Comparison of habitat-based indices of abundance with fishery-independent biomass estimates from bottom trawl surveys

Rockfish species are notoriously difficult to sample with multispecies bottom trawl survey methods. Typically, biomass estimates have high coefficients of variation and can fluctuate outside the bounds of biological reality from year to year. This variation may be due in part to their patchy distribution related to very specific habitat preferences. We successfully modeled the distribution of five commercially important and abundant rockf ish species. A two-stage modeling method (modeling both presence-absence and abundance) and a collection of important habitat variables were used to predict bottom trawl survey catch per unit of effort. The resulting models explained between 22% and 66% of the variation in rockfish distribution. The models were largely driven by depth, local slope, bottom temperature, abundance of coral and sponge, and measures of water column productivity (i.e., phytoplankton and zooplankton). A year-effect in the models was back-transformed and used as an index of the time series of abundance. The abundance index trajectories of three of five species were similar to the existing estimates of their biomass. In the majority of cases the habitat-based indices exhibited less interannual variability and similar precision when compared with stratified survey-based biomass estimates. These indices may provide for stock assessment models a more stable alternative to current biomass estimates produced by the multispecies bottom trawl survey in the Gulf of Alaska.

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.

A comparison of two fishery-independent survey programs used to define the population structure of American lobster (Homarus americanus) in the Gulf of Maine

The population structure and abundance of the American lobster (Homarus americanus) stock in the Gulf of Maine are defined by data derived from a fishery-independent trawl survey program conducted by the National Marine Fisheries Service (NMFS). Few sampling stations in the survey area are located inshore, in particular along coastal Maine. According to statistics, however, more than two thirds of the lobster landings come from inshore waters within three miles off the coast of Maine. In order to include an inshore survey program, complementary to the NMFS survey, the Maine Department of Marine Resources (DMR) initialized an inshore survey program in 2000. The survey was modeled on the NMFS survey program, making these two survey programs comparable. Using data from both survey programs, we evaluated the population structure of the American lobster in the Gulf of Maine. Our findings indicate that lobsters in the Gulf of Maine tend to have a size-dependent inshore-off-shore distribution; smaller lobsters are more likely to stay inshore and larger lobsters are more likely to stay offshore. The DMR inshore and NMFS survey programs focused on different areas in the Gulf of Maine and likely targeted different segments of the stock. We suggest that data from both survey programs be used to assess the lobster stock and to describe the dynamics of the stock in the Gulf of Maine.

Fishery-independent Bottom Trawl Surveys for Deep-water Fishes and Invertebrates of the U.S. Gulf of Mexico, 2002–08

From 2002 through 2008, the Mississippi Laboratories of the NMFS Southeast Fisheries Science Center, NOAA, conducted fishery-independent bottom trawl surveys for continental shelf and outer-continental shelf deep-water fishes and invertebrates of the U.S. Gulf of Mexico (50–500 m bottom depths). Five-hundred and ninety species were captured at 797 bottom trawl locations. Standardized survey gear and randomly selected survey sites have facilitated development of a fishery-independent time series that characterizes species diversity, distributions, and catch per unit effort. The fishery-independent surveys provide synoptic descriptions of deep-water fauna potentially impacted by various anthropogenic factors.

Temporal trends (2000–2011) and influences on fishery-independent catch rates for loggerhead sea turtles (Caretta caretta) at an important coastal foraging region in the southeastern United States

Seasonal trawling was conducted randomly in coastal (depths of 4.6–17 m) waters from St. Augustine, Florida, (29.9°N) to Winyah Bay, South Carolina (33.1°N), during 2000–03, 2008–09, and 2011 to assess annual trends in the relative abundance of sea turtles. A total of 1262 loggerhead sea turtles (Caretta caretta) were captured in 23% (951) of 4207 sampling events. Capture rates (overall and among prevalent 5-cm size classes) were analyzed through the use of a generalized linear model with log link function for the 4097 events that had complete observations for all 25 model parameters. Final models explained 6.6% (70.1–75.0 cm minimum straight-line carapace length [SCLmin]) to 14.9% (75.1–80.0 cm SCLmin) of deviance in the data set. Sampling year, geographic subregion, and distance from shore were retained as significant terms in all final models, and these terms collectively accounted for 6.2% of overall model deviance (range: 4.5–11.7% of variance among 5-cm size classes). We retained 18 parameters only in a subset of final models: 4 as exclusively significant terms, 5 as a mixture of significant or nonsignificant terms, and 9 as exclusively nonsignificant terms. Four parameters also were dropped completely from all final models. The generalized linear model proved appropriate for monitoring trends for this data set that was laden with zero values for catches and was compiled for a globally protected species. Because we could not account for much model deviance, metrics other than those examined in our study may better explain catch variability and, once elucidated, their inclusion in the generalized linear model should improve model fits.

Liver genomic responses to ciguatoxin: evidence for activation of Phase I and Phase II detoxification pathways following an acute hypothermic response in mice

Ciguatoxins (CTX) are polyether neurotoxins that target voltage-gated sodium channels and are responsible for ciguatera, the most common fish-borne food poisoning in humans. This study characterizes the global transcriptional response of mouse liver to a symptomatic dose (0.26 ng/g) of the highly potent Pacific ciguatoxin-1 (P-CTX-1). At 1 h post-exposure 2.4% of features on a 44K whole genome array were differentially expressed (p ≤ 0.0001), increasing to 5.2% at 4 h and decreasing to 1.4% by 24 h post-CTX exposure. Data were filtered (|fold change| ≥ 1.5 and p ≤ 0.0001 in at least one time point) and a trend set of 1550 genes were used for further analysis. Early gene expression was likely influenced prominently by an acute 4°C decline in core body temperature by 1 h, which resolved by 8 h following exposure. An initial downregulation of 32 different solute carriers, many involved in sodium transport, was observed. Differential gene expression in pathways involving eicosanoid biosynthesis and cholesterol homeostasis was also noted. Cytochrome P450s (Cyps) were of particular interest due to their role in xenobiotic metabolism. Twenty-seven genes, mostly members of Cyp2 and Cyp4 families, showed significant changes in expression. Many Cyps underwent an initial downregulation at 1 h but were quickly and strongly upregulated at 4 and 24 h post-exposure. In addition to Cyps, increases in several glutathione S-transferases were observed, an indication that both phase I and phase II metabolic reactions are involved in the hepatic response to CTX in mice.