availability (measured as drift). Growth rates of coastal age-0 fish averaged 0.1 mm/d in summer–fall and 0.2 mm/d in winter–spring. Growth rates of CV fish were up to 10 times faster than those of fish on the coast and had the opposite seasonal pattern, in which growth in summer–fall was faster than that in winter–spring. Fish growth also differed between CV rivers; the mean growth ra...

MORPHOLOGICAL FEATURES USED TO IDENTIFY CHINOOK SALMON SEX DURING FISH PASSAGE

Abstract We compared several external morphological features for determining sex of adult fall-run chinook salmon (Oncorhynchus tschawytscha) migrating to spawning grounds in the Central Valley of California. Adult fish carcasses of known sex were measured at fish hatcheries or during angler surveys. These data were used to develop predictive morphometric discriminant function models for potential incorporation in an automated monitoring system. The best predictor for determining sex of handled fish was snout length to fork length ratio, which correctly classified 96% of individuals tested. In contrast, adipose fin length to fork length ratio was the best predictor of sex when measurements were obtained from video images at a fish passage facility. Of these fish, 86% were correctly identified. Combining both ratios with a third (head length) increased model accuracy to 92% for video images.

Effects of predator and flow manipulation on Chinook salmon (Oncorhynchus tshawytscha) survival in an imperiled estuary

We evaluated the effects of non-native, piscivorous fish removal and artificial flow manipulation on survival and migration speed of juvenile Chinook salmon, Oncorhynchus tshawytscha, emigrating through the eastern Sacramento-San Joaquin Delta of California (Delta) using a Before-After-Control-Impact study design. Acoustically-tagged salmon survival increased significantly after the first predator reduction in the impact reach. However, survival estimates returned to pre-impact levels after the second predator removal. When an upstream control gate opened (increasing flow and decreasing tidal effect) juvenile salmon emigration time decreased and survival increased significantly through the impact reach. Though a short-term, single season experiment, our results demonstrate that predator control and habitat manipulation in the Delta tidal transition zone can be effective management strategies to enhance salmon survival in this highly altered system.