Early Ocean Distribution of Juvenile Chinook Salmon in an Upwelling Ecosystem

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life-history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California (37o 30’ N) to Newport, Oregon (44o 00’ N)) for a two-week period over three summers (2010-2012). At each station, we measured chlorophyll a as an indicator of primary productivity, acoustic-based metrics of zooplankton density as an indicator of potential prey availability, and physical characteristics such as bottom depth, temperature, and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91-98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using AIC to determine which covariates influenced salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with high chlorophyll a concentration and close to an individual’s natal river. Catch abundance was primarily influenced by year, mean fork length, and proximity to natal rivers. At the scale of sampling stations, presence and abundance was not related to acoustic indices of zooplankton density. In the weeks to months following ocean entry, California’s juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets

Effects of Tag Type and Environment on Migratory Success of Sockeye Salmon (Oncorhynchus nerka) Smolts Through a Counting Fence

Understanding behavior and quantifying survival is vital to the conservation of anadromous fishes. Sockeye Salmon (Oncorhynchus nerka) are one of the most economically and culturally important fish in the world, but some populations are declining, particularly in the Fraser River watershed in British Columbia, Canada. Within the Fraser River basin, Chilko Lake is one of the most prolific Sockeye Salmon populations, and Fisheries and Oceans Canada (DFO) has operated a counting fence at the mouth of the river for several decades to enumerate outmigrating smolts. Previous studies identified the clear water landscapes immediately downstream of the fence as high-risk, with high mortality of migrating smolts relative to larger, more turbid systems further downstream. In this thesis, I used passive integrative transponder (PIT, n = 358 age-1 smolts and n = 251 age-2 smolts) and acoustic telemetry (n = 208 age-2 smolts) to assess behavior and estimate survival of Chilko Lake Sockeye Salmon smolts in the 1.3-km upstream of the counting fence. Mark-recapture Cormack-Jolly-Seber models indicate that this 1.3-km stretch of the migration is high-risk (survival ranging from 37.7% - 62.2%). Survival estimates were similar among age classes and tag types, but age-2 fish may experience slightly higher survival than age-1 fish, with age-1 fish representing ~96% of the outmigrating population. Travel duration from release to the counting fence varied widely (1.3 hours – ~18 days days), suggesting complex behavioral patterns in this specific area. After investigating several covariates, fork length, mass, and a condition metric (residuals of a mass-length relationship) appeared correlated with survival, but the directions of relationships were not consistent across age and tag types. Further investigations of fine-scale behavioral patterns revealed that it is common for smolts to make several attempts to pass the fence, potentially causing delay and a depletion of energy stores. Consistent with previous studies, I presented evidence that increased co-migrant density appears to promote successful escapement at the fence. I identified a new high-mortality landscape and showed that a counting fence used by fisheries managers annually over the past 70 years is likely negatively affecting survival and the timely passage of out-migrating smolts