Observer-reported skate bycatch in the commercial groundfish fisheries of Alaska

We analyzed skate catch data collected by observers in the North Pacific Groundfish Observer Program (NPGOP) from 1998 through 2008 to document recent changes in the identification of skates by observers and to examine the species composition of observed skate catch in Alaska’s groundfish fisheries as well as recent trends in skate retention by commercial fishermen. Historically, almost all skate bycatch has been reported by NPGOP observers as “skate unidentified.” However, since 2004 observers have been trained to identify skates to the genus and species level. In 2008 over 95% of all skates were identified at least to the genus level, and over 50% were identified to species. The most common species of skates identified by observers in groundfish fisheries are Bathyraja parmifera (Alaska skate), Raja binoculata (big skate), and Bathyraja aleutica (Aleutian skate). Species composition of reported skate catch generally reflects recent survey-derived biomass estimates, with B. parmifera dominating the catches in the Bering Sea and, to a lesser extent, in the Aleutian Islands region, and species of the genus Raja dominating catches in the Gulf of Alaska. A relatively high percentage of the skate catch on longline vessels is still reported at the family or genus level because of difficulties in the identification of skates not brought onboard the vessel. For the larger skate species, the proportion retained for processing has increased in recent years as the market price for skate product has increased. Although observed skate catch does not give a complete account of skate bycatch in the fisheries of the region, observer data provide critical information for the appropriate management of skate populations in Alaska.

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm.

A 4500-year time series of Pacific cod (Gadus macrocephalus) size and abundance: archaeology, oceanic regime shifts, and sustainable fisheries

A 4500-year archaeological record of Pacific cod (Gadus macrocephalus) bones from Sanak Island, Alaska, was used to assess the sustainability of the modern fishery and the effects of this fishery on the size of fish caught. Allometric reconstructions of Pacific cod length for eight prehistoric time periods indicated that the current size of the nearshore, commercially fished Pacific cod stocks is statistically unchanged from that of fish caught during 4500 years of subsistence harvesting. This finding indicates that the current Pacific cod fishery that uses selective harvesting technolog ies is a sustainable commercial fishery. Variation in relative Pacific cod abundances provides further insights into the response of this species to punctuated changes in ocean climate (regime shifts) and indicates that Pacific cod stocks can recover from major environmental perturbations. Such palaeofisheries data can extend the short time-series of fisheries data (<50 yr) that form the basis for fisheries management in the Gulf of Alaska and place current trends within the context of centennial- or millennial-scale patterns.

Spatial and temporal distribution of North Atlantic right whales (Eubalaena glacialis) in Cape Cod Bay, and implications for management

Cape Cod Bay (Massachusetts) is the only known winter and early spring feeding area for concentrations of the endangered North Atlantic right whale (Eubalaena glacialis) population. During January–May, 1998–2002, 167 aerial surveys were conducted (66,466 km of total survey effort), providing a complete representation of the spatiotemporal distribution of right whales in the bay during winter and spring. A total of 1553 right whales were sighted; some of these sightings were multiple sightings of the same individuals. Right whale distribution and relative abundance patterns were quantified as sightings per unit of effort (SPUE) and partitioned into 103 23-km2 cells and 12 2-week periods. Significant interannual variations in mean SPUE and timing of SPUE maxima were likely due to physically forced changes in available food resources. The area of greatest SPUE expanded and contracted during the season but its center remained in the eastern bay. Most cells with SPUE>0 were inside the federal critical habitat (CH) and this finding gave evidence of the need for management measures within CH boundaries to reduce anthropogenic mortality from vessel strikes and entanglement. There was significant within-season SPUE variability: low in December−January, increasing to a maximum in late February−early April, and declining to zero in May; and these results provide support for management measures from 1 January

Spatial and temporal variability in the relative contribution of king mackerel (Scomberomorus cavalla) stocks to winter mixed fisheries off South Florida

King mackerel (Scomberomorus cavalla) are ecologically and economically important scombrids that inhabit U.S. waters of the Gulf of Mexico (GOM) and Atlantic Ocean (Atlantic). Separate migratory groups, or stocks, migrate from eastern GOM and southeastern U.S. Atlantic to south Florida waters where the stocks mix during winter. Currently, all winter landings from a management-defined south Florida mixing zone are attributed to the GOM stock. In this study, the stock composition of winter landings across three south Florida sampling zones was estimated by using stock-specific otolith morphological variables and Fourier harmonics. The mean accuracies of the jackknifed classifications from stepwise linear discriminant function analysis of otolith shape variables ranged from 66−76% for sex-specific models. Estimates of the contribution of the Atlantic stock to winter landings, derived from maximum likelihood stock mixing models, indicated the contribution was highest off southeastern Florida (as high as 82.8% for females in winter 2001−02) and lowest off southwestern Florida (as low as 14.5% for females in winter 2002−03). Overall, results provided evidence that the Atlantic stock contributes a certain, and perhaps a significant (i.e., ≥50%), percentage of landings taken in the management-defined winter mixing zone off south Florida, and the practice of assigning all winter mixing zone landings to the GOM stock should

Yellow (Perca flavescens) and Eurasian (P. fluviatilis) perch distinguished in fried fish samples by DNA analysis

DNA techniques are increasingly used as diagnostic tools in many fields and venues. In particular, a relatively new application is its use as a check for proper advertisement in markets and on restaurant menus. The identification of fish from markets and restaurants is a growing problem because economic practices often render it cost-effective to substitute one species for another. DNA sequences that are diagnostic for many commercially important fishes are now documented on public databases, such as the National Center for Biotechnology Information’s (NCBI) GenBank.1 It is now possible for most genetics laboratories to identify the species from which a tissue sample was taken without sequencing all the possible taxa it might represent.

Removing observational noise from fisheries-independent time series data using ARIMA models

Abundance indices derived from fishery-independent surveys typically exhibit much higher interannual variability than is consistent with the within-survey variance or the life history of a species. This extra variability is essentially observation noise (i.e. measurement error); it probably reflects environmentally driven factors that affect catchability over time. Unfortunately, high observation noise reduces the ability to detect important changes in the underlying population abundance. In our study, a noise-reduction technique for uncorrelated observation noise that is based on autoregressive integrated moving average (ARIMA) time series modeling is investigated. The approach is applied to 18 time series of finfish abundance, which were derived from trawl survey data from the U.S. northeast continental shelf. Although the a priori assumption of a random-walk-plus-uncorrelated-noise model generally yielded a smoothed result that is pleasing to the eye, we recommend that the most appropriate ARIMA model be identified for the observed time series if the smoothed time series will be used for further analysis of the population dynamics of a species.

Impacts of climate change and variability on fish value chains in Uganda

This study examines the vulnerability of fish pr oduction in Uganda, particularly as it r elates to the predicted impacts from climate change, using the concept of the value chain. The value chain approach has been recommended as a useful tool to study specific challenges facing a sector resulting from various drivers of change, including climate. Critically, such analyses can reveal context-specific response strategies to enhance a sector (Jacinto and Pomer oy 2010). The specific purpose of the study was to identify curr ent and potential impacts of climate change and corresponding adaptation strategies in fish value chains. The study builds upon information fr om earlier value chain analyses on fisheries and aquaculture production in Uganda to provide a more in-depth understanding of issues facing the fish industry, in particular, those to be incorporated in the CGIAR Resear ch Program Livestock and Fish.

Evaluating methods for estimating rare events with zero-heavy data: a simulation model estimating sea turtle bycatch in the pelagic longline fishery

Estimating rare events from zero-heavy data (data with many zero values) is a common challenge in fisheries science and ecology. For example, loggerhead sea turtles (Caretta caretta) and leatherback sea turtles (Dermochelys coriacea) account for less than 1% of total catch in the U.S. Atlantic pelagic longline fishery. Nevertheless, the Southeast Fisheries Science Center (SEFSC) of the National Marine Fisheries Service (NMFS) is charged with assessing the effect of this fishery on these federally protected species. Annual estimates of loggerhead and leatherback bycatch in a fishery can affect fishery management and species conservation decisions. However, current estimates have wide confidence intervals, and their accuracy is unknown. We evaluate 3 estimation methods, each at 2 spatiotemporal scales, in simulations of 5 spatial scenarios representing incidental capture of sea turtles by the U.S. Atlantic pelagic longline fishery. The delta-log normal method of estimating bycatch for calendar quarter and fishing area strata was the least biased estimation method in the spatial scenarios believed to be most realistic. This result supports the current estimation procedure used by the SEFSC.

Interdecadal change in growth of sablefish (Anoplopoma fimbria) in the northeast Pacific Ocean

Errors in growth estimates can affect drastically the spawner-perrecruit threshold used to recommend quotas for commercial fish catches. Growth parameters for sablefish (Anoplopoma fimbria) in Alaska have not been updated for stock assessment purposes for more than 20 years, although aging of sablefish has continued. In this study, length-stratified data (1981–93 data from the annual longline survey conducted cooperatively by the Fisheries Agency of Japan and the Alaska Fisheries Science Center of the National Marine Fisheries Service) were updated and corrected for discovered sampling bias. In addition, more recent, randomly collected samples (1996–2004 data from the annual longline survey conducted by the Alaska Fisheries Science Center) were analyzed and new length-at-age and weight-at-age parameters were estimated. Results were similar between this analysis with length-at-age data from 1981 to 2004 and analysis with updated longline survey data through 2010; therefore, we used our initial results from analysis done with data through 2004. We found that, because of a stratified sampling scheme, growth estimates of sablefish were overestimated with the older data (1981–93), and growth parameters used in the Alaskan sablefish assessment model were, thus, too large. In addition, a comparison of the bias-corrected 1981–93 data and the 1996–2004 data showed that, in more recent years, sablefish grew larger and growth differed among regions. The updated growth information improves the fit of the data to the sablefish stock assessment model with biologically reasonable results. These findings indicate that when the updated growth data (1996–2004) are used in the existing sablefish assessment model, estimates of fishing mortality increase slightly and estimates of female spawning biomass decrease slightly. This study provides evidence of the importance of periodically revisiting biological parameter estimates, especially as data accumulate, because the addition of more recent data often will be more biologically realistic. In addition, it exemplifies the importance of correcting biases from sampling that may contribute to erroneous parameter estimates.

Variation in trawl geometry due to unequal warp length

Survey standardization procedures can reduce the variability in trawl catch efficiency thus producing more precise estimates of biomass. One such procedure, towing with equal amounts of trawl warp on both sides of the net, was experimentally investigated for its importance in determining optimal trawl geometry and for evaluating the effectiveness of the recent National Oceanic and Atmospheric Administration (NOAA) national protocol on accurate measurement of trawl warps. This recent standard for measuring warp length requires that the difference between warp lengths can be no more than 4% of the distance between the otter doors measured along the bridles and footrope. Trawl performance data from repetitive towing with warp differentials of 0, 3, 5, 7, 9, 11, and 20 m were analyzed for their effect on three determinants of flatfish catch efficiency: footrope distance off-bottom, bridle length in contact with the bottom, and area swept by the net. Our results indicated that the distortion of the trawl caused by asymmetry in trawl warp length could have a negative inf luence on flatfish catch efficiency. At a difference of 7 m in warp length, the NOAA 4% threshold value for the 83112 Eastern survey trawl used in our study, we found no effect on the acous-tic-based measures of door spread, wing spread, and headrope height off-bottom. However, the sensitivity of the trawl to 7 m of warp offset could be seen as footrope distances off-bottom increased slightly (particularly in the center region of the net where flatfish escapement is highest), and as the width of the bridle path responsible for flatfish herding, together with the effective net width, was reduced. For this survey trawl, a NOAA threshold value of 4% should be considered a maximum. A more conservative value (less than 4%) would likely reduce potential bias in estimates of relative abundance caused by large differences in warp length approaching 7 m.

Sexual differentiation and gonad development in striped mullet (Mugil cephalus L.) from South Carolina estuaries*

This study examined the sexual differentiation and reproductive dynamics of striped mullet (Mugil cephalus L.) in the estuaries of South Carolina. A total of 16,464 specimens were captured during the study and histological examination of sex and maturity was performed on a subsample of 3670 fish. Striped mullet were sexually undifferentiated for the first 12 months, began differentiation at 13 months, and were 90% fully differentiated by 15 to 19 months of age and 225 mm total length (TL). The defining morphological characteristics for differentiating males was the elongation of the protogonial germ tissue in a corradiating pattern towards the center of the lobe, the development of primary and secondary ducts, and the lack of any recognizable ovarian wall structure. The defining female characteristics were the formation of protogonial germ tissue into spherical germ cell nests, separation of a tissue layer from the outer epithelial layer of the lobe-forming ovarian walls, a tissue bud growing from the suspensory tissue that helped form the ovary wall, and the proliferation of oogonia and oocytes. Sexual maturation in male striped mullet first occurred at 1 year and 248 mm TL and 100% maturity occurred at age 2 and 300 mm TL. Female striped mullet first matured at 2 years and 291 mm total length and 100% maturity occurred at 400 mm TL and age 4. Because of the open ocean spawning behavior of striped mullet, all stages of maturity were observed in males and females except for functionally mature females with hydrated oocytes. The spawning season for striped mullet recruiting to South Carolina estuaries lasts from October to April; the majority of spawning activity, however, occurs from November to January. Ovarian atresia was observed to have four distinct phases. This study presents morpholog ical analysis of reproductive ontogeny in relation to size and age in South Carolina striped mullet. Because of the length of the undifferentiated gonad stage in juvenile striped mullet, previous studies have proposed the possibility of protandric hermaphrodism in this species. The results of our study indicate that striped mullet are gonochoristic but capable of exhibiting nonfunctional hermaphroditic characteristics in differentiated mature gonads.

Incidental catch and estimated discards of pelagic sharks from the swordfish and tuna fisheries in the Mediterranean Sea

Large pelagic sharks are caught incidentally in the swordfish and tuna fisheries of the Mediterranean Sea. In our study, twelve shark species were documented as bycatch over three years from 1998 to 2000. Blue shark (Prionace glauca) was the predominant species in all gears and areas examined. Shortfin mako (Isurus oxyrinchus), common thresher shark (Alopias vulpinus), and tope shark (Galeorhinus galeus) were the next most abundant shark species—found in more than half of the areas sampled. Catch composition varied both in the areas and gears investigated. Sharks represented 34.3% in weight of total catches sampled in the Alboran Sea and 0.9% in the Straits of Sicily. Higher shark catches were observed in the swordfish longline fishery, where a nominal CPUE value reached 3.8 sharks/1000 hooks in the Alboran Sea. Size distribution by fishing gear varied significantly. Albacore longline catches consisted mainly of juveniles, whereas subadult and adult specimens were more frequent in the swordfish longline and driftnet fishery. The percentage of sharks brought onboard alive was exceptionally high; only 5.1% of the specimens died. Few discards (seven blue shark) were recorded in the Greek longline fleet during onboard sampling in the Aegean Se

Temporal and spatial distribution and abundance of flathead sole (Hippoglossoides elassodon) eggs and larvae in the western Gulf of Alaska

Data from ichthyoplankton surveys conducted in 1972 and from 1977 to 1999 (no data were collected in 1980) by the Alaska Fisheries Science Center (NOAA, NMFS) in the western Gulf of Alaska were used to examine the timing of spawning, geographic distribution and abundance, and the vertical distribution of eggs and larvae of flathead sole (Hippoglossoides elassodon). In the western Gulf of Alaska, flathead sole spawning began in early April and peaked from early to mid-May on the continental shelf. It progressed in a southwesterly direction along the Alaska Peninsula where three main areas of flathead sole spawning were indentified: near the Kenai Peninsula, in Shelikof Strait, and between the Shumagin Islands and Unimak Island. Flathead sole eggs are pelagic, and their depth distribution may be a function of their developmental stage. Data from MOCNESS tows indicated that eggs sink near time of hatching and the larvae rise to the surface to feed. The geographic distribution of larvae followed a pattern similar to the distribution of eggs, only it shifted about one month later. Larval abundance peaked from early to mid-June in the southern portion of Shelikof Strait. Biological and environmental factors may help to retain flathead sole larvae on the continental shelf near their juvenile nursery areas.

Fisheries potential of village dams in northern Ghana

Results of a twelve-month assessment of the fisheries and aquaculture potential of small waterbodies (SWBs) in the West Gonja District of Northern Ghana are presented. The primary objectives of the project were to established whether the fisheries within the reservoir basins in the West Gonja and Nanumba Districts (Northern Region) could be enhanced and aquaculture associated with the SWBs could be viable.