Since 1988, scientists at the Auke Bay Laboratories have been using the /Delta/ submarine for a wide range of research projects. Over 500 dives have been completed. The video collected during these projects provides valuable direct observations of seafloor habitat and biological attributes. This project is assembling a database that will include dive locations and basic biological and substrate information from each of the dives. To date, biological and substrate data have been processed for about 40% of the dives.

The web-posted Alaska Shore Station Database is a compilation of hundreds of intertidal sites that were visited and evaluated throughout the coastal waters of Alaska. At each station attempts are made to document all observed species and their assemblages, geomorphic features, measurements of beach length and slope, and gather photographic examples. This online database has been designed to integrate with the spatially explicit, Alaska ShoreZone web enabled GIS platform. The end result is a user friendly and accessible version of the Shore Station database with a queryable display of station locations, downloadable species lists and photos.

Genetic data were collected and prepared with the use of protein electrophoresis from 52 spawning locations in southeastern Alaska and northern British Columbia. Genetic relationships were examined from principal components analysis and unrooted trees constructed from genetic distances between collections. These descriptive analyses suggest a geographic basis to genetic divergence among populations. This geographic basis was confirmed using log-likelihood-ratio analysis and analyses of variance. Three groups of populations were observed: one from systems that drain into the inside waters of northern and central southeast Alaska; another from the far southeastern islands (including Prince of Wales Island); and the third in systems of the southern inside waters. Although the geographic structure was a statistically significant component of the overall genetic structure, gene diversity analysis indicates that only about 4.7% of the total genetic variability was attributable to genetic differences among those regions, whereas about 8.4% of the total was due to differences among populations within each region. The other 87.0% of the variation occurred, on average, within each collection.

Genetic data were collected and prepared with the use of protein electrophoresis from 52 spawning locations in southeastern Alaska and northern British Columbia. Genetic relationships were examined from principal components analysis and unrooted trees constructed from genetic distances between collections. These descriptive analyses suggest a geographic basis to genetic divergence among populations. This geographic basis was confirmed using log-likelihood-ratio analysis and analyses of variance. Three groups of populations were observed: one from systems that drain into the inside waters of northern and central southeast Alaska; another from the far southeastern islands (including Prince of Wales Island); and the third in systems of the southern inside waters. Although the geographic structure was a statistically significant component of the overall genetic structure, gene diversity analysis indicates that only about 4.7% of the total genetic variability was attributable to genetic differences among those regions, whereas about 8.4% of the total was due to differences among populations within each region. The other 87.0% of the variation occurred, on average, within each collection.

Genetics Herring Microsatellite Alaska PWS- SEAK 2007-08 ID 17243

The Southeast Alaska Coastal Monitoring (SECM) project in Alaska was initiated in 1997 by the Auke Bay Laboratory, National Marine Fisheries Service, to study the habitat use and early marine ecology of juvenile (age-0) Pacific salmon (Oncorhynchus spp.) and associated epipelagic ichthyofauna. This research has been conducted to meet several needs identified in the National Oceanic and Atmospheric Administration (NOAA) Fisheries 2006-2011 Strategic Plan, the North Pacific Anadromous Fisheries Commission (NPAFC) 20062010 Science Plan, and the Gulf of Alaska Global Ocean Ecosystem Dynamics (GLOBEC) Program.

A primary goal of the 2006-2011 NOAA Fisheries Strategic Plan is to Protect, Restore, and Manage the Use of Coastal and Ocean Resources Through an Ecosystem Approach to Management. SECM research addresses the five fundamental activities identified under this goal, which include: Monitor and observe the land, sea, atmosphere. Understand and describe how natural systems work together, Assess and predict the changes in natural systems, Engage, advise, and inform individuals, partners, communities, and industries, and, Manage coastal and ocean resources SECM research emphasizes long-term monitoring of coastal marine habitats used by juvenile salmon and associated epipelagic fishes, to understand how environmental variation affects the sustainability of these marine resources in an ecological context.

The study of juvenile anadromous stocks of salmon in ocean ecosystems is an important component of the NPAFC 2006-2010 Science Plan. This component recommends studies directed at understanding: seasonal distribution and migration route/timing of juvenile salmon; hydrological characteristics, primary production, and prey resources in the habitats; trophic linkages, growth rates and predation rates of juvenile salmon; and population size, survival rate and survival mechanism of juvenile salmon. SECM research focuses on each of these elements of this component. In particular, SECM examines the relationships among habitat use, marine growth, hatchery and wild stock interactions, year-class strength, and ocean carrying capacity of key juvenile salmon stocks in the Eastern Pacific rim.

Research under the GLOBEC program incorporates basin-scale studies to determine how plankton productivity and the carrying capacity for high-trophic level, pelagic carnivores in the North Pacific Ocean change in response to climate variations, and incorporates regional-scale ecosystem studies to compare how variations in ocean climate affect species dominance and fish populations in the coastal margins of the Pacific Rim. SECM research addresses the regional-scale component of the GLOBEC program by 1) collecting biological data on juvenile Pacific salmon and ecologically related fish species from surface rope trawl samples, 2) monitoring physical and biological oceanographic indices at sampling stations in marine habitats, and 3) conducting process studies focusing on bioenergetics, prey fields, and trophic relationships of juvenile salmon and associated fishes.

Radio telemetry was used to determine the distribution, locate spawning sites, and evaluate the tagging response of wild Chinook salmon Oncorhynchus tshawytscha returning to a large, free-flowing river basin. A total of 2,860 fish were radio tagged in the lower Yukon River and tracked upriver. Fish traveled to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging site. We found similar distribution patterns across years, suggesting that the major components of the return were identified. Most spawning fish were clustered in a number of principal tributaries, although small numbers of fish were located in other spatially-isolated areas. The cumulative contribution of these minor stocks was appreciable, making up 28-31% of the tagged sample. There was suggestive evidence of mainstem spawning in upper reaches of the basin. Large-scale elevation and physiographic data were useful in categorizing spawning areas, with most fish returning to relatively entrenched upland rivers. Fish were largely absent in lowland reaches characterized by meandering, low gradient, alluvial channels often associated with main river floodplains. The fish generally responded well to the capture, handling, and tagging procedures with most (2,790, 97.6%) resuming upriver movements, although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release. The duration of this response was relatively short (several days) and less severe as the fish moved upriver. The swimming speeds of radio-tagged fish after the initial delay were comparable to estimates for untagged fish, further suggesting that the capture, handling, and tagging methods used were relatively benign. Identifying the primary components of the run (including both major and minor stocks) and determining site-specific utilization patterns can fundamentally enhance salmon management in large river basins, and facilitate research and conservation efforts.

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.

The scientific objective of the Gulf of Alaska Survey (GOA Survey) is to assess Young of the Year (YOY) groundfish, salmon, plankton, and oceanographic conditions across the coastal, shelf, slope, and offshore waters of the GOA and to provide information on species distribution, ecosystem structure, and marine productivity in response to changes in season, region, and climate. Specific objectives are to 1) observe epi-pelagic fish communities by sampling with a rope trawl towed at the surface; 2) collect electronic oceanographic data including CTD (Conductivity-temperature-depth) vertical profiles of temperature, salinity, light transmission, chlorophyll a fluorescence, and photosynthetic available radiation (PAR); and 3) collect biological oceanographic samples (zooplankton and water) by oblique bongo tows and water sampling.

We studied young of the year sablefish Anoplopoma fimbria to collect basic life history information on their abundance, growth, and diet and to determine whether forecasting year class abundance based on young of the year surveys was practical. Surface gillnet surveys were conducted annually from 1995 to 2004 along the seaward edge of the continental shelf of Alaska. Otoliths were extracted from a random subset of juvenile sablefish sampled by gillnet. This data set includes voucher otoliths from these studies.