Use of SARIMA models to assess data-poor fisheries: a case study with a sciaenid fishery off Portugal

Research on assessment and monitoring methods has primarily focused on fisheries with long multivariate data sets. Less research exists on methods applicable to data-poor fisheries with univariate data sets with a small sample size. In this study, we examine the capabilities of seasonal autoregressive integrated moving average (SARIMA) models to fit, forecast, and monitor the landings of such data-poor fisheries. We use a European fishery on meagre (Sciaenidae: Argyrosomus regius), where only a short time series of landings was available to model (n=60 months), as our case-study. We show that despite the limited sample size, a SARIMA model could be found that adequately fitted and forecasted the time series of meagre landings (12-month forecasts; mean error: 3.5 tons (t); annual absolute percentage error: 15.4%). We derive model-based prediction intervals and show how they can be used to detect problematic situations in the fishery. Our results indicate that over the course of one year the meagre landings remained within the prediction limits of the model and therefore indicated no need for urgent management intervention. We discuss the information that SARIMA model structure conveys on the meagre lifecycle and fishery, the methodological requirements of SARIMA forecasting of data-poor fisheries landings, and the capabilities SARIMA models present within current efforts to monitor the world’s data-poorest resources.

Season- and depth-dependent variability of a demersal fish assemblage in a large fjord estuary (Puget Sound, Washington)

Fjord estuaries are common along the northeast Pacific coastline, but little information is available on fish assemblage structure and its spatiotemporal variability. Here, we examined changes in diversity metrics, species biomasses, and biomass spectra (the distribution of biomass across body size classes) over three seasons (fall, winter, summer) and at multiple depths (20 to 160 m) in Puget Sound, Washington, a deep and highly urbanized fjord estuary on the U.S. west coast. Our results indicate that this fish assemblage is dominated by cartilaginous species (spotted ratfish [Hydrolagus colliei] and spiny dogfish [Squalus acanthias]) and therefore differs fundamentally from fish assemblages found in shallower estuaries in the northeast Pacific. Diversity was greatest in shallow waters (<40 m), where the assemblage was composed primarily of flatfishes and sculpins, and lowest in deep waters (>80 m) that are more common in Puget Sound and that are dominated by spotted ratf ish and seasonally (fall and summer) by spiny dogfish. Strong depth-dependent variation in the demersal fish assemblage may be a general feature of deep fjord estuaries and indicates pronounced spatial variability in the food web. Future comparisons with less impacted fjords may offer insight into whether cartilaginous species naturally dominate these systems or only do so under conditions related to human-caused ecosystem degradation. Information on species distributions is critical for marine spatial planning and for modeling energy flows in coastal food webs. The data presented here will aid these endeavors and highlight areas for future research in this important yet understudied system.

Interactions of age-dependent mortality and selectivity functions in age-based stock assessment models

The natural mortality rate (M) of fish varies with size and age, although it is often assumed to be constant in stock assessments. Misspecification of M may bias important assessment quantities. We simulated fishery data, using an age-based population model, and then conducted stock assessments on the simulated data. Results were compared to known values. Misspecification of M had a negligible effect on the estimation of relative stock depletion; however, misspecification of M had a large effect on the estimation of parameters describing the stock recruitment relationship, age-specific selectivity, and catchability. If high M occurs in juvenile and old fish, but is misspecified in the assessment model, virgin biomass and catchability are often poorly estimated. In addition, stock recruitment relationships are often very difficult to estimate, and steepness values are commonly estimated at the upper bound (1.0) and overfishing limits tend to be biased low. Natural mortality can be estimated in assessment models if M is constant across ages or if selectivity is asymptotic. However if M is higher in old fish and selectivity is dome-shaped, M and the selectivity cannot both be adequately estimated because of strong interactions between M and selectivity.

A meta-analytic approach to quantifying scientific uncertainty in stock assessments

Quantifying scientific uncertainty when setting total allowable catch limits for fish stocks is a major challenge, but it is a requirement in the United States since changes to national fisheries legislation. Multiple sources of error are readily identifiable, including estimation error, model specification error, forecast error, and errors associated with the definition and estimation of reference points. Our focus here, however, is to quantify the influence of estimation error and model specification error on assessment outcomes. These are fundamental sources of uncertainty in developing scientific advice concerning appropriate catch levels and although a study of these two factors may not be inclusive, it is feasible with available information. For data-rich stock assessments conducted on the U.S. west coast we report approximate coefficients of variation in terminal biomass estimates from assessments based on inversion of the assessment of the model’s Hessian matrix (i.e., the asymptotic standard error). To summarize variation “among” stock assessments, as a proxy for model specification error, we characterize variation among multiple historical assessments of the same stock. Results indicate that for 17 groundfish and coastal pelagic species, the mean coefficient of variation of terminal biomass is 18%. In contrast, the coefficient of variation ascribable to model specification error (i.e., pooled among-assessment variation) is 37%. We show that if a precautionary probability of overfishing equal to 0.40 is adopted by managers, and only model specification error is considered, a 9% reduction in the overfishing catch level is indicated.

Demographics by depth: spatially explicit life-history dynamics of a protogynous reef fish

Distribution and demographics of the hogfish (Lachnolaimus maximus) were investigated by using a combined approach of in situ observations and life history analyses. Presence, density, size, age, and size and age at sex change all varied with depth in the eastern Gulf of Mexico. Hogfish (64–774 mm fork length and 0–19 years old) were observed year-round and were most common over complex, natural hard bottom habitat. As depth increased, the presence and density of hogfish decreased, but mean size and age increased. Size at age was smaller nearshore (<30 m). Length and age at sex change of nearshore hogfish were half those of offshore hogfish and were coincident with the minimum legal size limit. Fishing pressure is presumably greater nearshore and presents a confounding source of increased mortality; however, a strong red tide occurred the year before this study began and likely also affected nearshore demographics. Nevertheless, these data indicate ontogenetic migration and escapement of fast-growing fish to offshore habitat, both of which should reduce the likelihood of fishing-induced evolution. Data regarding the hogfish fishery are limited and regionally dependent, which has confounded previous stock assessments; however, the spatially explicit vital rates reported herein can be applied to future monitoring efforts.

Ichthyoplankton community structure and comparative trophodynamics in an estuarine transition zone

Surveys were conducted to evaluate and compare assemblage structure and trophodynamics of ichthyoplankton, and their variability, in an estuarine transition zone. Environmental gradients in the saltfront region of the Patuxent River subestuary, Chesapeake Bay, were hypothesized to define spatiotemporal distributions and assemblages of ichthyoplankton. Larval fishes, zooplankton, and hydrographic data were collected during spring through early summer 2000 and 2001. Larvae of 28 fish species were collected and species richness was similar each year. Total larval abundance was highest in the oligohaline region down-estuary of the salt front in 2000, but highest at the salt front in 2001. Larvae of anadromous fishes were most abundant at or up-estuary of the salt front in both years. Two ichthyoplankton assemblages were distinguished: 1) riverine—characterized predominantly by anadromous species (Moronidae and Alosinae); and 2) estuarine—characterized predominantly by naked goby (Gobiosoma bosc) (Gobiidae). Temperature, dissolved oxygen, salinity-associated variables (e.g., salt-front location), and concentrations of larval prey, specifically the calanoid copepod Eurytemora affinis and the cladoceran Bosmina longirostris, were important indicators of larval fish abundance. In the tidal freshwater region up-estuary of the salt front, there was substantial diet overlap between congeneric striped bass (Morone saxatilis) and white perch (M. americana) larvae, and also larvae of alewife (Alosa pseudoharengus) (overlap= 0.71–0.93). Larval abundance, taxonomic diversity, and dietary overlap were highest within and up-estuary of the salt front, which serves to both structure the ichthyoplankton community and control trophic relationships in the estuarine transition zone.

Age, growth, and spawning season of red bream (Beryx decadactylus) off the southeastern United States

Red bream (Beryx decadactylus) is a commercially important deep-sea benthopelagic fish with a circumglobal distribution on insular and continental slopes and seamounts. In the United States, small numbers are caught incidentally in the wreckfish (Polyprion americanus) fishery which operates off the southeastern coast, but no biological information exists for the management of the U.S. red bream population. For this study, otoliths (n=163) and gonads (n=161) were collected from commercially caught red bream between 2003 and 2008 to determine life history parameters. Specimens ranged in size from 410 to 630 mm fork length and were all determined to be mature by histological examination of the gonads. Females in spawning condition were observed from June through September, and reproductively active males were found year-round. Sectioned otoliths were difficult to interpret, but maximum age estimates were much higher than the 15 years previously reported for this species from the eastern North Atlantic based on whole-otolith analysis. Estimated ages ranged from 8 to 69 years, and a minimum lifespan of 49 years was validated by using bomb radiocarbon dating. Natural mortality was estimated at 0.06/yr. This study shows that red bream are longer lived and more vulnerable to overfishing than previously assumed and should be managed carefully to prevent overexploitation.

Measurements of resistance and reactance in fish with the use of bioelectrical impedance analysis: sources of error

New technologies can be riddled with unforeseen sources of error, jeopardizing the validity and application of their advancement. Bioelectrical impedance analysis (BIA) is a new technology in fisheries research that is capable of estimating proximate composition, condition, and energy content in fish quickly, cheaply, and (after calibration) without the need to sacrifice fish. Before BIA can be widely accepted in fisheries science, it is necessary to identify sources of error and determine a means to minimize potential errors with this analysis. We conducted controlled laboratory experiments to identify sources of errors within BIA measurements. We concluded that electrode needle location, procedure deviations, user experience, time after death, and temperature can affect resistance and reactance measurements. Sensitivity analyses showed that errors in predictive estimates of composition can be large (>50%) when these errors are experienced. Adherence to a strict protocol can help avoid these sources of error and provide BIA estimates that are both accurate and precise in a field or laboratory setting.

An evaluation of the effects of blue crab (Callinectes sapidus) behavior on the efficacy of crab pots as a tool for estimating population abundance

Crab traps have been used extensively in studies on the population dynamics of blue crabs to provide estimates of catch per unit of effort; however, these estimates have been determined without adequate consideration of escape rates. We examined the ability of the blue crab (Callinectes sapidus) to escape crab pots and the possibility that intraspecific crab interactions have an effect on catch rates. Approximately 85% of crabs that entered a pot escaped, and 83% of crabs escaped from the bait chamber (kitchen). Blue crabs exhibited few aggressive behavioral interactions in and around the crab pot and were documented to move freely in and out of the pot. Both the mean number and size of crabs caught were significantly smaller at deeper depths. Results from this study show that current estimates of catch per unit of effort may be biased given the high escape rate of blue crabs documented in this study. The results of this paper provide a mechanistic view of trap efficacy, and reveal crab behavior in and around commercial crab pots.

BotCam: a baited camera system for nonextractive monitoring of bottomfish species

A stereo-video baited camera system (BotCam) has been developed as a fishery-independent tool to monitor and study deepwater fish species and their habitat. During testing, BotCam was deployed primarily in water depths between 100 and 300 m for an assessment of its use in monitoring and studying Hawaiian bottomfish species. Details of the video analyses and data from the pilot study with BotCam in Hawai`i are presented. Multibeam bathymetry and backscatter data were used to delineate bottomfish habitat strata, and a stratified random sampling design was used for BotCam deployment locations. Video data were analyzed to assess relative fish abundance and to measure f ish size composition. Results corroborate published depth ranges and zones of the target species, as well as their habitat preferences. The results indicate that BotCam is a promising tool for monitoring and studying demersal fish populations associated with deepwater habitats to a depth of 300 m, at mesohabitat scales. BotCam is a flexible, nonextractive, and economical means to better understand deepwater ecosystems and improve science-based ecosystem approaches to management.

Larval abundance of summer flounder (Paralichthys dentatus) as a measure of recruitment and stock status

Summer flounder (Paralichthys dentatus) is one of the most economically and ecologically important estuarine-dependent species in the northeastern United States. The status of the population is currently a topic of controversy. Our goal was to assess the potential of using larval abundance at ingress as another fishery independent measure of spawning stock biomass or recruitment. Weekly long-term ichthyoplankton time series were analyzed from Little Egg Inlet, New Jersey (1989–2006) and Beaufort Inlet, North Carolina (1986–2004). Mean size-at-ingress and stage were similar between sites, whereas timing of ingress and abundance at ingress were not similar. Ingress primarily occurred during the fall at Little Egg Inlet and the winter at Beaufort Inlet. These findings agree with those from earlier studies in which at least two stocks (one north and one south of Cape Hatteras) were identified with different spawning periods. Larval abundance at Little Egg Inlet has increased since the late 1990s and most individuals now enter the estuary earlier during the season of ingress. Abundance at Little Egg Inlet was correlated with an increase in spawning stock biomass, presumably because spawning by larger, more abundant fish during the late 1990s and early 2000s provided increased larval supply, at least in some years. Larval abundance at ingress at Beaufort Inlet was not correlated with spawning stock biomass or with larval abundance at ingress at Little Egg Inlet, further supporting the hypothesis of at least two stocks. Larval abundance at Little Egg Inlet could be used as a fishery-independent index of spawning stock size north of Cape Hatteras in future stock assessments. Larval occurrence at Beaufort Inlet may provide information on the abundance of the stock south of Cape Hatteras, but additional stock assessment work is required.

The effect of temperature on the duration of spawning markers—migratory-nucleus and hydrated oocytes and postovulatory follicles—in the multiple-batch spawner Japanese flounder (Paralichthys olivaceus)

The duration of spawning markers (e.g. signs of previous or imminent spawnings) is essential information for estimating spawning frequency of fish. In this study, the effect of temperature on the duration of spawning markers (i.e., oocytes at early migratory nucleus, late migratory nucleus, and hydrated stages, as well as new postovulatory follicles) of an indeterminate multiple-batch spawner, Japanese f lounder (Paralichthys olivaceus), was evaluated. Cannulation was performed to remove samples of oocytes, eggs, and postovulatory follicles in individual females at 2–4 hour intervals over 27–48 hours. The duration of spawning markers was successfully evaluated in 14 trials ranging between 9.2° and 22.6°C for six females (total length 484–730 mm). The durations of spawning markers decreased exponentially with temperature and were seen to decrease by a factor of 0.16, 0.36, 0.30, and 0.31 as temperature increased by 10°C for oocytes at early migratory nucleus, late migratory nucleus, and hydrated stages, and new postovulatory follicles, respectively. Thus, temperature should be considered when estimating spawning frequency from these spawning markers, especially for those fish that do not spawn synchronously in the population.

Integrating methods for determining length-at-age to improve growth estimates for two large scombrids

Fish growth is commonly estimated from length-at-age data obtained from otoliths. There are several techniques for estimating length-at-age from otoliths including 1) direct observed counts of annual increments; 2) age adjustment based on a categorization of otolith margins; 3) age adjustment based on known periods of spawning and annuli formation; 4) back-calculation to all annuli, and 5) back-calculation to the last annulus only. In this study we compared growth estimates (von Bertalanffy growth functions) obtained from the above five methods for estimating length-at-age from otoliths for two large scombrids: narrow-barred Spanish mackerel (Scomberomorus commerson) and broad-barred king mackerel (Scomberomorus semifasciatus). Likelihood ratio tests revealed that the largest differences in growth occurred between the back-calculation methods and the observed and adjusted methods for both species of mackerel. The pattern, however, was more pronounced for S. commerson than for S. semifasciatus, because of the pronounced effect of gear selectivity demonstrated for S. commerson. We propose a method of substituting length-at-age data from observed or adjusted methods with back-calculated length-at-age data to provide more appropriate estimates of population growth than those obtained with the individual methods alone, particularly when faster growing young fish are disproportionately selected for. Substitution of observed or adjusted length-at-age data with back-calculated length-at-age data provided more realistic estimates of length for younger ages than observed or adjusted methods as well as more realistic estimates of mean maximum length than those derived from backcalculation methods alone.

Age validation, growth, mortality, and demographic modeling of spotted gully shark (Triakis megalopterus) from the southeast coast of South Africa

This study documents validation of vertebral band-pair formation in spotted gully shark (Triakis megalopterus) with the use of fluorochrome injection and tagging of captive and wild sharks over a 21-year period. Growth and mortality rates of T. megalopterus were also estimated and a demographic analysis of the species was conducted. Of the 23 OTC (oxytetracycline) -marked vertebrae examined (12 from captive and 11 from wild sharks), seven vertebrae (three from captive and four from wild sharks) exhibited chelation of the OTC and fluoresced under ultraviolet light. It was concluded that a single opaque and translucent band pair was deposited annually up to at least 25 years of age, the maximum age recorded. Reader precision was assessed by using an index of average percent error calculated at 5%. No significant differences were found between male and female growth patterns (P>0.05), and von Bertalanffy growth model parameters for combined sexes were estimated to be L∞=1711.07 mm TL, k=0.11/yr and t0=–2.43 yr (n=86). Natural mortality was estimated at 0.17/yr. Age at maturity was estimated at 11 years for males and 15 years for females. Results of the demographic analysis showed that the population, in the absence of fishing mortality, was stable and not significantly different from zero and particularly sensitive to overfishing. At the current age at first capture and natural mortality rate, the fishing mortality rate required to result in negative population growth was low at F>0.004/ yr. Elasticity analysis revealed that juvenile survival was the principal factor in explaining variability in population growth rate.

Ontogenetic and temporal variability in the fat content and fatty acid composition of Atlantic herring (Clupea harengus) from the Bay of Fundy, Canada

Atlantic herring (Clupea harengus) is an ecologically and economically valuable species in many food webs, yet surprisingly little is known about the variation in the nutritional quality of these fish. Atlantic herring collected from 2005 through 2008 from the Bay of Fundy, Canada, were examined for variability in their nutritional quality by using total lipid content (n=889) and fatty acid composition (n=551) as proxies for nutritional value. A significant positive relationship was found between fish length and total lipid content. Atlantic herring also had significantly different fatty acid signatures by age. Fish from 2005 had significantly lower total lipid content than fish from 2006 through 2008, and all years had significantly different fatty acid signatures. Summer fish were significantly fatter than winter fish and had significantly different fatty acid signatures. For all comparisons (ontogenetic, annual, and seasonal) percent concentrations of omega-3, -6, and long-chain monounsaturated fatty acids were the most important for distinguishing between the fatty acid signatures of fish. This study underscores the importance of quantifying variation in prey quality synoptically with prey quantity in food webs over ontogenetic and temporal scales when evaluating the effect of prey nutritional quality on predators and on modeling trophic dynamics.