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.

An experimental bottom longline survey was conducted at depths >1,000 m in the western Gulf of Alaska in August 2008. The objective was to investigate the abundance and biological characteristics of giant grenadier (Albatrossia pectoralis) and sablefish (Anoplopoma fimbria) in deep waters of the Gulf of Alaska that have not been previously sampled in fishery surveys. Several difficulties were encountered during the fishing operations which indicate special problems may occur when fishing longlines at these depths, including substantial gear drift after setting and hang-ups on the bottom that caused the longline to part. Although results were not conclusive because only stations in the western Gulf of Alaska were sampled, there was consistency in the results which provides an indication of fish abundance and distribution in depths >1,000 m. Catch rates of giant grenadier were relatively high, although not as large as those in nearby longline survey stations in depths <1,000 m. Female giant grenadier were much larger in size at the deep-water stations, and their weight averaged 69% greater than females at depths <1,000 m. Males, which comprise a low percentage of the catch in shallower water, were caught in much higher numbers at the deep-water stations. Catch rates for sablefish at the deep-water stations were extremely low, and it appears abundance of sablefish is negligible in the western Gulf of Alaska at depths >1,000 m. Besides giant grenadier, Pacific grenadier (Coryphaenoides acrolepis) was the only other species caught in substantial numbers. At one deep-water station, Pacific grenadier were extremely abundant and were caught on 56% of the longlines hooks.

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.

Data is available from annual bottom longline surveys conducted cooperatively by Japan (1979-1994) and the U.S. National Marine Fisheries Service, Alaska Fisheries Science Center (1988-present). Starting in 1988, the U.S. started conducting the survey, creating overlap between the two countries between1988-1994. Since 1994, the U.S. has conducted the survey independently. Stations are spaced systematically (~20-30 km apart) along the slope from the eastern Gulf of Alaska west to the Aleutian Islands and north into the eastern Bering Sea. At each station, depths from ~150-1000 meters are sampled. Each year the captain attempts to set the gear along the same path. The same stations are sampled each year except in the Aleutian Islands and the Bering Sea, which are sampled every other year at the beginning of the survey (last week of May-early June). Since 1995, in odd years the Bering Sea stations are sampled and in even years the Aleutian Islands are sampled. The status of each hook is recorded. Lengths are taken from major species including, sablefish, giant grenadier, Pacific grenadier, Greenland turbot, arrowtooth flounder, Pacific cod, shortspine thornyhead, and all rockfish caught.

Variable mesh gillnets were used to evaluate the abundance of young of the year sablefish during 1995-2002. Data include. Vessel, cruise, station. Species caught, and lengths of fish caught. The data were collected to be able to forecast year-class strength of sablefish.

In November, 2006, Oceanographic observations were initiated during the resupply cruises to the Little Port Walter Research Station on lower Baranof Island, Southeast Alaska. Six sampling stations were selected starting at mid channel, Stephans Passage near Snettisham Inlet then, near the intersection of Stephans Passage and Fredrick Sound by Brothers Islands, then, near the intersection of Fredrick Sound and Chatham Strait off of Kingsmill Point and then three stations across lower Chatham Strait just north of the latitude of Little Port Walter. An SBE19plus conductivity, temperature and depth recorder was used to take water samples at a speed of approximately one meter per second from the surface to a depth of 250 meters. These observations are intended to be part of the Southeast Alaska Ocean Observing System (SEAOOS). Data are stored as CNV files, HEX files and jpg files on Frank Throwers computer.

The Southeast Fisheries Science Center Mississippi Laboratories conducts standardized fisheries independent resource surveys in the Gulf of Mexico, South Atlantic, and U.S. Caribbean to provide abundance and distribution information to support regional and international stock assessments. In 2015, an experimental longline survey was conducted to provide additional sampling opportunities outside the annual bottom longline survey time frame and standard protocols, including testing the effects of variable bait type, leader material and covering a larger depth range.

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.

In order to manage vulnerable benthic habitats, such as deep-sea corals and sponges, the impacts of human activity including commercial fishing must be known and accounted for. One type of fishing gear whose impact has rarely been studied is commercial longline gear. We performed a series of experiments in 2013 and 2014 to address this knowledge gap using inertial measurement units and underwater cameras. These data area stored as image files, .bcs files and as .csv files.

The Southeast Fisheries Science Center Mississippi Laboratories conducts standardized fisheries independent resource surveys off the east coast of the United States to provide abundance and distribution information to support regional and international stock assessments. A pilot pelagic longline survey was conducted in 2006 off the U.S. east coast. The objective of the survey was to examine the feasibility of using pelagic longline gear to collect fisheries independent data on stocks of offshore fishes and to establish protocols for future use of data. Additional objectives included examining the distribution and relative abundance of pelagic fishes in the region and to collect biological and environmental data.