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Fisheries scientists provide stock, ecosystem, habitat, and climate assessments to support interdisplinary fisheries management in the US and worldwide. These assessment activities have evolved different models, using different review standards, and are communicated using different vocabulary. Recent research shows that spatio-temporal models can estimate population density for multiple locations, times, and species, and that this is a “common currency” for addressing core goals in stock, ecosystem, habitat, and climate assessments. I therefore review the history and “design principles” for one spatio-temporal modelling package, the Vector Autoregressive Spatio-Temporal (VAST) package. I then provide guidance on fifteen major decisions that must be made by users of VAST, including: whether to use a univariate or multivariate model; when to include spatial and/or spatio-temporal variation; how many factors to use within a multivariate model; whether to include density or catchability covariates; and when to include a temporal correlation on model components. I finally demonstrate these decisions using three case studies. The first develops indices of abundance, distribution shift, and range expansion for arrowtooth flounder (Atheresthes stomias) in the Eastern Bering Sea, showing the range expansion for this species. The second involves “species ordination” of eight groundfishes in the Gulf of Alaska bottom trawl survey, which highlights the different spatial distribution of flathead sole (Hippoglossoides elassodon) relative to sablefish (Anoplopoma fimbria) and dover sole (Microstomus pacificus). The third involves a short-term forecast of the proportion of coastwide abundance for five groundfishes within three spatial strata in the US West Coast groundfish bottom trawl survey, and predicts large interannual variability (and high uncertainty) in the distribution of lingcod (Ophiodon elongatus). I conclude by recommending further research exploring the benefits and limitations of a “common currency” approach to stock, ecosystem, habitat, and climate assessments, and discuss extending this approach to optimal survey design and economic assessments.

Between 2001 and 2013 the southeastern Bering Sea alternated between multi-year periods of relatively warm (2001–2005) and relatively cold (2007–2013) years. Adult Flathead Sole Hippoglossoides elassodon in the southeastern Bering Sea shift their spatial distribution pattern in relation to bottom water temperature indicating the importance of the thermal environment in determining fish habitat. The objective of this study was to infer Flathead Sole spawning area in the southeastern Bering Sea in May from ichthyoplankton surveys of their eggs using generalized additive models to assess how warm (2002, 2003, and 2005) and cold (2008, 2009, 2010, and 2012) years affected the location of their spawning site. Three mechanisms through which temperature could affect egg distribution were investigated: 1) additively, assuming a similar effect of temperature across the spatial domain, 2) as a spatially variable term, assuming that the effect of temperature changes across locations, and 3) as a threshold effect on the spatial distribution of eggs, assuming the distribution of eggs changes abruptly in relation to the annual average temperature. The model including temperature as a spatially variable effect had the smallest AIC score and therefore was chosen as the best fit. This model showed that the effect of temperature on egg density varied across the study area and indicated a northeastward expansion of the spawning site as temperature increased. The area of expansion may correspond with the outer reach of a cold-water mass (called the cold pool) that extends in the Bering Sea middle domain during late spring and summer, and forms as a result of the previous winter ice coverage. Flathead Sole are known to avoid temperatures colder than 2 °C that is also used as the boundary for the cold pool, thus spawning fish may have moved relative to the spatial extent of the cold pool.

Stock of demersal fish species at the depths of 20–386 m in the northwestern Bering Sea, as well as pelagic and anadromous fishes in the bottom biotopes, are considered on the data of the bottom trawl survey conducted within the West-Bering and Chukchi fishery districts in the summer of 2017. The total accounted biomass of demersal fish was 1756,870 t, including 1578,430 t in the West-Bering and 178,440 t in the Chukchi district. The mean distribution density was similar in both districts: 11331.8 and 10748.0 kg/km 2 , respectively. Pacific cod formed the bulk of the demersal fish biomass — 1227,300 t. Among other species, the stocks were considerable for flathead sole — 96,310 t, great sculpin — 79,160 t, alaska plaice — 71,200 t, and arrowtooth flounder — 40,630 t, and the summary biomass of all others was 242,270 t. The total biomass of pelagic and anadromous fish species presented in the bottom biotopes was estimated as 3884,150 t, including 3555,930 t in the West-Bering and 328,220 t in the Chukchi district. They had higher distribution density in the West-Bering district — 25527.9 kg/km 2 vs 19769.9 kg/km2 in the Chukchi district. Walleye pollock prevailed among these species with the total biomass 3884,150 t (assessed with the catchability coefficient for adults k = 0.4), including 36,080 t of accounted yearlings (k = 0.1). Biomasses of other pelagic fishes in the bottom biotopes were 415,380 t for pacific herring, 18,680 t for arctic cod, 920 t for capelin, and 260 t for all others in sum. Comparing these new assessments with the data of analogous survey in 2015, the stocks of pacific herring, rock sole, alaska plaice, and ray Bathyraja parmifera have decreased and the stocks of arctic cod, saffron cod, pacific cod, walleye pollock (both adults and yearlings), flathead sole, and yellowfin sole have increased. Positive and negative anomalies from the standard curves of size composition for some species could be considered as a basement for forecasting of their stocks tendencies in the nearest future.

Biological features of the seven abundant commercial species—the Pacific halibut Hippoglossus stenolepis, the Greenland halibut Reinhardtius hippoglossoides, the Alaska plaice Pleuronectes quadrituberculatus, the northern rock sole Lepidopsetta polyxystra, the yellowfin sole Limanda aspera, the flathead sole Hippoglossoides elassodon, and the Bering flounder H. robustus (Pleuronectidae)—have been studied for a 20-year period (1995−2015). These species are present in the northwestern Bering Sea in the summer–autumn season; they form the gatherings in Olyutorsky-Navarin region. The size-weight spectra of the fish caught by different fishing gear has been analyzed, the peculiarities of the linear growth and the weight gain, as well as the spawning period and scale and the spawning conditions, have been described. The largest halibut specimens have been registered in the bottom setlines and gill nets, while flounders were in snurrevad catches; the smallest specimens have been observed in trawl catches. The abundant year-class in most of the studied species is seen well on the long-term plots of the fish size spectra and is tracked by the decrease of their biological parameters. The species that demand vast growing grounds (Pacific halibut, Alaska plaice, northern rock sole, and yellowfin sole) are characterized by a smaller average body size of the fish sampled in the coastal waters due to the prevalence of the young specimens in this area.

Cited and archive data on fecundity of 31 flatfish species are generalized for the North Pacific. General characterization of the fecundity is presented and correlation between absolute individual fecundity of the females and their body length or age is analyzed and formalized in equation form. Spatial variability of fecundity is described for different species: pacific halibut and starry flounder have the highest absolute fecundity in the eastern Bering Sea and Okhotsk Sea, greenland halibut, yellowfin sole, alaska plaice, sakhalin flounder, longhead dab, and flathead sole - in the Okhotsk Sea, northern rock sole - in the waters at East and West Kamchatka. kamchatka flounder - in the Bering Sea, arrowtooth flounder - in the Pacific waters at North America. So, the Okhotsk Sea is the area where the absolute fecundity of majority wide-spread flatfish species can reach the maximal level. However, the maximal fecundity of longsnouted flounder is higher in the Japan Sea than in the Okhotsk Sea.

Stocks of demersal fishes on the depths of 20-200 m in the northwestern Bering Sea are considered, excluding walleye pollock Theragra chalcogramma , on the data of 10 bottom trawl surveys conducted in the summer-fall of 1985-2015. The mean total biomass of demersal fish in two parts of this area (Western Bering Sea zone and Chukchi zone) in this period was 747.78 . 10 3 and 119.83 . 10 3 t, with almost equal density distribution: 5757 and 5709 kg/km 2 , respectively. The biomass had some redistributions in recent times: the assessments were 832.97 . 10 3 and 69.88 . 10 3 t in 2012, and 946.31 . 10 3 and 141.40 . 10 3 t in 2015, respectively. Pacific cod Gadus macrocephalus is usually the dominant species in the Western Bering Sea zone (up to 57 % of the total biomass in 2015) followed by subdominant species as alaska plaice Pleuronectes quadrituberculatus , flathead sole Hippoglossoides spp., alaska skate Bathyraja parmifera , and great sculpin Myoxocephalus polyacanthocephalus with portions of each species between 5-13 %. Generally, the ichthyocenosis of both zones was monodominant; the polydominant structure was observed in the Western Bering Sea zone only in 2001 and 2005, in conditions of abnormally low cod abundance. The total stock of demersal fish is determined mostly by state of the cod stock. It was very high in the middle 1980s, then had a significant decline in the late 1990s - early 2000s, but rises again since the middle 2000s. A considerable part of the mass demersal species migrate in summer from the Western Bering Sea to the Chukchi zone for feeding that is the background for significant fluctuations of their biomass assessments, which depend on the environments variability. The densest aggregations of the mass demersal fish form mainly in the area between Cape Olyutorsky and Cape Navarin and in the Anadyr Bay in the waters of the Navarin Current.

In this analysis we demonstrate how preferred fish habitat can be predicted and mapped for juveniles of two Alaskan groundfish species – Pacific halibut (Hippoglossus stenolepis) and flathead sole (Hippoglossoides elassodon) – at five sites (Kiliuda Bay, Izhut Bay, Port Dick, Aialik Bay, and the Barren Islands) in the central Gulf of Alaska. The method involves using geographic information system (GIS) software to extract appropriate information from National Ocean Service (NOS) smooth sheets that are available from NGDC (the National Geophysical Data Center). These smooth sheets are highly detailed charts that include more soundings, substrates, shoreline and feature information than the more commonly-known navigational charts. By bringing the information from smooth sheets into a GIS, a variety of surfaces, such as depth, slope, rugosity and mean grain size were interpolated into raster surfaces. Other measurements such as site openness, shoreline length, proportion of bay that is near shore, areas of rocky reefs and kelp beds, water volumes, surface areas and vertical cross-sections were also made in order to quantify differences between the study sites. Proper GIS processing also allows linking the smooth sheets to other data sets, such as orthographic satellite photographs, topographic maps and precipitation estimates from which watersheds and runoff can be derived. This same methodology can be applied to larger areas, taking advantage of these free data sets to describe predicted groundfish essential fish habitat (EFH) in Alaskan waters.

Flatfishes support a number of important fisheries in Alaskan waters and represent major pathways of energy flow through the ecosystem. Despite their economic and ecological importance, little is known about the use of habitat by juvenile flatfishes in the eastern Bering Sea. This study describes the habitat characteristics of juvenile flatfishes in coastal waters along the Alaska Peninsula and within the Port Moller–Herendeen Bay system, the largest marine embayment in the southern Bering Sea. The two most abundant species, northern rock sole and yellowfin sole, differed slightly in habitat use with the latter occupying slightly muddier substrates. Both were more common along the open coastline than they were within the bay, whereas juvenile Alaska plaice were more abundant within the bay than along the coast and used shallow waters with muddy, high organic content sediments. Juvenile Pacific halibut showed the greatest shift in distribution between age classes: age-0 fish were found in deeper waters (~ 30 m) along the coast, whereas older juveniles were found in the warmer, shallow waters within the bay, possibly due to increased thermal opportunities for growth in this temperature-sensitive species. Three other species, starry flounder, flathead sole, and arrowtooth flounder, were also present, but at much lower densities. In addition, the habitat use patterns of spring-spawning flatfishes (northern rock sole, Pacific halibut, and Alaska plaice) in this region appear to be strongly influenced by oceanographic processes that influence delivery of larvae to coastal habitats. Overall, use of the coastal embayment habitats appears to be less important to juvenile flatfishes in the Bering Sea than in the Gulf of Alaska.

According to the nursery size hypothesis, flatfish recruitment is constrained by nursery area. Thus, if resource selection models can be shown to accurately predict the location and geographic extent of flatfish nursery areas, they will become important tools in the management and study of flatfish population dynamics. We demonstrate that some resource selection models derived previously to predict the presence and absence of juvenile flatfishes near shore were applicable to the broader continental shelf. For other age-species groups, derivation of new models for the continental shelf was necessary. Our study was conducted in the western Gulf of Alaska (GoA) during October 2011 on four groups of age-0 juvenile flatfishes: Pacific halibut (Hippoglossus stenolepis), arrowtooth flounder (Atheresthes stomias), northern rock sole (Lepidopsetta polyxystra), and flathead sole (Hippoglossoides elassodon); and three groups of age-1 juvenile flatfishes: northern rock sole, flathead sole, and yellowfin sole (Limanda aspera). Sampling occurred at 33 sites across the continental shelf. Fish were collected using a 3-m beam trawl, and a midwater trawl. Environmental data were collected on sediment composition and water temperature and depth. Many of the age-species groups co-occurred in the Shumagin and Barnabus sea valleys; however, age-0 arrowtooth flounder occurred at more locations than other juveniles, perhaps due to a relatively broad tolerance of environmental conditions and to the utilization of midwater habitat. Thus, the large nursery area of arrowtooth flounder may be one reason why they are currently the most abundant GoA flatfish. In fact, among all species, mean recruitment at age 3 increased with the percent occurrence of age-0 juveniles at the 33 sites, a proxy for relative nursery area, in accordance with the nursery size hypothesis, suggesting that mean recruitment among GoA flatfishes is structured by nursery size.

Female Yellowfin Sole Limanda aspera, Alaska Plaice Pleuronectes quadrituberculatus, and Flathead Sole Hippoglossoides elassodon were collected from the eastern Bering Sea during known prespawning, spawning, and postspawning periods in 2012 and 2013, and their ovaries and otoliths were sampled for use in histological analysis to update historical maturity estimates. For fisheries management, new information on maturity at age can lead to possible changes in estimated reproduction potential (measured as female spawning stock biomass [SSB]) and values of fishing mortality reference points. Our analysis indicated that Yellowfin Sole currently mature at an age similar to that estimated in a study conducted 20 years ago. An evaluation of impacts on the stock assessment indicated that updated estimates of Yellowfin Sole SSB were over 7% higher, but the reference points only changed slightly. The first histologically derived maturity estimates for Alaska Plaice were close to the anatomically derived esti...

The objectives of this study were to examine levels of arsenic, cadmium, lead, mercury and selenium in edible tissue of seven species of marine fish collected from several Aleutian islands (in 2004) to determine: (1) interspecific differences, (2) locational differences (among Aleutian Islands), (3) size-related differences in any metal levels within a species, and (4) potential risk to the fish or to predators on the fish, including humans. We also compared metals levels to those of three other fish species previously examined in detail, as well as examining metals in the edible tissue of octopus (Octopus dofleini). Octopus did not have the highest levels of any metal. There were significant interspecific differences in all metal levels among the fish species, although the differences were less than an order of magnitude, except for arsenic (mean of 19,500 ppb in Flathead sole, Hippoglossoides elassodon). Significant intraisland variation occurred among the four sites on Amchitka, but there was not a consistent pattern. There were significant interisland differences for some metals and species. Mercury levels increased significantly with size for several species; lead increased significantly for only one fish species; and cadmium and selenium decreased significantly with size for halibut (Hippoglossus stenolepis). The Alaskan Department of Health and Social Services supports unrestricted consumption of most Alaskan fish species for all people, including pregnant women. Most mean metal concentrations were well below the levels known to adversely affect the fish themselves, or predators that consume them (including humans), except for mercury in three fish species (mean levels just below 0.3 ppm), and arsenic in two fish species. However, even at low mercury levels, people who consume fish almost daily will exceed guideline values from the Centers for Disease Control and the Environmental Protection Agency.

Stomach content analysis of eastern North Pacific groundfish has been conducted routinely by researchers interested in understanding trophic interactions between key predator species and their prey. Identification of prey by traditional morphological methods has limitations however, due to the loss of identifiable characters from digestion and morphological similarities between taxa. Furthermore, some forage fish ( e.g ., osmerids, ammodytids, and juvenile gadids), common prey of Bering Sea and Gulf of Alaska groundfish, are difficult to distinguish because of their slender or fusiform shape, disarticulating easily during digestion. DNA-based identification methods were developed to differentiate among 18 fish species, some that are found at depths greater than 200 m, from four taxonomic families: Ammodytidae and Osmeridae (forage fish), Pleuronectidae (flatfish), and Gadidae (gadid fish). Polymerase chain reaction (PCR) amplification of a 739 basepair section of mitochondrial DNA cytochrome c oxidase I and an 862 basepair section of mitochondrial DNA cytochrome b was followed by restriction digest assays and resulted in species level resolution for 16 of 18 species of interest. PCR restriction digest assays applied to fish prey from stomach contents of groundfish indicated the presence of several target species, eulachon ( Thaleichthys pacificus ), walleye pollock ( Gadus chalcogrammus ), searcher ( Bathymaster signatus ), rock sole ( Lepidopsetta bilineata ), yellowfin sole ( Limanda aspera ) and either Bering flounder ( Hippoglossoides robustus ) or flathead sole ( H. elassodon ). The PCR restriction digest protocols improved the identification rate of predated fish from stomach contents compared to identification by conventional taxonomic methods alone, and DNA sequence analysis further resolved identification of unknown prey fish samples.

This study provides a retrospective analysis of the relationship between physical oceanography, biology and recruitment of three Eastern Bering Sea flatfish stocks: flathead sole ( Hippoglossoides elassodon ), northern rock sole ( Lepidopsetta polyxystra ), and arrowtooth flounder ( Atheresthes stomias ) during the period 1978–2005. Stock assessment model estimates of recruitment and spawning stock size indicate that temporal patterns in productivity are consistent with decadal scale (or shorter) patterns in climate variability, which may influence marine survival during the early life history phases. Density-dependence (through spawning stock size) was statistically significant in a Ricker stock-recruit model of flatfish recruitment that included environmental terms. Wind-driven advection of northern rock sole and flathead sole larvae to favorable nursery grounds was found to coincide with years of above-average recruitment. Ocean forcing of Bristol Bay surface waters during springtime was mostly on-shelf (eastward) during the 1980s and again in the early 2000s, but was off-shelf (westerly) during the 1990s, corresponding with periods of good and poor recruitment, respectively. Finally, the Arctic Oscillation was found to be an important indicator of arrowtooth flounder productivity. Model results were applied to IPCC (Intergovernmental Panel on Climate Change) future springtime wind scenarios to predict the future impact of climate on northern rock sole productivity and indicated that a moderate future increase in recruitment might be expected because the climate trends favor on-shelf transport but that density-dependence will dampen this effect such that northern rock sole abundance will not be substantially affected by climate change.

Flatfish condition indices and distribution were examined along the U.S. west coast (55–1280 m) in relation to environmental variability and biomass using data from ten frequently occurring species collected in annual groundfish surveys from 2003 to 2010. The study was conducted during a period characterized by a cooling trend in the northern California Current system and by declining biomass for flatfish in general. Annual condition indices for six species (arrowtooth flounder, Dover sole, English sole, Pacific sanddab, petrale sole, and rex sole) were significantly related either to large-scale climatic indices (Pacific Decadal Oscillation, Multivariate El Nino–Southern Oscillation Index, North Pacific Gyre Oscillation) and/or annual biomass levels. Condition was most closely related to environmental effects rather than either biomass alone or both variables, with condition typically higher during cool climatic conditions. A similar analysis revealed that changes in distribution (measured as variation in annual catch-weighted mean latitude, longitude, depth and temperature) tended to be best described by models incorporating environmental effects and biomass rather than either variable alone. Linear trends in the center of distribution along a southeast–northwest axis were significant for seven species (arrowtooth flounder, deepsea sole, Dover sole, flathead sole, Pacific sanddab, petrale sole, and slender sole) with a tendency for flatfish to be displaced towards the southeast as environmental conditions shifted from warm to cooler conditions and biomass declined. A spatial distribution analysis indicated that for the majority of species (80%) the greatest magnitude of displacement (km) occurred when the centers of biomass were compared between environmental phases (average annual displacement 34 km) rather than changing biomass levels (average displacement 24 km). Taken together both approaches revealed that environmental changes and variation in biomass play significant roles in flatfish distribution.

North Pacific flatfishes are gaining increased popularity on the German market. Isoelectric focusing of sarcoplasmic proteins and PCR-based DNA analysis were applied to identify fillets of nine Alaskan Flatfish species: Artheresthes stomias (Arrow-tooth flounder), Limanda aspera (Yellowfin sole), Isopsetta isolepis (Butter sole), Lepidopsetta bilineata (Southern rock sole), Lepidopsetta polyxystra (Northern rock sole), Hippoglossus stenolepis (Pacific halibut), Hippoglossoides elassodon (Flathead sole), Platichthys stellatus (Starry flounder), and Glyptocephalus zachirus (Rex sole). Characteristic protein patterns were obtained for raw fillets of several species. Reactivity of flatfish DNA against five pairs of primers was tested, amplifying segments of the mitochondrial cytochrome b, cytochrome oxidase subunit I, 16S rRNA gene, as well as the nuclear parvalbumin gene. Amplicons of the cytochrome b gene were sequenced and used for single-strand conformation polymorphism analysis. The survey of deep-frozen commercial yellowfin sole fillets resulted in the detection of 17% of the fillets being mislabelled; Northern rock sole, butter sole and flathead sole had been used as substitutes.

Two similar appearing congeners, Hippoglossoides robustus (Bering flounder) and H. elassodon (flathead sole), inhabit the Bering Sea and are harvested together during the commercial fishery. In order to establish more precise overfishing limits, the annual spawning biomass must be estimated. Spawning biomass is modelled using the best estimate of the age and length at which 50% of the stock is expected to reach maturity (A 50, L 50). The major objective of this study was to establish the first maturity estimates for Bering flounder. Females matured at a similar age for Bering flounder (A 50, 9 years) and flathead sole (A 50, 10 years). However, the body length at which females matured was significantly smaller for Bering flounder (L 50, 238 mm) compared to flathead sole (L 50, 320 mm). The difference in the length-at-maturity was probably caused by growth differences, which significantly differed between species. The distribution and spawning locations of both species in the eastern Bering Sea su...

The general warming of the eastern Bering Sea (EBS) and the wide range of abundance exhibited by several eastern Bering Sea flatfish motivated an examination of how density-dependent and density-independent factors may influence the spatial distributions of EBS flatfish. In this study, EBS trawl survey data from 1982 to 2006 were used to examine how temporal changes in the distributions of six flatfish species groups [yellowfin sole (Limanda aspera), rock sole (Lepidopsetta sp.), flathead sole (Hippoglossoides sp.), Alaska plaice (Pleuronectes quadrituberculatus), arrowtooth flounder (Atheresthes sp.), and Greenland turbot (Reinhardtius hippoglossoides)] are related to temporal changes in the location of the ‘cold pool’ (bottom water < 2� C), and how the area occupied by flatfish are related to the cold pool and population abundance. Rock sole and flathead sole distributions have generally moved northwest since 1982 and are significantly correlated with the movement of the cold pool, whereas arrowtooth flounder avoid the cold pool and their area occupied is inversely related to the size of the cold pool. The area occupied by arrowtooth flounder and rock sole are also significantly related to stock abundance. Multivariate statistical models indicate that the location of rock sole is more strongly related to stock abundance than to the cold pool, whereas the area occupied by arrowtooth flounder is more strongly related to the area of the cold pool rather than abundance. The temperatures occupied by several flatfish stocks indicate a substantial variability in suitable temperatures. These results suggest that a complex suite of density-dependent and density-independent factors may determine the response of EBS flatfish spatial distributions to increasing temperatures.

Yeung, C., and McConnaughey, R. A. 2008. Using acoustic backscatter from a sidescan sonar to explain fish and invertebrate distributions: a case study in Bristol Bay, Alaska. – ICES Journal of Marine Science, 65: 242–254. Environmental variables that are ecologically relevant and easily measured over large areas are useful for modelling species distributions and habitats. Continuous acoustic, sonar-backscatter data convey information about physical properties of the seabed, and hence could be a valuable addition to that suite of variables. We tested the potential utility of acoustic backscatter for improving habitat models of marine species using data from a pilot sidescan-sonar survey. Raw digital-backscatter data were processed with QTC SIDEVIEW and CLAMS software. Resultant acoustic variables—Q-values (Q1, Q2, and Q3), representing the first three principal components of the data derived from image analysis of backscatter echoes, and a complexity metric (compx) measuring the variance of Q-values in a geographic area—were used in multiple linear regression to model individual species abundance from bottom-trawl survey data. Habitat models for flathead sole (Hippoglossoides elassodon), Pacific cod (Gadus macrocephalus), walleye pollock (Theragra chalcogramma), red king crab (Paralithodes camtschaticus), basket star (Gorgonocephalus eucnemis), and sponges (Porifera) included acoustic variables as significant predictors. For these six taxa, full models explained 67–86% of variability in abundance, with 9–54% of that total contributed by the acoustic predictors, suggesting that acoustic data could advance habitat research for some bottom-associated marine species.

Increasingly there is a need to assess the contaminant levels in fish as indicators of the health and well-being of both the fish and their consumers, including humans. This paper examines the levels of arsenic, cadmium, chromium, lead, manganese, mercury, and selenium in the kidney, liver, and muscle of great sculpin and flathead sole from Adak Island in the Aleutian Islands, Alaska. Both species are consumed by the local Aleuts and others. There were significant differences in the levels of heavy metals as a function of tissue for both fish species; the liver of sculpin and sole generally had the highest levels of most metals, except for arsenic, lead, and selenium. Sole had significantly higher mean levels of arsenic in kidney (32,384 vs. 531 ppb, wet weight), liver (18,954 vs. 2532 ppb), and muscle (19,452 vs. 1343 ppb) than did sculpin. Sole also had higher mean levels of cadmium (230 vs. 63 ppb), lead (1236 vs. 48 ppb), mercury (150 vs. 107 ppb), and selenium (5215 vs. 1861 ppb) in kidney than did sculpin. There were significant correlations among weight and length measurements for both species. However, except for mercury, there were few significant correlations among tissue types for most metals. Only mercury and manganese levels were significantly correlated with size for sculpin (but not for sole). Levels of arsenic, lead, and mercury may pose a risk to predators that consume them, and arsenic and mercury may pose a risk to human consumers.

Concentrations of three non-essential elements (cadmium (Cd), mercury (Hg), and lead (Pb)) were determined in sediment and fish from several locations in Alaska (AK) and California (CA) and used to examine differences in bioaccumulation within and between geographic locations. We analyzed tissue (liver, muscle, gill, and stomach contents) from white croaker (Genyonemus lineatus) and English sole (Pleuronectes vetulus) in California and flathead sole (Hippoglossoides elassodon) in Alaska, in addition to several species of invertebrates (mercury only). As found in previous work on arsenic (As) [Meador et al., 2004], Cd in fish liver exhibited a negative correlation with sediment concentrations. No such correlations were found for Hg and Pb when fish liver and sediment were compared; however, these metals did exhibit a positive relationship between liver and organic carbon normalized sediment concentrations, but only for the CA sites. Sediment concentrations of Hg at the AK sites were lower than those for the CA sites; however, AK invertebrates generally bioaccumulated more Hg than CA invertebrates. Conversely, Hg bioaccumulation was higher in CA fish. Even though ratios of total metal/acid volatile sulfides (AVS) in sediment were one to two orders of magnitude higher for the AK sites, bioaccumulation of these elements was much higher in fish from the CA sites. Bioaccumulation factors ([liver]/[sediment]) (BAFs) were highest at relatively clean sites (Bodega Bay and Monterey), indicating that elements were more bioavailable at these sites than from more contaminated locations. The observation of high BAFs for As in fish from Alaska and low BAFs for the California fish, but reversed for Cd, Hg, and Pb in this study, implies that differences in fish species are less important than the unique geochemical features at each site that control bioavailability and bioaccumulation and the potential sources for each element. Additionally, these data were also used to examine the metal depletion hypothesis, which describes the inverse relationship between elements and organic contaminants documented in some monitoring studies. Our results suggest that the enhanced bioavailability of the metals at some uncontaminated sites is the main determinant for the inverse correlation between metal and organic contaminants in tissue.

This study describes a method for modeling and predicting, from biological and physi- cal variables, habitat use by a commercially harvested groundfish species. Models for eastern Bering Sea flathead sole Hippoglossoides elassodon were developed from 3 relationships describing the response of organism abundance along a resource continua. The model was parameterized for 1998 to 2000 trawl survey data and tested on 2001 and 2002 data. Catch per unit effort (CPUE) of flathead sole had a curvilinear relationship with depth, peaking at 140 m, a proportional relationship with bot- tom water temperature, a positive curvilinear relationship with potential cover (invertebrate shelter- ing organisms such as anemones, corals, sponges, etc.), a negative relationship with increasing mud:sand ratio in the sediment, and an asymptotic relationship with potential prey abundance. The predicted CPUE was highly correlated (r 2 = 0.63) to the observations (1998 to 2000) and the model accurately predicted CPUE (r 2 = 0.58) in the test data set (2001 and 2002). Because this method of developing habitat-based abundance models is founded on ecological relationships, it should be more robust for predicting fish distributions than statistically based models. Thus, the model can be used to examine the consequences of fishing activity (e.g. reduction in sheltering organisms), changes in temperature (e.g. climate effects) and interaction between variables, and can be modified to incorporate new variables as more information is collected about a species.

Female flathead sole Hippoglossoides elassodon maturity appears not to be area dependent since the total length (L T ) at which 50% were mature (L T50 ) was similar for the central Gulf of Alaska (333 mm) and south-eastern Bering Sea (320 mm) areas. Likewise the age at which 50% were mature (A 50 ) was similar in the south-eastern Bering Sea (9.7 years) and central Gulf of Alaska (8.7 years). The timing of female flathead sole spawning may also be similar between areas. Batch or serial spawning was indicated for flathead sole. Female flathead sole grew at a similar rate in both the Gulf of Alaska and Bering Sea. In contrast, males grew faster in the Bering Sea than in the Gulf of Alaska. Males grew more slowly than females in both areas after 5 years of age, and reached a smaller maximum L T . The growth of both sexes was similar during 1993 and 1996 in the Gulf of Alaska.

The effect of speed through water on the footrope capture efficiency of a survey bottom trawl was experimentally investigated by repetitively towing at three vessel speeds (2.5, 3.0 and 3.5 knots) with an auxiliary net attached underneath the trawl footrope to capture fish escaping beneath the trawl. Length-dependent capture efficiencies were then computed from the number of fish caught in both the trawl and auxiliary net. Capture efficiencies for Pacific cod Gadus macrocephalus, walleye pollock Theragra chalcogramma and Pacific halibut Hippoglossus stenolepis were not affected by fish length or trawl speed. Capture efficiency for skates Bathyraja spp. decreased with increasing trawl speed but was not affected by fish length. Capture efficiencies for arrowtooth flounder Atheresthes stomias and flathead sole Hippoglossoides elassodon increased with fish length and decreased with increasing trawl speed. Our results indicate that in areas of variable current, variation in survey catch per unit effort could be reduced for some species by standardizing towing speed to speed through water or by reducing footrope lift by the addition of sufficient weight to the trawl footrope.

This paper compiles data from bottom trawl surveys using variations on a 400-mesh eastern trawl gear into a 38-year time series (1963–2000), using a robust index of median catch per unit effort (CPUE) as an indicator of regional abundance. Time series are presented for three index sites in the southeastern Bering Sea: the inner shelf in Bristol Bay, the middle shelf north of Unimak Island, and the outer shelf near the Pribilof Islands. All three sites show strong evidence of a shift in benthic biomass and community structure in the early to mid-1980s. During this period, all three sites showed substantial increases in the abundances of walleye pollock, Pacific cod, rock sole, flathead sole, cartilaginous fishes (skates) and non-crab benthic invertebrates. Species composition, especially of flatfish, differs at the three sites, but the trend for groundfish abundance to increase was consistent at all three sites. The similarity in trends both across the region and across both commercial and unexploited groups suggests to us that a complete reorganization of benthic and demersal food webs may have taken place. The timing of change in trawl catch weight is consistent with effects of the strong regime shift observed in climate indices in 1976–1977. There is little evidence of similar biological responses to subsequent, less pronounced changes in climate. Our data are also consistent with recently documented shifts in ecosystem dynamics resulting from changes in ice cover and thermal structure in the eastern Bering Sea. Our analysis indicates that there was a much higher biomass of groundfish at all three sites during 1980–2000 than in 1960–1980. This result provides evidence against the hypothesis that the overall productivity of the eastern Bering Sea has decreased. The precipitous decline of the endangered Steller sea lion in this region from 1975–1985 was concurrent with an overall increase in abundance of groundfish prey.

This paper provides a retrospective analysis of the relationship of physical oceanography and biology and recruitment of three Eastern Bering Sea flatfish stocks: flathead sole (Hippoglossoides elassodon), northern rock sole (Lepidopsetta polyxystra), and arrowtooth flounder (Atheresthes stomias) for the period 1978–1996. Temporal trends in flatfish production in the Eastern Bering Sea are consistent with the hypothesis that decadal scale climate variability influences marine survival during the early life history period. Density-dependence (spawning stock size) is statistically significant in a Ricker model of flatfish recruitment, which includes environmental terms. Wind-driven advection of flatfish larvae to favorable nursery grounds was also found to coincide with years of above-average recruitment through the use of an ocean surface current simulation model (OSCURS). Ocean forcing of Bristol Bay surface waters during springtime was mostly shoreward (eastward) during the 1980s and seaward (westerly) during the 1990s, corresponding with periods of good and poor recruitment. Distance from shore and water depth at the endpoint of 90-day drift periods (estimated time of settlement) were also found to correspond with flatfish productivity.

Net efficiency, or the proportion of fish within the path of a trawl net that are captured, of the 83-112 Eastern bottom trawl was estimated for four flatfish and one roundfish species encountered on the stock assessment surveys of the eastern Bering Sea. Net efficiency data was collected by repeatedly towing with an experimental trawl consisting of the usual trawl net with an auxiliary net attached underneath which is designed to capture all fish escaping under the trawl footrope. Efficiency was estimated by the ratio of the catch from the trawl net to the combined catch from both nets. Estimates of net efficiency as a function of fish length were obtained by sequentially fitting a nested hierarchy of statistical models to the efficiency and length data for each species and choosing the best model using likelihood ratio tests. For flathead sole, Hippoglossoides elassodon; northern rock sole, Lepidopsetta sp. cf. bilineata; Pacific halibut, Hippoglossus stenolepis and Pacific cod, Gadus macrocephalus, net efficiency did not vary with body length and was always >0.94. For yellowfin sole, Limanda aspera, net efficiency increased with body length and reached an asymptotic maximum of 0.77.

A variety of eastern Bering Sea (EBS) flatfish including yellowfin sole (Limanda aspera), rock sole (Lepidopsetta bilineata), flathead sole (Hippoglossoides elassodon), and Alaska plaice (Pleuronectes quadrituberculatus), co-occur in various degrees in EBS trawl fisheries, impeding attempts to obtain single-species management targets. A further complication is the bycatch of Pacific halibut (Hippoglossus stenolepis); halibut bycatch limits, rather than single-species catch quotas, have been the primary factor regulating EBS flatfish harvest in recent years. To examine bycatch interactions among the EBS flatfish listed above, an equilibrium mixed-species multifishery model was developed. Equilibrium yield curves, scaled by recent average recruitment, are flat topped or asymptotically increasing, reflecting low fishing selectivity during the first several years of life and low growth relative to natural mortality. A linear programming analysis indicated that relaxation of the halibut bycatch constraint at the optimal solution of catch by fishery would produce approximately 20 times more flatfish yield than a similar relaxation of any flatfish catch quota. A strategy for establishing halibut bycatch limits that considers the foregone revenue in the halibut and flatfish trawl fisheries reveals how the choice of halibut bycatch limit is affected by the management goal for the flatfish complex.

An underwater video system is under investigation by the National Marine Fisheries Service for use in studying the capture efficiency of a survey bottom trawl’s footrope in diverse habitats commonly sampled during surveys. This system utilizes a 50-watt quartz halogen light since most survey stations are at depths greater than natural light can penetrate for low-light camera use. One potential shortcoming to this approach is that the light emitted might alter fish behaviour and thereby bias estimates of escapement. The light effect on escapement was examined by attaching the video system onto a trawl fitted with an auxiliary capture bag to retain those fish which would have otherwise escaped beneath. A paired towing experiment (unlit vs. lit) was conducted to test the hypothesis that there is no effect on capture proportion due to the addition of artificial light. ANOVA was used to test for the effect both fish length and water depth had on escapement. Since neither length nor depth were significant, a paired t test (α=0.05) was used to test the null hypothesis. For five of the six species examined, we found no effect of the light on fish escapement. Only flathead sole (Hippoglossoides elassodon) showed a statistically significant difference in capture proportion due to artificial light, the proportion decreasing by 0.0698.

Because it is unrealistic to assess fishes in all locations, models are needed to characterize the nursery habitats of flatfish species. Descriptive habitat models of species presence and categorical analysis regression tree (CART) models of species abundance have been developed in previous studies. Based on collections around Kodiak Island, Alaska in 1991 and 1992, these models have been developed for: age-0 flathead sole (Hippoglossoides elassodon); age-0 Pacific halibut (Hippoglossus stenolepis); age-1 yellowfin sole (Pleuronectes asper); and age-0 rock sole (Pleuronectes bilineatus). In 1995, collections were made in bays along the Alaska Peninsula (an area never before sampled for juvenile flatfishes) and were compared with the previous models developed for Kodiak Island in 1991 and 1992. Very simple descriptive models for Kodiak Island ( Norcross et al., 1995 , Neth. J. Sea Res. 34: 161–175) accurately predicted the abundance along the Alaska Peninsula of flathead sole (78%), Pacific halibut (96%), yellowfin sole (75%) and rock sole (99%) in specific depth ranges and on specific substrate types. More complex CART models of species abundance ( Norcross et al., 1997 , Fish. Bull. (US) 95: 504–520) were more precise but not as accurate as the descriptive models because some parameters were not always available at the test locations. Flathead sole were found at temperatures ≤ 8.9°C on mud and mixed mud substrates in similar proportions in 1995 (66%) as in 1991–92 (71%). Similarly, Pacific halibut were ≤ 7.9 km inside bays and at depths ≤ 40 m in 93% of the sites of this study, compared with 89% previously. Seventy-five per cent of yellowfin sole were at depths ≤ 28 m on mixed substrates in both study periods. Rock sole were found on sand and muddy sand substrates at temperatures above 8.7°C in 52% of the sites in present and 69% of the sites in previous studies. This field test demonstrated that both descriptive and CART models were very useful at identifying juvenile habitat parameters, but are insufficient for areas not previously sampled. The resource-selection models verified the importance of a subset of parameters used in earlier models and provided a statistical means (78–87% correct) for prediction of fish distribution in similar areas of the eastern North Pacific.

The influence of trawl width on the ability of a survey trawl to capture groundfish was tested by comparing catch rates between paired tows with and without a constraint line that reduced the operating width of the trawl. The vertical distribution of fish near and above the seafloor was recorded with an echo sounder to test for the incidence of fish diving into the path of the trawl during the tows. Arrowtooth flounder (Atheresthes stomias), flathead sole (Hippoglossoides elassodon) and walleye pollock (Theragra chalcogramma) were captured at higher rates (fish per area swept) by a survey trawl fished in the restricted (narrow) configuration. The greatest difference occurred for pollock. The difference in catch rates was consistent across size groups within each species. Correlations detected between catch rates of pollock and echo-integration values for targets well above the trawl height indicated that some of these fish may have been diving from midwater into the path of the trawl. Differences between the correlation patterns with and without constraint lines indicate that the diving behavior may be affected by the presence of the line.

Three transects in Kachemak Bay, Alaska, were sampled in September 1994, May and August 1995, and February, May, and August 1996. Juvenile flathead sole, Hippoglossoides elassodon, and rock sole, Pleuronectes bilineatus, were the most abundant flatfishes, comprising 65–85% of all flatfishes captured at any period. Collections of fish and sediments were made at regular depth contour intervals of 10 m. Habitat distribution was described by depth at 10 m increments and sediment percent weights of gravel, sand, and mud. Year-round habitat of flathead sole age-0 was primarily from 40 to 60 m, and age-1 habitat was primarily from 40 to 80 m. Summer habitat of rock sole age-0 and -1 was from 10 to 30 m, and in winter they moved offshore to depths of up to 150 m. Both age classes of flathead sole were most abundant on mixed mud sediments, while age-1 were also in high abundance on muddy sand sediments. Rock sole age-0 and-1 were most abundant on sand, though age-1 were also found on a variety of sediments both finer and coarser grained than sand. Flathead sole and rock sole had distinctive depth and sediment habitats. When habitat overlap occurred between the species, it was most often due to rock sole moving offshore in the winter. Abundances were not significantly different among seasons for age-1 flatfishes.

Juveniles of four species of pleuronectid flatfishes were abundant in bays and nearshore areas around Kodiak Island, Alaska during August 1991. Flatfish nursery areas located in deep water bays such as those surrounding Kodiak Island have not been previously reported. Age-0 rock sole (Pleuronectes bilineatus), flathead sole (Hippoglossoides elassodon), Pacific halibut (Hippoglossus stenolepis) and age-1 yellowfin sole (Pleuronectes asper) were collected close to one another and at first appeared to share nursery areas. Closer examination of associated within-bay distribution, depth, substrate, temperature and salinity data revealed characteristics which limited nursery area overlap. The major concentrations of juveniles of these species could usually be segregated by one or more of the physical parameters investigated. Based on the physical characteristics found to be most important in determining distribution of juveniles for each species, we hypothesize the following relationships. Age-0 rock sole are found predominantly in water depths less than 50 m, on sand or mixed sand substrate outside of or within bays. Age-0 flathead sole are found predominantly in water depths greater than 40 m, on mud or mixed mud substrate throughout bays. Age-0 Pacific halibut are found predominantly in water depths less than 40 m, on mixed sand substrate near or outside mouths of bays. Age-1 yellowfin sole are found predominantly in water depths less than 40 m, on mixed substrates at upper reaches of bays. These hypotheses will be field tested, after which the relationships may be considered for application to broader geographic areas.

Fish larvae were collected at 6 depths in Auke Bay, southeastern Alaska, USA, on 4 days in May and June 1987. On 3 dates samples were collected between 08:OO and 13:00 h , on the other date samples were collected every 4 h during 24 h. Vertical distributions of light, temperature, salinity, chlorophyll and copepod nauplii were also measured. Wind speed data were available from a nearby station. Smelt (Osmeridae) larvae, the most abundant larval fish taxon, migrated to the surface at midnight, whereas walleye pollock, flathead sole, rock sole, poacher (Agonidae) and northern smoothtongue moved deeper at dusk. During the day, most fish larvae were concentrated from 5 to 15 m, broadly overlapping the highest abundances of copepod nauplii, although poacher and northern smoothtongue were consistently deeper (15 to 25 m) . Diurnally, smelt larvae were shallow (5 to 10 m) , and pycnocllne depth accounted for more variabhty in their mean depth than any other biotic or physical vanable. Mean depths of the other 5 most abundant taxa were in the same rank order by depth in all 4 sets of daytime samples, and depth of isotherms below the pycnocline accounted for more vanation in their mean depths than did any other variable. The diurnal depth distributions we observed apparently result from temperature preferences among marine larval fishes, with descent at dusk as the most common form of diel vertical migration

Field studies on ovarian development in English sole from urban and nonurban sites in Puget Sound, Washington, USA, demonstrated that animals with elevated levels of fluorescent aromatic compounds (FACs) in bile were less likely to enter vitellogenesis and had lower plasma concentrations of estradiol than female sole with low levels of contaminant exposure. Biliary FACs were positively correlated with hepatic P450 activity, which was also elevated in sole showing inhibited ovarian development. These findings suggest that contaminant exposure may disrupt vitellogenesis in female fish. Results of the field study were supported by laboratory experiments showing that pretreatment of gravid female English sole with extracts of contaminated sediment decreased levels of endogenous estradiol. A similar response was observed in rock sole and flathead sole treated with Prudhoe Bay crude oil. However, exposure of English sole to sediment extracts had little effect on the activity of hepatic-steroid-metabolizing enzymes, indicating that some mechanism other than enhanced steroid metabolism may be responsible for reductions in endogenous circulating-steroid levels. Our recent studies suggest that reductions in endogenous estradiol levels may result from depressed ovarian steroidogenesis, as contaminant-associated reductions in in-vitro ovarian estradiol production were observed in English sole, rock sole, and flathead sole. Preliminary studies on winter flounder and white croaker indicate that they may also experience reproductive impairment as a result of exposure to contaminants, but the phase of the reproductive cycle that is most severely impacted varies from species to species.

Exposure and possible adverse effects of the Exxon Valdez oil spill (EVOS) at depth were studied between 1989 and 1991 on several species of crustaceans, molluscs, and finfish that are characterized by ontogenetic shifts in distribution from meroplanktonic larvae to benthic and demersal juveniles and adults. The authors approach was to search for (1) evidence of exposure to Exxon Valdez crude oil (EVC) at depth (generally between 20 to 150 m) and (2) measurable perturbations at both the individual and population levels. Primary species targeted were Tanner crab (Chionoecetes bairdi), several pandalid shrimps (Pandalus platyceros, P. hypsinotus, P. borealis), flathead sole (Hippoglossoides elassodon), and several bivalves including scallops (Chlamys rubida) and infaunal clams (Nuculana, Yoldia, and Macoma spp.). The survey design provided a comparison between variables measured in oiled bays around Knight Island and non-oiled bays at other locations within Prince William Sound. Polycyclic aromatic hydrocarbons (PAHs) of petrogenic origin were measured in all bays sampled in this study and levels of PAHs derived from EVC were elevated in the oiled bays following the spill, yet attenuated to less than 200 ng/g sediment by 1991. 95 refs., 22 figs., 6 tabs.

Considerable attention has been devoted to contaminants (mainly PCBs and mercury) in subsistence foods (particularly fish) from various parts of the world. However, relatively little attention has been devoted to examining mercury levels in a full range of subsistence foods from a particular region. While managers and scientists compute risk based on site-specific data on contaminant levels and consumption rates, a first step in making risk decisions by subsistence peoples is knowledge about the relative levels of mercury in the foods they eat. This study examined levels of mercury in subsistence foods (edible components) from several islands in the western Aleutians of Alaska, including algae (4 species), invertebrates (9 species), fish (15 species) and birds (5 species). Samples were gathered by both subsistence hunters/fishers and by scientists using the same equipment. Another objective was to determine if there were differences in mercury levels in subsistence foods gathered from different Aleutian islands. We tested the null hypotheses that there were no interspecific and interisland differences in mercury levels. Because of variation in distribution and the nature of subsistence hunting and fishing, not all organisms were collected from each of the islands. There were significant and important differences in mercury levels among species, but the locational differences were rather small. There was an order of magnitude difference between algae/some invertebrates and fish/birds. Even within fish, there were significant differences. The highest mean mercury levels were in flathead sole (Hippoglossoides elassodon, 0.277 ppm), yellow irish lord (Hemilepidotus jardani, 0.281 ppm), great sculpin (Myoxocephalus polyacanthocephalus, 0.366 ppm), glaucous-winged gull (Larus glaucescens, 0.329 ppm) and its eggs (0.364 ppm), and pigeon guillemot (Cepphus columba, 0.494 ppm). Mercury levels increased with increasing weight of the organisms for limpets (Tectura scutum), and for 11 of the 15 fish species examined. Nine of the 15 fish species had some samples over the 0.3 ppm level, and 7 of 15 fish had some samples over 0.5 ppm. For birds, 95% of the pigeon guillemot muscle samples were above the 0.3 ppm, and 43% were above 0.5 ppm. While health professionals may argue about the risk and benefits of eating fish, and of eating alternative protein sources, the public should be provided with enough information for them to make informed decisions. This is particularly true for subsistence people who consume large quantities of self-caught foods, particularly for sensitive sub-populations, such as pregnant women. We argue that rather than giving people blanket statements about the health benefits or risks from eating fish, information on mean and maximum mercury levels should also be provided on a wide range of subsistence foods, allowing informed decisions, especially by those most at risk.

Past studies determined that concentrations of arsenic in the liver of flathead sole from Alaska were generally higher than those found in fish from other locations sampled along the west coast of the United States (Meador et al. 1994). A study was conducted to examine arsenic concentrations and patterns of bioaccumulation in fish and potential prey species from two geographic locations. Flathead sole were collected from four sites in the Gulf of Alaska and white croaker and English sole were collected from five sites in California. Potential prey species from each site were also examined and found to contain high concentrations of arsenic. In California, the sites with the lowest sediment concentrations of arsenic, total organic carbon, and acid-volatile sulfides (AVS) contained invertebrates with the highest tissue concentrations. Regression analysis determined that arsenic in polychaetes was highly correlated to sediment concentrations of arsenic normalized to AVS but was higher overall for the California samples. Even though invertebrates from several of the California sites exhibited much higher concentrations of arsenic than invertebrates from the Alaska sites, liver and muscle tissue from flathead sole collected in Alaska usually exhibited higher concentrations than fish from the California sites. When concentrations of arsenic in fish liver were plotted against concentrations of arsenic in sediment normalized to AVS levels, a very high correlation was obtained for all sites. This suggests that AVS, or some factor correlated with AVS, may have been responsible for controlling arsenic bioaccumulation in these fish species through dietary uptake and exposure to arsenic in water. Based on the available data, it appears that dietary uptake may be related to fish tissue concentrations, but uptake of aqueous arsenic may be responsible for the higher tissue concentrations in fish from Alaska.