The Auke Lake system has endemic populations of pink, chum, sockeye and coho salmon, and supports populations of Dolly Varden char and cutthroat and steelhead trout. The National Marine Fisheries Service (NMFS), and its predecessor agency, U.S. Bureau of Commercial Fisheries, began salmon research at Auke Creek, near Juneau, Alaska, in 1961. There are emigrant and immigrant counts of several species over nearly five decades (Appendices 1 and 2). Pink salmon fry populations at Auke Creek were estimated annually, 1972-79, and counted at the weir since 1980. Fyke nets were used capture sockeye salmon smolts leaving Auke Lake, and estimates are available for some years between 1961 and 1979. Total sockeye smolt counts are available since 1980. Chum salmon fry were counted annually since 1985. Coho salmon smolt estimates were made in 1976, 1977, and 1979, and the total coho smolt emigration was counted since 1980. Dolly Varden char and cutthroat trout were counted in 1970 and since 1980. Steelhead emigrants were counted since 1990. Weir counts of sockeye salmon adults at Auke Creek began in 1963; pink and chum salmon were counted 1967-68, and all salmon were counted since 1971. Chinook salmon entered Auke Creek since 1987 as a result of releases of juveniles from other hatcheries. Immigrant Dolly Varden and cutthroat and steelhead trout were counted from 1997-2006. Auke Creek is the site of many research projects on wild and hatchery salmonids. The present weir at Auke Creek was constructed in 1980, and provided the capability to capture all emigrant and immigrant salmonids. Annual operations and maintenance costs associated with Auke Creek Research Station are provided by NMFS through the salmon research program of Auke Bay Laboratory. Projects at Auke Creek between 1971 and 1983 operated under several cooperative agreements. An interagency cooperative agreement relating to Auke Creek weir was established in 1983 between the NMFS, University of Alaska-Fairbanks (UAF), and Alaska Department of Fish and Game (ADFG). The agreement provided the authority to jointly fund a full-time person to assist with the operation of the fish counting weir at Auke Creek. The primary objective is to operate the weir on a daily basis and maintain the long-term data collections on migrant salmonids. Auke Creek weir usually operates from early March through late October. A report of fish counts from daily weir operations and other information related to salmonid research involving the facilities at the weir is prepared each year. The annual fish count data are available in the Auke Creek data file at the NMFS Auke Bay Laboratory. Data collected on specific projects outside the scope of the cooperative agreements are usually not included in the annual report. Those data may be available from project investigators or their respective agencies.

A database describing a 67-year time series for Sashin Creek pink salmon (Oncorhynchus gorbuscha) data is presented. The database details the survival and other biological parameters of the pink salmon population living in Sashin Creek, a pristine environment in Little Port Walter, Baranof Island, Alaska. We assembled all the published and unpublished biological and environmental data pertaining to this population, which has been evaluated almost continually by researchers since 1934. We developed a database using Microsoft Access that includes annual estimates of the freshwater and saltwater survival for these fish. The database contains the daily counts of the number of emigrating fry and escaping adults during their annual migrations since 1934, and their lengths, weights, or fecundity. Environmental parameters in the database include stream temperature, stream discharge, daily minimum and maximum air temperatures, and precipitation where Sashin Creek enters seawater at Little Port Walter. All records have been evaluated and transformed to ensure comparability. References for all data are provided, including unpublished sources. The Sashin Creek Weir Database (SCWDATA) can be accessed through the Internet.

Herring is one of the most energy-rich fish in the Alaskan ecosystem, and when populations struggle over time, such as the Lynn Canal population, there is management concern. Prior to 1983, Lynn Canal herring supported a productive sac roe fishery, a bait fishery, and a winter food and bait fishery. All commercial fisheries were closed in 1983 and remain so today. The purpose of this study was to examine the genetic structure of Lynn Canal herring and determine if it was discrete from other collections in southeast Alaska. We used microsatellite DNA to examine both spawning and non-spawning aggregates (collected in two consecutive years) in Lynn Canal, and compared them to two Southeast Alaska populations: Prince of Wales Island (southernmost waters) and Sitka Sound on Baranof Island (outer-coast). In addition we examined two collections from Prince William Sound (approx. 850 km NW) as a means to compare extent of divergence over large tracts of unsuitable spawning habitat. Because the geographic location of Lynn Canal is somewhat isolated and schools are known to over-winter in the area, we hypothesized that Lynn Canal herring experience reduced gene flow. The results of our study showed allele frequencies from 16 loci were highly similar across all collections, including the distant Prince William Sound. This investigation concurs with previous studies that there is a large amount of movement among herring in the Gulf of Alaska. We conclude that Lynn Canal herring are part of a meta-population that is possibly Gulf wide or larger.

Diel epipelagic sampling for juvenile Pacific salmon (Oncorhynchus spp.), rockfish (Sebastes spp.), sablefish (Anoplopoma fimbria), and associated species was conducted in order to identify factors that may affect year-class success of these commercially important species. Sampling occurred in offshore marine habitats of the coastal northeast Pacific Ocean from 10-20 August 2005 and was conducted with a surface trawl fishing the upper 20 m of the water column along transects up to78 km offshore near 58 N. Three habitats were sampled along each transect over a 24-hr period: the continental shelf (<200 m depth), the continental slope (400-750 m depth), and the abyss (>2,000 m depth). A total of 38,747 fish and squid representing 24 species were sampled in 56 trawl hauls. Of the targeted juvenile fish species, a total of 587 salmon, 11 rockfish, and 70 sablefish were captured. Sampling during day (1500-1900) and night (2200-0200) periods indicated that biomass of fish and squid was 2-4 times higher at night at (each?)all habitat types pooled across transects. No distinct patterns between day or night occurrence were noted for juvenile pink salmon (O. gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), or coho salmon (O. kisutch), however, juvenile Chinook salmon (O. tshawytscha) were encountered only at night. Catches of juvenile rockfish and juvenile sablefish were quite low in this study, and larger sample sizes of these fish are needed to adequately determine their diel distribution. Diel differences were apparent with forage species such as Pacific herring (Clupea pallasi), capelin (Mallotus villosus), and eulachon (Thaleichthys pacificus) that were almost exclusively sampled at night. The offshore distribution patterns of target species were distinctly different, with the most common occurrences of juvenile salmon over continental shelf habitats, juvenile sablefish over continental shelf and slope habitats, and juvenile rockfish over slope and abyss habitats. Pacific herring, capelin, eulachon, and Pacific sardines (Sardinops sagax) were found over continental shelf habitats, whereas small squid and myctophids occurred primarily at slope and abyssal habitats. The greatest overall catch biomass was of gelatinous species (jellyfish), which was consistently higher than that of all fish and squid combined, usually by an order of magnitude. Individual fish or squid species with highest average weight per haul were pomfret (Brama japonica), adult coho salmon, Humboldt squid (Dosidicus gigas), and blue sharks (Prionace glauca). The occurrence of the latter two warm-water species and Pacific sardines were of interest because this study occurred during an anomalously warm year and the capture of Pacific sardines and Humboldt squid represent northern range extensions for these species. Stomach content analysis of potential predator species of the target species showed that only adult coho salmon were predating on juvenile salmon and sablefish, and only pomfret were predating on juvenile rockfish. Further sampling of the target species is needed in these habitats during more normal environmental conditions to validate these observations.

Pacific salmon (Oncorhynchus spp.) runs in rivers that flow into the eastern Bering Sea have been inconsistent and at times very weak. Low returns of chinook (O. tshawytscha) and chum (O. keta) salmon to the Yukon River, Kuskokwim River, and Norton Sound areas of Alaska prompted the state of Alaska to restrict commercial and subsistence fisheries during 2000 and declare the region a fisheries disaster area. Weak salmon returns to these river systems follow several years of low sockeye (O. nerka) salmon returns to Bristol Bay, which was declared a fisheries disaster region during 1998 by both the State of Alaska and the U.S. Department of Commerce. Causes of the poor salmon returns to these river systems are not known however, the regional-scale decline of these stocks indicates that the marine environment may play a critical role. Ocean conditions, particularly in the first few months after the salmon leave fresh water, are known to significantly affect salmon survival (Holtby et al. 1990; Friedland et al. 1996; Beamish and Mahnken 2001). Mechanisms affecting marine survival of the eastern Bering Sea salmon stocks are unknown, principally due to the lack of marine life history information on western Alaska salmon. To improve understanding of the marine life-history stage of salmon in the Bering Sea, the North Pacific Anadromous Fish Commission (NPAFC) began an internationally coordinated research program on salmon in the Bering Sea called the Bering-Aleutian Salmon International Survey (BASIS) (NPAFC 2001). As part of BASIS, scientists from the National Marine Fisheries Service (NMFS), Ocean Carrying Capacity (OCC) program conducted a fall survey on the eastern Bering Sea shelf to provide key ecological data for eastern Bering Sea salmon stocks during their juvenile life-history stage. The goal of the OCC/BASIS salmon research cruise was to understand mechanisms underlying the effects of environment on distribution, migration, and growth of juvenile salmon on the eastern Bering Sea shelf. Primary objectives of BASIS include: 1) to determine the extent of offshore migrations of juvenile salmon from rivers draining into the eastern Bering Sea, 2) to describe the physical environment of the eastern and northeastern Bering Sea shelf occupied by juvenile salmon, and 3) to collect biological information on other ecologically important species. Summaries of previous Bering Sea juvenile salmon research cruises can be found in Farley et al. (1999, 2000, 2001, 2002, 2004, 2005).

Electrophoretic analysis of Asian even brood-year pink salmon stocks has shown regional heterogeneity (Noll et al. in review). Hypothetical mixed fisheries were created using data from 24 variable loci from Noll et al. in review. The mixture was analyzed to test the accuracy and precision of this baseline data for potential use in mixed fishery analyses. Thirteen stocks were separated into four management regions: Japan, Sakhalin, eastern Kamchatka, and western Kamchatka. Simulations were varied in sample size, number of loci, and percent regional contribution. The simulated mixtures were analyzed using the Conditional Maximum Likelihood Estimate (MLE). The mean estimate, standard deviation, and coefficient of variation were calculated for standardized comparison by both stock and region. Computed MLEs showed that estimates for the Noll et al. baseline improved in accuracy and precision with increased sample size and retention of important loci. When 24 loci and a minimum of 200 samples in a mixture were used, the baseline was approximately 80% accurate in its ability to distinguish regions from a mixture.

This layer is intended to represent the geographic extent of NOAA Fisheries’ Juvenile Salmon and Ocean Ecosystem Survey stations. The Juvenile Salmon and Ocean Ecosystem Survey (JSOES) started in 1998 and is led by NMFS Northwest Fisheries Science Center. This survey is the longest running salmon survey on the U.S. West Coast. The primary goal of our work is to develop a mechanistic understanding of how trophic dynamics and conditions in the ocean and Columbia River plume affect survival of juvenile salmonids. JSOES collects juvenile salmon and other open-ocean animals which allows identification of shifts in abundance, distribution, and growth/condition of migrating juvenile salmon. JSOES has demonstrated correlations between ocean conditions and the distribution, abundance, and survival of juvenile Columbia River salmon in the Northern California Current nearshore ecosystem to provide context for efforts by states, tribes, and others to restore and enhance salmon production. The samples from this survey improve salmon forecasts in a quantitative rather than qualitative manner, and decouple the effects of mitigation efforts in the freshwater environment from the effects of a changing ocean environment. The survey is conducted two times a year (late May and late June) for roughly ten days each. This study utilizes a surface trawl. A surface trawl collects juvenile salmon and other open-ocean animals during sampling.

Understanding the processes that regulate early marine survival of salmon is a major goal of the Global Ocean Ecosystems Dynamics (GLOBEC) Northeast Pacific (NEP) program. Faster growth and larger body size are generally associated with higher marine survival for most species of juvenile salmon, which experience relatively high mortality rates during early marine life. The interaction between the temporal-spatial distribution of juvenile salmon, growth performance, environmental conditions, and stage-specific survival are critical to understanding how physical and biological factors contribute to production and survival, and influence the mechanisms, magnitude, location, and timing of marine mortality. The northern Coastal Gulf of Alaska (CGOA) is a highly productive, down-welling based system where freshwater runoff and winds dominate the physical processes on the shelf. The physical environment changes at different spatial and temporal scales, which is believed to influence inter-annual variability in distribution, feeding, growth, and survival of juvenile salmon. Pink salmon are the upper trophic level target species of GLOBEC, however, the overarching programmatic goal is to enhance our understanding of the processes driving the physical structure and biological productivity of the highly dynamic CGOA system.

This work involves 1) synthesizing information from the literature and 2) modeling impacts of climate change on specific aspects of salmon life history and viability. Annual literature reviews summarize information from peer-reviewed journals and major technical reports relevant to managing Pacific salmon, with an emphasis on information that is most relevant for salmon in the Pacific Northwest and the Columbia River Basin. Original research involves modeling exploration of changes in climate on spawner to smolt productivity, juvenile survival, upstream migration survival and timing, prespawn mortality, and whole life cycle population viability. Collection of data collected by numerous other sources (e.g., tribes, states) managed and made public by NWFSC.

This study is a cooperative effort between Douglas Island Pink & Chum (DIPAC), the University of Alaska Fairbanks, School of Fisheries and Ocean Sciences (UAF, SFOS), the National Oceanic & Atmospheric Administration, Auke Bay Lab (ABL), and the Alaska Department of Fish & Game (ADF&G) to determine the potential for interactions between DIPAC hatchery chum salmon (Oncorhynchus keta) fry and wild chum salmon fry in Taku Inlet, Southeast Alaska. We analyzed patterns in spatial and temporal distribution, size, and condition of juvenile chum salmon collected in the littoral and neritic waters of Taku Inlet in 2004 and 2005. Energy density and diet of wild and hatchery chum salmon fry in Taku Inlet were analyzed and compared to data obtained later in the season for chum salmon stocks caught in Icy Strait. The greatest potential for wild/hatchery interactions was in the outer inlet, directly following early hatchery releases (May 9-11). Peak outmigration for wild chum salmon fry coincided with early hatchery releases; in contrast, most wild chum salmon fry had already emigrated from the estuary by the time of late hatchery fry release (May 22 June 1). In both years, hatchery fry were rare in the inner inlet, but comprised over 95% of the catch in the outer estuary during the peak of outmigration. Hatchery chum salmon were significantly larger than wild fry in both beach and neritic samples. Wild and early hatchery chum salmon were smaller in the littoral than the neritic habitat, indicating that both groups moved from shallow to deeper water with ontogeny. In spite of large differences in abundance, no negative correlation between abundance of hatchery fish and condition of wild fish was identified. Both wild and early hatchery chum salmon fry showed apparent growth through the season, while late hatchery fry appeared to leave the estuary soon after release. Regardless of origin, most chum salmon juveniles emigrated from the study area in late May and early June, indicating a high probability for mixed-stock schools. Hatchery chum salmon juveniles were initially larger and had greater energy content than wild fish; however, energetic values converged by mid-June in Taku Inlet. In Icy Strait, energetic condition of wild and hatchery chum salmon juveniles was also similar. Multivariate analysis of 54 prey measures indicated that diets of the two groups were distinctly different throughout the season in all Taku Inlet locations and converged in Icy Strait.