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.

The project consisted of a nearshore fish, invertebrate, and habitat survey in northern Bristol Bay, Alaska. A 32-ft. gillnet vessel, the F/V Willow was chartered for the survey, and we also used a 20-ft. aluminum skiff with 90-hp. motor for shallow water work. The survey was staged out of Dillingham, Alaska and took place from July 26-August 8, 2009.The main gear types used during the survey were a beach seine and a bottom beam trawl. A surface pair trawl (towed by the vessel and the skiff) was deployed in one location. Using these gear types, we sampled from the shoreline to 17 m depth, as well as surface waters ~1 km from the shoreline. Catches were sorted to species, enumerated, and when possible weighed using spring scales. Length measurements were taken for most species. Voucher specimens were preserved in 10% formalin for confirmation of species identification. A small number of samples were frozen for age and energetics analysis . Photographs were taken of most species. Small, datalogging conductivity-temperature-depth recorders (CTDs) were deployed on the trawl gear, and also placed on temporary moorings in several locations to study fluctuations in temperature and salinity over tidal cycles. We also recorded habitat variables at beach seine sites according to the methodology used in the Nearshore Fish Atlas of Alaska. During July 26-August 1, 2009 sampling was conducted in Nushagak Bay. High wind and waves hampered the sampling throughout this entire week and largely determined possible sampling locations. Two days were completely lost due to weather. On August 3 we traveled from Dillingham to the west side of the Nushagak and from August 4-8 sampling was conducted along the Nushagak Peninsula and in Kulukak, Nunavachak, Ungalikthluk, and Togiak Bays. During most of this time we experienced high winds but they did not hamper the sampling to the same degree as in the Nushagak. On August 8 we traveled back to Dillingham.

Between 2004 and 2006 we conducted four harbor seal tagging trips in Cook Inlet during the months of October and May. In total, we captured and released 93 harbor seals, 77 of which were tagged with satellite transmitters. Each transmitter was glued to the hair on the back of the seal using durable epoxy. Fourteen of the seals were also equipped with specially developed transmitters that were attached to one of the rear flippers. Transmissions from the 91 tags resulted in 178,536 location estimates and 310,593 dive and haul-out behavior records. These data formed the basis for the development of novel analysis techniques. Johnson et al. (2008) described a novel continuous-time correlated random walk (CTCRW) method for predicting animal locations from satellite tags. Higgs and Ver Hoef (2011) described a new statistical method for analyzing dive behavior based on dive histogram recordings obtained from satellite tags. The data files within this dataset represent the 'raw' data obtained from the Wildlife Computers data portal. Each deployment (unique tag id + animal id combination) is provided as a zipped archive. The root folder also includes additional documentation. The various files and detailed column descriptions are described in the 'Spreadsheet-File-Descriptions.pdf' which was downloaded from Wildlife Computers (https://wildlifecomputers.com/support/downloads/). The '00_cookinletpv_get_data.Rmd' file is an RMarkdown file that provides code and documentation of the data retrieval process. The corresponding '00_cookinlet_get_data.hml' file is autogenerated from the RMarkdown file.

The objectives of these Arctic nearshore fish surveys is to measure seasonal changes in the distribution, demographics, trophic position and nutritional status of forage fish during the partial and complete ice-free season near Pt. Barrow, along the nearshore Chukchi and Beaufort Seas including Elson Lagoon, Alaska. These data will be related to biological and physical conditions observed near the Chukchi and Beaufort coasts and Elson Lagoon. Arctic Cod (Boreogadus saida), Saffron Cod (Eleginus gracilis), Capelin (Mallotus villosus), Sand Lance (Ammodytes hexapterus), Coregonids and sculpins will serve as the primary forage species targeted in the proposed work. The physical features to be measured include salinity, temperature, current direction and speed, wind direction and speed and bathymetry, but most importantly we seek a better understanding of how weather (wind) would affect the transport through the multi-inlet Elson Lagoon and its relation to coastal currents. Biological features include the community composition, abundance, distribution and quality of zooplankton prey available to forage fish. The catch data in this database include sampling efforts from 3 complimentary studies using similar gear in similar areas: ACES (Arctic Coastal Ecosystem Survey) and SHELFZ (Shelf Habitat and EcoLogy of Fish and Zooplankton), Ecology of Forage Fishes in the Arctic Nearshore. Data will be comparable to NOAAs previous efforts in the nearshore near Pt. Barrow (e.g. Thedinga et al. 2013). Combining these historical data with the proposed work will lead to an improved understanding of the relationship between forage fish and their nearshore habitats during the partial and complete ice-free period. The information developed by this proposed project is needed by those engaged in predicting impacts of climate change, developing oil and gas resources, managing foraging habitat of marine mammals, and planning for increased marine transportation.

Floating glacial ice serves as a haul-out substrate for a significant number (10-15%) of Alaskan harbor seals, and thus surveying tidewater glacial fjords is an important component of statewide efforts to estimate seal abundance. Surveys conducted during pupping suggest that glacial haul outs have higher than average productivity and thus may serve as important source populations statewide. The availability of ice for hauling out varies with seasonal glacial dynamics, but over decades of climate change most tidewater glaciers are now retreating toward eventual grounding with many already ceasing to calve ice into the water. Compounding glacial retreat and thinning is the trend at most of these sites toward increasing tourism and a low compliance of tour vessels to seal approach guidelines and regulations. It is thus important to track glacial populations over the long-term especially as various impacts may degrade seal habitat leading to fewer glacial seals and potential impacts to the population state-wide. There are currently 28 glacial sites that have at least one actively calving tidewater glacier and in turn seals that haul out on the ice during the seals’ molting period, when most surveys have occurred. Due to concerns about vessel disturbance, Disenchantment and Icy Bays have been surveyed during molting almost annually between 2001-2011 (ex 2003); surveys occurred during pupping and molting in 2004 and 2005, and have occurred just during molting apx. every other year since 2011. Johns Hopkins Inlet in Glacier Bay has been surveyed annually using these methods since 2007, with surveys occurring during both pupping and molting. The remaining 25 sites have been surveyed on an opportunistic schedule (based on weather and aircraft availability), which for most sites equates to about every 2-3 years. Some of the smallest sites have been surveyed on a 4-5 year schedule. These schedules will likely continue with more abundant sites in Prince William Sound (e.g., College Fjord and Columbia) and Southeast Alaska (Tracy Arm, Endicott Arm, LeConte Bay, and Glacier Bay) having higher priority and contingent on management concerns.

A total of 105 stations were occupied. There were two sample grids (southeast Alaska and Yakutat Bay) and two transects in the vicinity of Kayak Island. At each station we sampled using paired 20 and 60 cm Bongo frames (150 and 500 micron mesh nets, respectively) and a Sameoto neuston sampler (500 micron mesh net) to estimate the abundance of zoo- and ichthyoplankton. A SeaBird SeaCat (SBE 19 plus) was used with the bongo frames to determine the depth of the samplers in real time and to measure temperature and conductivity. At a few selected stations depth-stratified plankton were obtained with a 1 meter squared MOCNESS (500 micron mesh nets) and at other selected stations microzooplankton were sampled with vertical tows of a CalVET net (53 micron mesh).

A total of 105 stations were occupied. There were two sample grids (southeast Alaska and Yakutat Bay) and two transects in the vicinity of Kayak Island. At each station we sampled using paired 20 and 60 cm Bongo frames (150 and 500 micron mesh nets, respectively) and a Sameoto neuston sampler (500 micron mesh net) to estimate the abundance of zoo- and ichthyoplankton. A SeaBird SeaCat (SBE 19 plus) was used with the bongo frames to determine the depth of the samplers in real time and to measure temperature and conductivity. At a few selected stations depth-stratified plankton were obtained with a 1 meter squared MOCNESS (500 micron mesh nets) and at other selected stations microzooplankton were sampled with vertical tows of a CalVET net (53 micron mesh).

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.

The dataset contains records of fish eggs and larvae collected during FOCI assessment surveys. Records include all data pertinent to identify where specimens were collected (lat, lon, date, gear used, max depth of gear, water depth). Specific data on specimens includes scientific name, stage of development, number collected (whole numbers and CPUE), lengths of larvae, and diameters and stages of eggs. In addition, there are comments that explain any irregularities that may have occurred during sample collection; depending on the reason data is being extracted, comments may indicate a sample is not suitable for consideration.

The Alaska Fisheries Science Center's Status of Stocks and Multispecies Assessment (SSMA) Programs Fishery Interaction Team (FIT) conducted a fish survey in the marine offshore waters of the Beaufort Sea during the month of August, 2008. The Mineral Management Service (MMS) provided funding for the survey. The results of the survey provided estimates of abundance, species composition and biological information of marine fish and invertebrates, oceanographic properties and information on the macro- and micro- zooplankton communities.