Annual report chinook salmon spawner stocks in California's central valley, 1991

This report covers the 39th annual inventory of chinook salman, Oncorhynchus tshawytscha, spawner populations in the Sacramento-San Joaquin River system." It is a compilation of reports estimating the fall-, winter-, late-fall-, and spring-run salman spawner populatiens fer streams which were surveyed. Estimates were made from counts of fish entering hatcheries and migrating past dams, from surveys of dead and live fish and redds on spawning areas, and from aerial counts. The estimated 1991 total escapement of chinook salmon in the Central Valley was 147,080 fish. This total consisted of 132,571 fall-, 5,921 spring-, 190 winter-, and 8,398 late-fall-run spawners. All of the spring-, late-fall-, and winter-run salmon were estimated to be in the Sacramento River system, while 1,176 fish of the fall run were in the San Joaquin River system. Spawner populations in all individual tributaries (except the American River) and the Sacramento River mainstem were lower than in 1990; but it should be noted that fall run populations in the Feather and Yuba rivers, two of the larger tributaries, were not surveyed that year. The winter run in the mainstem Sacramento River was at a record low level. (PDF contains 42 pages.)

Food habits of Steller sea lions (Eumetopias jubatus) off Oregon and northern California, 1986–2007

We described the diet of the eastern stock of Steller sea lions (Eumetopias jubatus) from 1416 scat samples collected from five sites in Oregon and northern California from 1986 through 2007. A total of 47 prey types from 30 families were identified. The most common prey was Pacific hake (Merluccius productus), followed by salmonids (Oncorhynchus spp.), skates (Rajidae), Pacific lamprey (Lampetra tridentata), herrings (Clupeidae), rockfish (Sebastes spp.), and northern anchovy (Engraulis mordax). Steller sea lion diet composition varied seasonally, annually, and spatially. Hake and salmonids were the most commonly identified prey in scats collected during the summer (breeding season), whereas hake and skate were most common in the nonbreeding season. Continued research on Steller sea lion diet and foraging behavior in the southern extent of their range is necessary to address issues such as climate change, interaction with competing California sea lions, and predation impacts on valuable or sensitive fish stocks.

Ocean distribution of the American shad (Alosa sapidissima) along the Pacific coast of North America

We examined the incidental catches of American shad (Alosa sapidissima) taken during research cruises and in commercial and recreational landings along the Pacific coast of North America during over 30 years of sampling. Shad, an introduced species, was mainly found over the shallow continental shelf, and largest catches and highest frequency of occurrences were found north of central Oregon, along the coasts of Washington and Vancouver Island, and in California around San Francisco Bay. Migrations to the north off Washington and Vancouver were seen during spring to fall, but we found no evidence for large-scale seasonal migrations to the south during the fall or winter. The average weight of shad increased in deeper water. Sizes were also larger in early years of the study. Most were caught over a wide range of sea surface temperatures (11–17°C) and bottom temperatures (6.4–8.0°C). Abundance of shad on the continental shelf north of 44°N was highly correlated with counts of shad at Bonneville Dam on the Columbia River in the same year. Counts were negatively related to average weights and also negatively correlated with the survival of hatchery coho salmon (Oncorhynchus kisutch), indicating that survival of shad is favored by warm ocean conditions. Examining the catch during research cruises and commercial and recreational landings, we concluded that American shad along the Pacific coast have adapted to the prevailing environmental conditions and undertake only moderate seasonal migrations compared with the long seasonal migrations of shad along the Atlantic coast of North America. We suggest that the large spawning populations in the Columbia River and San Francisco Bay areas explain most of the distributional features along the Pacific coast.

Mechanisms of Toxicity of Ag Nanoparticles in Comparison to Bulk and Ionic Ag on Mussel Hemocytes and Gill Cells

Silver nanoparticles (Ag NPs) are increasingly used in many products and are expected to end up in the aquatic environment. Mussels have been proposed as marine model species to evaluate NP toxicity in vitro. The objective of this work was to assess the mechanisms of toxicity of Ag NPs on mussel hemocytes and gill cells, in comparison to ionic and bulk Ag. Firstly, cytotoxicity of commercial and maltose stabilized Ag NPs was screened in parallel with the ionic and bulk forms at a wide range of concentrations in isolated mussel cells using cell viability assays. Toxicity of maltose alone was also tested. LC50 values were calculated and the most toxic Ag NPs tested were selected for a second step where sublethal concentrations of each Ag form were tested using a wide array of mechanistic tests in both cell types. Maltose-stabilized Ag NPs showed size-dependent cytotoxicity, smaller (20 nm) NPs being more toxic than larger (40 and 100 nm) NPs. Maltose alone provoked minor effects on cell viability. Ionic Ag was the most cytotoxic Ag form tested whereas bulk Ag showed similar cytotoxicity to the commercial Ag NPs. Main mechanisms of action of Ag NPs involved oxidative stress and genotoxicity in the two cell types, activation of lysosomal AcP activity, disruption of actin cytoskeleton and stimulation of phagocytosis in hemocytes and increase of MXR transport activity and inhibition of Na-K-ATPase in gill cells. Similar effects were observed after exposure to ionic and bulk Ag in the two cell types, although generally effects were more marked for the ionic form. In conclusion, results suggest that most observed responses were due at least in part to dissolved Ag.

Stanford University’s John Otterbein Snyder: Student, Collaborator, and Colleague of David Starr Jordan and Charles Henry Gilbert

John Otterbein Snyder (1867–1943) was an early student of David Starr Jordan at Stanford University and subsequently rose to become an assistant professor there. During his 34 years with the university he taught a wide variety of courses in various branches of zoology and advised numerous students. He eventually mentored 8 M.A. and 4 Ph.D. students to completion at Stanford. He also assisted in the collection of tens of thousands of fish specimens from the western Pacific, central Pacific, and the West Coast of North America, part of the time while stationed as “Naturalist” aboard the U.S. Fish Commission’s Steamer Albatross (1902–06). Although his early publications dealt mainly with fish groups and descriptions (often as a junior author with Jordan), after 1910 he became more autonomous and eventually rose to become one of the Pacific salmon, Oncorhynchus spp., experts on the West Coast. Throughout his career, he was especially esteemed by colleagues as “a stimulating teacher,” “an excellent biologist,” and “a fine man.

The Ragfish, Icosteus aenigmaticus Lockington, 1880: A Synthesis of Historical and Recent Records From the North Pacific Ocean and the Bering Sea

Knowledge of the distribution and biology of the ragfish, Icosteus aenigmaticus, an aberrant deepwater perciform of the North Pacific Ocean, has increased slowly since the first description of the species in the 1880’s which was based on specimens retrieved from a fish monger’s table in San Francisco, Calif. As a historically rare, and subjectively unattractive appearing noncommercial species, ichthyologists have only studied ragfish from specimens caught and donated by fishermen or by the general public. Since 1958, I have accumulated catch records of >825 ragfish. Specimens were primarily from commercial fishermen and research personnel trawling for bottom and demersal species on the continental shelves of the eastern North Pacific Ocean, Gulf of Alaska, Bering Sea, and the western Pacific Ocean, as well as from gillnet fisheries for Pacific salmon, Oncorhynchus spp., in the north central Pacific Ocean. Available records came from four separate sources: 1) historical data based primarily on published and unpublished literature (1876–1990), 2) ragfish delivered fresh to Humboldt State University or records available from the California Department of Fish and Game of ragfish caught in northern California and southern Oregon bottom trawl fisheries (1950–99), 3) incidental catches of ragfish observed and recorded by scientific observers of the commercial fisheries of the eastern Pacific Ocean and catches in National Marine Fisheries Service trawl surveys studying these fisheries from 1976 to 1999, and 4) Japanese government research on nearshore fisheries of the northwestern Pacific Ocean (1950–99). Limited data on individual ragfish allowed mainly qualitative analysis, although some quantitative analysis could be made with ragfish data from northern California and southern Oregon. This paper includes a history of taxonomic and common names of the ragfish, types of fishing gear and other techniques recovering ragfish, a chronology of range extensions into the North Pacific and Bering Sea, reproductive biology of ragfish caught by trawl fisheries off northern California and southern Oregon, and topics dealing with early, juvenile, and adult life history, including age and growth, food habits, and ecology. Recommendations for future study are proposed, especially on the life history of juvenile ragfish (5–30 cm FL) which remains enigmatic.

A Brief History of Bycatch Management Measures for Eastern Bering Sea Groundfish Fisheries

Bycatch management measures instituted for groundfish fisheries of the eastern Bering Sea have focused on reducing the incidental capture and injury of species traditionally harvested by other fisheries. These species include king crab, Paralithodes and Lithodes spp.; Tanner crab, Chionoecetes spp.; Pacific herring, Clupea harengus pallasi; Pacific halibut, Hippoglossus stenolepis; and Pacific salmon and steelhead trout, Oncorhynchus spp. Collectively, these species are called "prohibited species," as they cannot be retained as bycatch in groundfish fisheries and must be discarded with a minimum of injury.

Trace metals in common marine foods of the Pacific Coast

Trace metal analysis of 23 species of common Pacific Coast marine foods revealed high cadmium values for Bent-nosed clams (Macoma nasuta), Bay mussels (Mytilus edulis), Bay oysters (Osrtrea lurida), Pacific oysters (Crassostrea gigas), and Littleneck clams (Protothaca staminea). Metals were found to concentrate in the gills, heart, and visceral mass of all 10 species of bivalve mollusks examined. Swordfish (Xiphias gladius) and Salmon (Oncorhynchus tshawytscha) demonstrated the highest cadmium values for fish flesh.

Age and length composition of Columbia Basin chinook, sockeye, and coho salmon at Bonneville Dam in 2001

In 2001, representative samples of adult Columbia Basin chinook (Oncorhynchus tshawytscha), sockeye (O. nerka), and coho salmon (O. kisutch) populations at Bonneville Dam were collected. Fish were trapped, anesthetized, sampled for scales and biological data, revived, and then released adult migrating salmonids. Scales were examined to estimate age composition; the results contributed to an ongoing database for age class structure of Columbia Basin salmon populations. Based on scale analysis of chinook salmon, four-year-old fish (from brood year [BY] 1997) comprised 88% of the spring chinook, 67% of the summer chinook, and 42% of the Bright fall chinook salmon population. Five-year-old fish (BY 1996) comprised 9% of the spring chinook, 14% of the summer chinook, and 9% of the fall chinook salmon population. The sockeye salmon population at Bonneville was predominantly four-year-old fish (81%), with 18% returning as five-year-olds in 2001. The coho salmon population was 96% three-year-old fish (Age 1.1). Length analysis of the 2001 returns indicated that chinook salmon with a stream-type life history are larger (mean length) than the chinook salmon with an ocean-type life history. Trends in mean length over the sampling period for returning 2001 chinook salmon were analyzed. Chinook salmon of age classes 0.2 and 1.3 show a significant increase in mean length over time. Age classes 0.1, 0.3, 0.4, 1.1, 1.2, and 1.4 show no significant change over time. A year class regression over the past 12 years of data was used to predict spring, summer, and Bright fall chinook salmon population sizes for 2002. Based on three-year-old returns, the relationship predicts four-year-old returns of 132,600 (± 46,300, 90% predictive interval [PI]) spring chinook and 44,200 (± 11,700, 90% PI) summer chinook salmon for the 2002 runs. Based on four-year-old returns, the relationship predicts five-year-old returns of 87,800 (± 54,500, 90% PI) spring, 33,500 (± 11,500, 90% PI) summer, and 77,100 (± 25,800, 90% PI) Bright fall chinook salmon for the 2002 runs. The 2002 run size predictions should be used with caution; some of these predictions are well beyond the range of previously observed data.

Age and length composition of Columbia Basin chinook, sockeye, and coho salmon at Bonneville Dam in 2000

In 2000, representative samples of adult Columbia Basin chinook (Oncorhynchus tshawytscha), sockeye (O. nerka), and coho salmon (O. kisutch), populations were collected at Bonneville Dam. Fish were trapped, anesthetized, sampled for scales and biological data, allowed to revive, and then released. Scales were examined to estimate age composition and the results contribute to an ongoing database for age class structure of Columbia Basin salmon populations. Based on scale analysis, four-year-old fish (from brood year (BY) 1996) were estimated to comprise 83% of the spring chinook, 31% of the summer chinook, and 32% of the upriver bright fall chinook salmon population. Five-year-old fish (BY 1995) were estimated to comprise 2% of the spring chinook, 26% of the summer chinook, and 40% of the fall chinook salmon population. Three-year-old fish (BY 1997) were estimated to comprise 14% of the spring chinook, 42% of the summer chinook, and 17% of the fall chinook salmon population. Two-year-olds accounted for approximately 11% of the fall chinook population. The sockeye salmon population sampled at Bonneville was predominantly four-year-old fish (95%), and the coho salmon population was 99.9% three-year-old fish (Age 1.1). Length analysis of the 2000 returns indicated that chinook salmon with a stream-type life history are larger (mean length) than the chinook salmon with an ocean-type life history. Trends in mean length over the sampling period were also analysis for returning 2000 chinook salmon. Fish of age classes 0.2, 1.1, 1.2, and 1.3 have a significant increase in mean length over time. Age classes 0.3 and 0.4 have no significant change over time and age 0.1 chinook salmon had a significant decrease in mean length over time. A year class regression over the past 11 years of data was used to predict spring and summer chinook salmon population sizes for 2001. Based on three-year-old returns, the relationship predicts four-year-old returns of 325,000 (± 111,600, 90% Predictive Interval [PI]) spring chinook and 27,800 (± 29,750, 90% PI) summer chinook salmon. Based on four-year-old returns, the relationship predicts five-year-old returns of 54,300 (± 40,600, 90% PI) spring chinook and 11,000 (± 3,250, 90% PI) summer chinook salmon. The 2001 run size predictions used in this report should be used with caution, these predictions are well beyond the range of previously observed data.

Age and length composition of Columbia Basin chinook, sockeye, and coho salmon at Bonneville Dam in 2002

In 2002, representative samples of migrating Columbia Basin chinook (Oncorhynchus tshawytscha), sockeye (O. nerka), and coho salmon (O. kisutch) adult populations were collected at Bonneville Dam. Fish were trapped, anesthetized, sampled for scales and biological data, revived, and then released. Scales were examined to estimate age composition; the results contributed to an ongoing database for age class structure of Columbia Basin salmon populations. Based on scale analysis of chinook salmon, four-year-old fish (from brood year [BY] 1998) comprised 86% of the spring chinook, 51% of the summer chinook, and 51% of the bright fall chinook salmon population. Five-year-old fish (BY 1997) comprised 13% of the spring chinook, 43% of the summer chinook, and 11% of the bright fall chinook salmon population. The sockeye salmon population at Bonneville was predominantly five-year-old fish (55%), with 40% returning as four-year-olds in 2002. For the coho salmon population, 88% of the population was three-year-old fish of age class 1.1, while 12% were age class 1.0. Length analysis of the 2002 returns indicated that chinook salmon with a stream-type life history are larger (mean length) at age than the chinook salmon with an ocean-type life history. Trends in mean length over the sampling period for returning 2002 chinook salmon were analyzed. Chinook salmon of age classes 1.2 and 1.3 show a significant increase in mean length over the duration of the migration. A year class regression over the past 14 years of data was used to predict spring, summer, and bright fall chinook salmon population sizes for 2003. Based on three-year-old returns, the relationship predicts four-year-old returns of 54,200 (± 66,600, 90% predictive interval [PI]) spring chinook, 23,800 (± 19,100, 90% PI) summer, and 169,100 (± 139,500, 90% PI) bright fall chinook salmon for the 2003 runs. Based on four-year-old returns, the relationship predicts five-year-old returns of 36,300 (± 35,400, 90% PI) spring, 63,800 (± 10,300, 90% PI) summer, and 91,100 (± 69,400, 90% PI) bright fall chinook salmon for the 2003 runs. The 2003 run size predictions should be used with caution; some of these predictions are well beyond the range of previously observed data.

Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary

The transition between freshwater and marine environments is associated with high mortality for juvenile anadromous salmonids, yet little is known about this critical period in many large rivers. To address this deficiency, we investigated the estuarine ecology of juvenile salmonids and their associated fish assemblage in open-water habitats of the lower Columbia River estuary during spring of 2007–10. For coho (Oncorhynchus kisutch), sockeye (O. nerka), chum (O. keta), and yearling (age 1.0) Chinook (O. tshawytscha) salmon, and steelhead (O. mykiss), we observed a consistent seasonal pattern characterized by extremely low abundances in mid-April, maximum abundances in May, and near absence by late June. Subyearling (age 0.0) Chinook salmon were most abundant in late June. Although we observed interannual variation in the presence, abundance, and size of juvenile salmonids, no single year was exceptional across all species-and-age classes. We estimated that >90% of juvenile Chinook and coho salmon and steelhead were of hatchery origin, a rate higher than previously reported. In contrast to juvenile salmonids, the abundance and composition of the greater estuarine fish assemblage, of which juvenile salmon were minor members, were extremely variable and likely responding to dynamic physical conditions in the estuary. Comparisons with studies conducted 3 decades earlier suggest striking changes in the estuarine fish assemblage—changes that have unknown but potentially important consequences for juvenile salmon in the Columbia River estuary.

New insights into the diets of harbor seals (Phoca vitulina) in the Salish Sea revealed by analysis of fatty acid signatures

Harbor seals (Phoca fvitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available informationon harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

Fish consumption by harbor seals (Phoca vitulina) in the San Juan Islands, Washington

The harbor seal (Phoca vitulina) is a large-bodied and abundant predator in the Salish Sea ecosystem, and its population has recovered since the 1970s after passage of the Marine Mammal Protection Act and the cessation of bounties. Little is known about how this large predator population may affect the recovery of fish stocks in the Salish Sea, where candidate marine protected areas are being proposed. We used a bioenergetics model to calculate baseline consumption rates in the San Juan Islands, Washington. Salmonids (Oncorhynchus spp.) and herring (Clupeidae) were the 2 most energetically important prey groups for biomass consumed by harbor seals. Estimated consumption of salmonids was 783 (±380 standard deviation [SD]) metric tons (t) in the breeding season and 675 (±388 SD t in the nonbreeding season. Estimated consumption of herring was 646 (±303 SD) t in the breeding season and 2151 (±706 SD) t in the nonbreeding season. Rockfish, a depressed fish stock currently in need of population recovery, composed one of the minor prey groups consumed by harbor seals (84 [±26 SD] t in the nonbreeding season). The variables of seal body mass and proportion of prey in seal diet explained >80% of the total variation in model outputs. Prey groups, such as rockfish, that are targeted for recovery may still be affected by even low levels of predation. This study highlights the importance of salmonids and herring for the seal population and provides a framework for refining consumption estimates and their confidence intervals with future data.

Assessment of contaminant body burdens and histopathology of fish and shellfish species frequently used for subsistence food by Alaskan Native communities

Subsistence food items can be a health concern in rural Alaska because community members often rely on fish and wildlife resources not routinely monitored for persistent bioaccumulative contaminants and pathogens. Subsistence activities are a large part of the traditional culture, as well as a means of providing protein in the diets for Tribal members. In response to the growing concerns among Native communities, contaminant body burden and histopathological condition of chum and sockeye salmon (Oncorhynchus keta and Oncorhynchus nerka) and the shellfish cockles and softshell clams (Clinocardium nuttallii and Mya arenaria) were assessed. In the Spring of 2010, the fish and shellfish were collected from traditional subsistence harvest areas in the vicinity of Nanwalek, Port Graham, and Seldovia, AK, and were analyzed for trace metals and residues of organic contaminants routinely monitored by the NOAA National Status & Trends Program (NS&T). Additionally, the fish and shellfish were histologically characterized for the presence, prevalence and severity of tissue pathology, disease, and parasite infection. The fish and shellfish sampled showed low tissue contamination, and pathologic effects of the parasites and diseases were absent or minimal. Taken together, the results showed that the fish and shellfish were healthy and pose no safety concern for consumption. This study provides reliable chemistry and histopathology information for local resource managers and Alaska Native people regarding subsistence fish and shellfish use and management needs.