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

Accuracy of ARGOS Locations of Pinnipeds at-Sea Estimated Using Fastloc GPS

Background: ARGOS satellite telemetry is one of the most widely used methods to track the movements of free-ranging marine and terrestrial animals and is fundamental to studies of foraging ecology, migratory behavior and habitat-use. ARGOS location estimates do not include complete error estimations, and for many marine organisms, the most commonly acquired locations (Location Class 0, A, B, or Z) are provided with no declared error estimate.Methodology/Principal Findings: We compared the accuracy of ARGOS locations to those obtained using Fastloc GPS from the same electronic tags on five species of pinnipeds: 9 California sea lions (Zalophus californianus), 4 Galapagos sea lions (Zalophus wollebaeki), 6 Cape fur seals (Arctocephalus pusillus pusillus), 3 Australian fur seals (A. p. doriferus) and 5 northern elephant seals (Mirounga angustirostris). These species encompass a range of marine habitats (highly pelagic vs coastal), diving behaviors (mean dive durations 2&ndash;21 min) and range of latitudes (equator to temperate). A total of 7,318 ARGOS positions and 27,046 GPS positions were collected. Of these, 1,105 ARGOS positions were obtained within five minutes of a GPS position and were used for comparison. The 68th percentile ARGOS location errors as measured in this study were LC-30.49 km, LC-2 1.01 km, LC-1 1.20 km, LC-0 4.18 km, LC-A 6.19 km, LC-B 10.28 km. Conclusions/Significance: The ARGOS errors measured here are greater than those provided by ARGOS, but within the range of other studies. The error was non-normally distributed with each LC highly right-skewed. Locations of species that make short duration dives and spend extended periods on the surface (sea lions and fur seals) had less error than species like elephant seals that spend more time underwater and have shorter surface intervals. Supplemental data (S1) are provided allowing the creation of density distributions that can be used in a variety of filtering algorithms to improve the quality of ARGOS tracking data.<br /

Foraging Behavior and Success of a Mesopelagic Predator in the Northeast Pacific Ocean: Insights from a Data-Rich Species, the Northern Elephant Seal

The mesopelagic zone of the northeast Pacific Ocean is an important foraging habitat for many predators, yet few studies have addressed the factors driving basin-scale predator distributions or inter-annual variability in foraging and breeding success. Understanding these processes is critical to reveal how conditions at sea cascade to population-level effects. To begin addressing these challenging questions, we collected diving, tracking, foraging success, and natality data for 297 adult female northern elephant seal migrations from 2004 to 2010. During the longer post-molting migration, individual energy gain rates were significant predictors of pregnancy. At sea, seals focused their foraging effort along a narrow band corresponding to the boundary between the sub-arctic and sub-tropical gyres. In contrast to shallow-diving predators, elephant seals target the gyre-gyre boundary throughout the year rather than follow the southward winter migration of surface features, such as the Transition Zone Chlorophyll Front. We also assessed the impact of added transit costs by studying seals at a colony near the southern extent of the species’ range, 1,150 km to the south. A much larger proportion of seals foraged locally, implying plasticity in foraging strategies and possibly prey type. While these findings are derived from a single species, the results may provide insight to the foraging patterns of many other meso-pelagic predators in the northeast Pacific Ocean

Cumulative human impacts on marine predators

Stressors associated with human activities interact in complex ways to affect marine ecosystems, yet we lack spatially explicit assessments of cumulative impacts on ecologically and economically key components such as marine predators. Here we develop a metric of cumulative utilization and impact (CUI) on marine predators by combining electronic tracking data of eight protected predator species (n=685 individuals) in the California Current Ecosystem with data on 24 anthropogenic stressors. We show significant variation in CUI with some of the highest impacts within US National Marine Sanctuaries. High variation in underlying species and cumulative impact distributions means that neither alone is sufficient for effective spatial management. Instead, comprehensive management approaches accounting for both cumulative human impacts and trade-offs among multiple stressors must be applied in planning the use of marine resources

Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California

Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta. We use a quantile regression forest approach to create a risk forecasting tool, which can inform adjustments of diversions based on near real-time predictions. Models were trained using historical entrainment data (Water Years 1999–2019) for Sacramento River winter-run Chinook Salmon or Central Valley Steelhead and a suite of environmental and water operations metrics. A range of models was developed; their performance was evaluated by comparison of a quantile loss metric. The models were validated through examination of partial dependence plots, cross-validation procedures, and further evaluated through WY 2019 pilot testing, which integrated real-world uncertainty in environmental parameters into model predictions. For both species, the strongest predictor of loss was the previous week’s entrainment loss. In addition, risk increased with higher water exports and more negative Old and Middle Rivers (OMR) flows. Point estimates of loss were modestly correlated with observations (R2 0.4 to 0.6), but the use of a quantile regression approach provided reliable prediction intervals. For both species, the predicted 75th quantile appears to be a robust and conservative estimator of entrainment risk, with overprediction occurring in fewer than 20% of cases. This quantile balances the magnitude of over- and under-prediction and results in a low probability (&lt; 5% of predictions) of unexpected high-take events. These models, and the web-based application through which they are made accessible to non-technical users, can provide a useful and complementary approach to the current system of managing entrainment risk

From drought to deluge: spatiotemporal variation in migration routing, survival, travel time and floodplain use of an endangered migratory fish

We developed a novel statistical model to relate the daily survival and migration dynamics of an endangered anadromous fish to river flow and water temperature during both extreme drought and severe flooding in an intensively managed river system. Our Bayesian temporally stratified multistate mark recapture model integrates over unobserved travel times and route transitions to efficiently estimate covariate relationships and includes an adjustment for telemetry tag battery failure. We applied the model to acoustic-tagged juvenile Sacramento river winter-run Chinook salmon (Oncorhynchus tshawytscha) and found that survival decreased with decreasing river flows and increased water temperatures. We found that fish were likely to enter at a large floodplain during flood conditions and that survival in floodplain was comparable to the mainstem Sacramento river. Our study demonstrates the response of an endangered anadromous fish population to extreme spatial and temporal variability in habitat accessibility and quality. The general model framework we introduce here can be applied to telemetry of migratory fish through systems with multiple routes to efficiently estimate spatiotemporal variation in survival, travel time, and routing.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) North of the San Francisco Estuary

Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the SFE at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a metapopulation. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River and detected no Longfin Smelt in the Klamath and Mad Rivers, while in the dry winter of 2020, we detected larvae in two additional estuaries. Elevated freshwater outflow in 2019 possibly increased transport rates to sea, resulting in observed low larval recruitment. Our results sugget that, although populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under sampled or are not permanently inhabited by Longfin Smelt. Longfin Smelt in the SFE may therefore lack resilience normally afforded by metapopulations. Increased monitoring over their coastal range under varying hydrologic conditions is needed to assess gene flow between populations

Effects of age, adipose percent, and reproduction on PCB concentrations and profiles in an extreme fasting North Pacific marine mammal.

Persistent organic pollutants, including polychlorinated biphenyls (PCBs), are widely distributed and detectable far from anthropogenic sources. Northern elephant seals (Mirounga angustirostris) biannually travel thousands of kilometers to forage in coastal and open-ocean regions of the northeast Pacific Ocean and then return to land where they fast while breeding and molting. Our study examined potential effects of age, adipose percent, and the difference between the breeding and molting fasts on PCB concentrations and congener profiles in blubber and serum of northern elephant seal females. Between 2005 and 2007, we sampled blubber and blood from 58 seals before and after a foraging trip, which were then analyzed for PCBs. Age did not significantly affect total PCB concentrations; however, the proportion of PCB congeners with different numbers of chlorine atoms was significantly affected by age, especially in the outer blubber. Younger adult females had a significantly greater proportion of low-chlorinated PCBs (tri-, tetra-, and penta-CBs) than older females, with the opposite trend observed for hepta-CBs, indicating that an age-associated process such as parity (birth) may significantly affect congener profiles. The percent of adipose tissue had a significant relationship with inner blubber PCB concentrations, with the highest mean concentrations observed at the end of the molting fast. These results highlight the importance of sampling across the entire blubber layer when assessing contaminant levels in phocid seals and taking into account the adipose stores and reproductive status of an animal when conducting contaminant research

Climate-scale Hydrographic Features Related to Foraging Success in a Capital Breeder, the Northern Elephant Seal Mirounga angustirostris

Published by and copyright by Endangered Species ResearchIn marine ecosystems, physical and biological processes act at multiple temporal and\ud spatial scales to influence the distribution of prey species and subsequently habitat selection of foraging\ud apex predators. Understanding how apex predators may respond to climate changes requires\ud knowledge of habitat selection in relation to measures of foraging success at spatio-temporal scales\ud relevant to the question and analytical approach. In this study, we used satellite telemetry from\ud 75 adult female northern elephant seals Mirounga angustirostris, coupled with point measures of foraging\ud success (energy gain), to examine habitat selection at large temporal and spatial scales. The\ud main hydrographic ecoregion used on the post-moult (PM) migration was the Transition Zone, while\ud on the post-breeding (PB) migration, females focused on the Subarctic Gyre. Characteristics of arearestricted\ud search (ARS) behaviours, as determined by the fractal landscape method (such as time\ud spent in ARS, total distance travelled in ARS and number of ARS) also differed significantly between\ud the PM and PB migrations. Underlying differences in prey composition and/or distribution may drive\ud the differences seen in searching behaviour and foraging success of elephant seals at large scales.\ud Despite these differences, seals showed comparable levels of foraging success across both migrations\ud and in all ecoregions. Foraging success was notably greater than measured in previous studies. These\ud results highlight the benefits of a capital breeding strategy to a relatively slow-moving, large vertebrate\ud predator allowing individuals to exploit large areas of the heterogeneous North Pacific

Effects of age, adipose percent, and reproduction on PCB concentrations and profiles in an extreme fasting north pacific marine mammal

Persistent organic pollutants, including polychlorinated biphenyls (PCBs), are widely distributed and detectable far from anthropogenic sources. Northern elephant seals ( Mirounga angustirostris ) biannually travel thousands of kilometers to forage in coastal and open-ocean regions of the northeast Pacific Ocean and then return to land where they fast while breeding and molting. Our study examined potential effects of age, adipose percent, and the difference between the breeding and molting fasts on PCB concentrations and congener profiles in blubber and serum of northern elephant seal females. Between 2005 and 2007, we sampled blubber and blood from 58 seals before and after a foraging trip, which were then analyzed for PCBs. Age did not significantly affect total PCB concentrations; however, the proportion of PCB congeners with different numbers of chlorine atoms was significantly affected by age, especially in the outer blubber. Younger adult females had a significantly greater proportion of low-chlorinated PCBs (tri-, tetra-, and penta-CBs) than older females, with the opposite trend observed for hepta-CBs, indicating that an age-associated process such as parity (birth) may significantly affect congener profiles. The percent of adipose tissue had a significant relationship with inner blubber PCB concentrations, with the highest mean concentrations observed at the end of the molting fast. These results highlight the importance of sampling across the entire blubber layer when assessing contaminant levels in phocid seals and taking into account the adipose stores and reproductive status of an animal when conducting contaminant researc