Development of Bayesian stock assessment methods for Namibian orange roughy Hoplostethus atlanticus

Bayesian methods are useful in fisheries stock assessment because they provide a conceptually elegant and statistically rigorous approach to making decisions under uncertainty. The application of Bayesian stock assessment methods in the management of Namibian orange roughy Hoplosthethus atlanticus within the 200 mile EEZ of Namibia is reviewed. Time-series of relative abundance are short and their reliability in indicating abundance trends is uncertain. The development of informative prior probability density functions (pdfs) for the constants of proportionality (q) for hydro-acoustic, commercial trawl swept area, and research trawl swept area indices produced statistically consistent prior estimates of absolute abundance for each of the three grounds where more than one index of abundance was available. The posterior pdfs for stock assessment model parameters were used to account for uncertainty in evaluations of the potential consequences of alternative harvesting policies under a stock reduction model in which catch removals were assumed to account for any declines. It appears that all orange roughy stocks off Namibia have been depleted below the limit reference point (50% of long-term unfished biomass). However, the stock reduction model could not easily account for the large declines in indices on the four fishing grounds over the period from 1995 until 1999 when the informative priors for q were applied. In the 2000 stock assessment, the Bayesian procedure was updated to account formally for uncertainty in model structures that could explain the decline in abundance. The possibility of very low stock abundance could still not be discounted when these uncertainties were accounted for. Although this most recent methodology applies more statistical rigour, its complexity has hindered its acceptance in Namibia. However, if it is worth quantifying risks and uncertainties in future stock assessments for the provision of precautionary management advice, it is proposed that the assessment protocols adopted be probabilistic to account for uncertainty in model parameters, that careful attention be given to subjective judgements about their inputs and the representation of uncertainty within them, and that, where appropriate, alternative hypotheses about stock abundance and mechanisms for catchability and stock decline be taken into account.     

Comparison of horse mackerel length frequencies obtained from research vessels and commercial midwater trawlers: implications for biomass estimation

The validity of abundance estimates from hydroacoustic surveys relies, inter alia, on the ability of the fishing gear on the research vessel to sample non-selectively. This study compares the length frequencies of Cape horse mackerel Trachurus trachurus capensis taken in Namibian waters by the R.V. Welwitchia and commercial midwater trawlers. Results indicate that the length distributions of catches taken by the Welwitchia were significantly different from those from commercial trawlers, with a greater proportion of fish >25 cm being sampled by the latter. Also, the biomass estimated per length-class from hydroacoustic surveys over the period 1994–2000 was compared with those from annual landings of the commercial fishery. The length distribution of horse mackerel in purse-seine catches compares favourably with those from the research vessel. However, comparisons with the midwater trawl catches indicated that the length frequencies obtained from research vessels during the years 1994–1997 underestimated the number of large fish in the population and biased the biomass in those years. From 1998 to 2000 the bias was negligible. The magnitude of the error varied between years, but it remained fairly low. To compensate for this bias, length distribution data from midwater trawlers should be integrated into the acoustic biomass calculation procedure.     

A review of orange roughy Hoplostethus atlanticus fisheries,estimation methods,biology and stock structure

Orange roughy Hoplostethus atlanticus are unusual fish. They form dense aggregations that have fuelled lucrative fisheries at great depths (600–1 400 m), especially off Namibia, New Zealand and Australia. They are thought to be very long-lived (>100 years, maturity at 22 – 40 years), and to have exceptionally low natural mortality (M = 0.045–0.064 year^?1) and slow growth rates (K = 0.055–0.070 year^?1). In addition, they spawn large eggs and have low fecundity. These factors combine to make orange roughy highly susceptible to overfishing; most stocks are below 30% of pristine levels. Assessments are obtained from indices of catch rate and trawl, acoustic and egg surveys. Acoustic estimates are the most direct, but are confounded by the species' low target strength (?50 to ?53 dB)–attributable to the wax-filled swim bladder. Extracellular wax esters are stored in abundance and comprise mostly mono-unsaturated fatty acids, with low concentrations of the ω-3 fatty acid family. This unusual composition (resultant from the species' diet) ensures neutral buoyancy. Stock separation has been inferred mainly from biological studies, but genetic studies have also found differences among stocks within New Zealand and Australia. Deep-water habitat may be damaged by trawling operations and may take many years to recover, so in some quarters there is a call for a portion of suitable habitat to be set aside for preservation. Although Namibian orange roughy are shallower, smaller and younger than those in other stocks, the Namibian fishery sustained high catches for only a few years before quotas were reduced, from 12 000 to 1 875 tons. Three management lessons are suggested for developing orange roughy fisheries based on the Namibian experience: (1) imposition of catch limits during exploratory fishing; (2) starting the acoustic surveys earlier in the fishery, if possible; (3) greater reliance on trends in catch rate until a survey series has been established.     

The abundance and distribution of euphausiids and zero-age pollock on the inner shelf of the southeast Bering Sea near the Inner Front in 1997–1999

Acoustic data and net samples were collected during late spring and early fall 1997–1999 to assess zooplankton and micronekton abundance and distribution relative to the Inner Front at three sampling grids (Port Moller, Cape Newenham and Nunivak Island) on the inner shelf of the southeast Bering Sea. Epibenthic scattering layers were observed during May–June and August–September in all three years. Acoustic data were scaled to euphausiid biomass using target strength models. Mean euphausiid biomass determined acoustically for each transect line was 0.7–21 g m⁻², with most values below 5 g m⁻². There was no consistent relationship between the distribution and biomass of euphausiids and the location of the Inner Front. Zero age pollock were observed on the inner shelf in August–September during all years, but were confined primarily to the stratified side of the Inner Front and to the frontal regime. The acoustic data for pollock were scaled to biomass using laboratory measurements of gas bladder dimensions and target strength models. Acoustic determinations of mean transect biomass for euphausiids did not differ from literature values for the inner shelf of the southeast Bering Sea, and pollock biomass on the inner shelf did not differ from that around the Pribilof Islands. Despite recent anomalies in climate and oceanographic conditions on the inner shelf, and high mortality of shorttail shearwaters during 1997, we found no evidence of significant interannual differences in the biomass of euphausiids or zero-age pollock on the inner shelf of the southeast Bering Sea.     

The orange roughy fishery of Namibia: lessons to be learned about managing a developing fishery

Exploration for orange roughy Hoplostethus atlanticus in Namibia started in 1994 and within 12 months several aggregations had been discovered, suggesting the existence of a biomass sufficient to support a viable fishery. At that early stage it was realized that few, if any, recognized management procedures existed for newly developing fisheries, especially with the paucity of data such as existed on Namibian orange roughy. The development of the Namibian orange roughy fishery is reviewed to document the management strategies implemented and how the management of the fishery evolved. The first six years of the fishery are described, including the three-year exploration phase, several years of profitable exploitation, and the severe decline in catch rates. Whether the decline is attributable to fishing mortality or to change in the aggregating behaviour of orange roughy, or both, is not clear. Although many aspects of the precautionary approach were followed, a risk analysis applied and a number of innovative management methods implemented (e.g. incentives to promote exploratory fishing, use of Bayesian statistical methods, implementation of a management plan for long-term total allowable catches), the aggregating biomass declined to between 10 and 50% of virgin levels within the six years. The management methods applied are evaluated in the light of the severe decline in catch rate experienced in 1998 and 1999, so that others may learn from the experience.     

The role of acoustic surveys in the assessment of pelagic fish resources on the South African continental shelf

Acoustic data on the abundance and distribution of anchovy Engraulis capensis, pilchard Sardinops ocellatus and round herring Etrumeus whiteheadi on the South African continental shelf have been collected from 21 echo-integrator surveys between 1984 and 1991. Most effort has been concentrated on estimating adult biomass of anchovy and pilchard in November (spring) and anchovy recruitment in autumn. Distribution maps from all surveys are presented and the biomass estimates considered most reliable documented. A series of distribution maps tracing movements of three anchovy year-classes over a four-year period is presented to illustrate the usefulness of the surveys in migration studies. The major findings of the survey programme have been that anchovy are generally considerably more abundant and widespread than was thought to be the case prior to the surveys, that the pilchard resource has recovered substantially in recent years, and that the round herring resource, about which little was known prior to the surveys, is probably of the same order of magnitude as the anchovy resource and is probably underexploited. The anchovy and pilchard resources are currently managed through procedures based largely on the acoustic estimates of biomass and their estimated precision. The role of these estimates in the management procedures is discussed in some detail.     

Letter to the editor

It is a common observation that the mean length in a fish population progressively decreases as the biomass is reduced by fishing. However, this has not happened with the population of orange roughy (Hoplostethus atlanticus) on the Chatham Rise, New Zealand, even though the biomass is estimated to have declined by almost 80%. Because orange roughy are slow growing it might be expected that mean age (or its proxy, mean otolith weight) would be a more sensitive indicator of biomass decline than mean length. A simulation study shows that this is not true. With equal sample sizes, all three indicators are equally sensitive; on an equal cost basis, mean length is more sensitive than the others. A log transformation increases the sensitivity of age and otolith weight, but it is not clear whether this increase is sufficient to outweigh the much greater costs of measuring age and otolith weight, compared to length. Under the assumption of constant recruitment, it is more likely than not (P = 0.55–0.8) that a change in mean length would have been detected in the Chatham Rise population, given the estimated biomass decline.     

Fisheries for orange roughy (Hoplostethus atlanticus) on seamounts in New Zealand

Major commercial fisheries for orange roughy (Hoplostethus atlanticus) occur on seamount features, which are widely distributed throughout the New Zealand region. When the fishery developed in the late 1970s to early 1980s, it occurred mainly on flat bottom, but over time has become more focused on seamounts. In the 1995–1996 fishing year, it is estimated that about 70 % of the catch of orange roughy within the New Zealand EEZ was taken from seamounts. Seamounts on the Chatham Rise have been fished for over ten years. Examination of commercial catch and effort data show strong declines in catch rates over time, and a pattern of serial depletion of seamount populations, with the fishery moving progressively eastwards to unfished seamounts along the southern margins of the Rise. Catch rates on seamounts in other regions of New Zealand have also generally shown a similar pattern of rapid decline. There is growing concern over the impact of trawling on seamounts, and the effects this can have on the benthic habitat and fauna, and the long-term sustainability of associated commercial fisheries.     

Acoustic study on the abundance and distribution of anchovy spawners and recruits in South African waters

Direct surveys of Cape anchovy Engraulis capensis spawner and recruit biomass in South African coastal waters were made with a 38-kHz calibrated echo-sounder and custom-built digital echo-integrator. The spawning surveys were conducted each November between 1983 and 1985, predominantly on the Agulhas Bank. Recruit surveys were conducted in autumn 1985 and 1986, mainly on the West Coast. The spawning fish were widely distributed across the continental shelf, whereas recruit concentrations were highest close inshore. Employing a target strength per kilogramme expression for herring Clupea harengus, the spawning biomass in 1984 was estimated at 1,06 million tons and that in 1985 at 0,98 million tons. Similarly, recruit biomass in May/June 1985 and June 1986 was estimated at 310 and 466 thousand tons respectively. From an analysis of error in the latter two estimates, it was considered approximately 80 per cent certain that the recruitment in 1986 was greater than in 1985. The estimates of spawning biomass are 3–4 times higher than earlier estimates made by Virtual Population Analysis (VPA) of commercial catch data, and suggest that the stock is less seriously threatened by present catch levels than was indicated by VPA. It is concluded from the distribution and age structure of the spawning population that the VPA estimates are invalid because of the failure of commercial vessels to sample the major part of the adult population.     

Absolute Calibration of TOPEX/Poseidon and Jason-1 Using GPS Buoys in Bass Strait, Australia

An absolute calibration of the TOPEX/Poseidon (T/P) and Jason-1 altimeters has been undertaken during the dedicated calibration phase of the Jason-1 mission, in Bass Strait, Australia. The present study incorporates several improvements to the earlier calibration methodology used for Bass Strait, namely the use of GPS buoys and the determination of absolute bias in a purely geometrical sense, without the necessity of estimating a marine geoid. This article focuses on technical issues surrounding the GPS buoy methodology for use in altimeter calibration studies. We present absolute bias estimates computed solely from the GPS buoy deployments and derive formal uncertainty estimates for bias calculation from a single overflight at the 40-45 mm level. Estimates of the absolute bias derived from the GPS buoys is -10 ± 19 mm for T/P and +147 ± 21 mm for Jason-1 (MOE orbit) and +131 ± 21 mm for Jason-1 (GPS orbit). Considering the estimated error budget, our bias values are equivalent to other determinations from the dedicated NASA and CNES calibration sites.     

Fine-scale population structure in a deep-sea teleost (orange roughy, Hoplostethus atlanticus)

Microsatellite and otolith chemistry variability were analysed to assess fine scale genetic structure in the deep-sea teleost orange roughy (Hoplostethus atlanticus). The Porcupine Bank located on the continental shelf west of Ireland, comprises a complex system of mounds and flat areas that are broken up by canyons. Orange roughy form spawning aggregations on mounds and flat areas, and were heavily fished until the resource was depleted. By analysing adults in spawning condition and juvenile orange roughy from six mounds and one flat area, shallow but significant genetic population structure was evident (F_ST=0.0031, D_est across loci=0.0306 and G-test). Most of the structure was accounted for by inclusion of a sample from the flats (six of ten significant pairwise F_ST estimates and G-tests, and five of the highest D_est estimates included the flat sample). While the flat sample contributed most to the genetic structure, there was still significant (albeit weaker) structure among mound samples. The observed structure was supported by otolith analyses. Fish caught as late juveniles in either the flat or mound areas showed consistent differences in chemistry at the otolith core throughout the initial 10 years of growth, which could indicate site fidelity. We hypothesise that seafloor topographic structures (mounds and flats) may provide discrete spawning areas for orange roughy and that the limited gene flow between these spawning areas is insufficient to counteract genetic drift.     

Size‐fecundity relationships in the smooth oreo,Pseudocyttus maculatus,and the black oreo,Allocyttus niger (Pisces: Oreosomatidae) (note)

Fecundity estimates were made from 72 smooth oreo (Pseudocyttus maculatus Gilchrist, 1906) and 77 black oreo (Allocyttus niger James, Inada & Nakamura, 1988) with oocytes in late vitellogenesis, captured from the south Chatham Rise during November 1986. Absolute fecundities ranged from 6000 to 84 000 for smooth oreo and 5000 to 62 000 for black oreo, with relative fecundities of 10 800 and 17 500 eggs per kg body weight for smooth and black oreos, respectively. Both species have absolute and relative fecundities within the same order of magnitude as orange roughy, but one to two orders of magnitude lower than six other commercially exploited fish species from the New Zealand continental shelf or slope region. The comparatively low fecundity of the oreo species could contribute to susceptibility to overfishing.     

Juvenile life history of NE Atlantic orange roughy from otolith stable isotopes

Otoliths of pre-recruit orange roughy (Hoplostethus atlanticus) were sampled from different deep-water habitats (‘flat’ and ‘hill’) and areas (north and south) on the Porcupine Bank. Age-based profiles for stable isotopes of carbon (δ¹³C) and oxygen (δ¹⁸O) in these otoliths were developed, which provide a fish life-history record of water depth and metabolic activity. These profiles were consistent among all individuals implying endogenous (ontogenic) influences on the pattern. The data indicate that post-larval orange roughy are mesopelagic active foragers, early juvenile fish move into a low energy deep-demersal phase, and older pre-recruit orange roughy assume the habitat depth and metabolic rate typical of adults. Comparison of otolith stable isotope profiles among areas and habitats on the Porcupine Bank suggest that juvenile orange roughy from South ‘hill’ and ‘flat’ habitats experience differing temperature and metabolic status at certain life stages. This may reflect oceanographic and ecological divergence between the two environments and suggests fine-scale population structure that may reduce resilience to exploitation.     

Revised estimates of abundance of South African sardine and anchovy from acoustic surveys adjusting for echosounder saturation in earlier surveys and attenuation effects for sardine

Hydro-acoustic surveys have been used to provide annual estimates of May recruitment and November spawner biomass of the South African sardine Sardinops sagax and anchovy Engraulis encrasicolus resources since 1984. These time-series of abundance estimates form the backbone of the assessment of these resources, and consequently the management of the South African sardine and anchovy is critically dependent on them. Upgrades to survey equipment over time have resulted in recent surveys providing more accurate estimates of abundance, yet in order to maintain comparability across the full time-series, estimates of biomass mimicking the old equipment were used for a number of years. In this paper we develop a method to revise the earlier part of the time-series to correct for receiver saturation in the older generation SIMRAD EK400 and EKS-38 echo sounders and to account for attenuation in dense sardine schools. This is applied to provide a revised time-series of biomass estimates for the South African sardine and anchovy resources with associated variance–covariance matrices. Furthermore, the time-series presented here are based on updated acoustic target strength estimates, making this the most reliable time-series currently available for both resources.     

Evaluation of a class of possible simple interim management procedures for the Namibian hake fishery

During 1997, considerable scientific differences arose about the status of the Namibian hake (Merluccius capensis and M. paradoxus) resource, and as to whether the hake Total Allowable Catch (TAC) should be substantially decreased or increased. These differences revolved primarily around whether or not abundance estimates from the swept-area trawl surveys by the Norwegian research vessel Dr Fridtjof Nansen should be considered as reliable measures of biomass in absolute (as distinct from relative) terms. The paper relates the computations underlying the Interim Management Procedure (IMP) approach that was put forward at that time as a basis to resolve this impasse. The anticipated performance, in terms of catch and risk of resource depletion, of a number of simple candidate IMPs for the Namibian hake resource is evaluated. The IMPs depend on two parameters, whose values are to be chosen by decision-makers, and adjust the TAC up or down from one year to the next according to whether trends in recent commercial catch rate and survey indices of abundance are positive or negative. Performances are evaluated across the then current wide range argued for resource abundance and status. Trade-offs in performance across the candidates considered are discussed. One of the candidates was subsequently selected by a joint meeting of scientists, industry and Ministry officials in February 1998 and served as the basis for scientific recommendations for the TAC for the hake resource for the following three years.     

Comparison of anchovy biomass estimates measured by trawls,egg production methods and hydro-acoustics in the Chesapeake Bay and the Korea Strait

We compared estimates of anchovy biomass derived from trawl surveys, egg production method (EPM) and acoustic surveys, conducted in two remote regions. Biomass density of bay anchovy Anchoa mitchilli was estimated in Chesapeake Bay, USA, by trawls, EPM and acoustics from 1989 to 2000. Biomass density of Pacific anchovy Engraulis japonicus was estimated in the Korea Strait using EPM, simulation-based daily cohort analysis and acoustics from 1984 to 2006. Most of the existing estimates already had considered body-size-dependent gear selectivity, highlyvariable instantaneous natural mortality of anchovy eggs, and avoidance of trawl nets by adult anchovy. Despite great variability in the ratio of trawl to acoustic biomass estimates (0.034–8.35), annually-averaged biomass density of young-ofthe-year individuals derived by the two methods were similar for bay anchovy in Chesapeake Bay and Pacific anchovy in the Korea Strait (0.83 and 0.70 g m^?3, respectively). Results suggested that, despite substantial uncertainty, anchovy biomass estimates are generally compatible between EPM and acoustics. However, reported estimates of biomass density derived from the two acoustic surveys in the Korea Strait differed by a factor of 28, suggesting that further improvements in calibrations are required to reliably estimate anchovy biomass. The comparisons suggested that all biomass estimates could be biased and will require comparison and validation by other, independent sampling methods.     

Performance evaluation of fixed-station sampling design for a fishery-independent survey with multiple objectives

Fixed-station sampling design was widely used in fishery-independent surveys because of its characteristics of convenient sampling station setting, but the non-probabilistic(fixed) nature made it more uncertainty of drawing inferences on population. The performance of fixed-station sampling design for multispecies survey has not been evaluated, and we are uncertain if the design could detect the temporal trends of different populations in multispecies fishery-independent survey. In this study, s...     

Calibration of JASON-1 Altimeter over Lake Erie Special Issue: Jason-1 Calibration/Validation

This article describes absolute calibration results for both JASON-1 and TOPEX Side B (TSB) altimeters obtained at the Lake Erie calibration site, Marblehead, Ohio, USA. Using 15 overflights, the estimated JASON altimeter bias at Marblehead is 58 ± 38 mm, with an uncertainty of 19 mm based on detailed error analysis. Assuming that the TSB bias is negligible, relative bias estimates using both data from the TSB-JASON formation flight period and data from 48 water level gauges around the entire Great Lakes confirmed the Marblehead results. Global analyses using both the formation flight data and dual-satellite (TSB and JASON) crossovers yield a similar relative bias estimate of 146 ± 59 mm, which agrees well with open ocean absolute calibration results obtained at Harvest, Corsica, and Bass Strait (e.g., Watson et al. 2003). We find that there is a strong dependence of bias estimates on the choice of sea state bias (SSB) models. Results indicate that the invariant JASON instrument bias estimated oceanwide is 71 mm, with additional biases of 76 mm or 28 mm contributed by the choice of Collecte Localisation Satellites (CLS) SSB or Center for Space Research (CSR) SSB model, respectively. Similar analysis in the Great Lakes yields the invariant JASON instrument bias at 19 mm, with the SSB contributed biases at 58 mm or 13 mm, respectively. The reason for the discrepancy is currently unknown and warrants further investigation. Finally, comparison of the TOPEX/POSEIDON mission (1992–2002) data with the Great Lakes water level gauge measurements yields a negligible TOPEX altimeter drift of 0.1 mm/yr.     

Calibration of JASON-1 Altimeter over Lake Erie

This article describes absolute calibration results for both JASON-1 and TOPEX Side B (TSB) altimeters obtained at the Lake Erie calibration site, Marblehead, Ohio, USA. Using 15 overflights, the estimated JASON altimeter bias at Marblehead is 58 ± 38 mm, with an uncertainty of 19 mm based on detailed error analysis. Assuming that the TSB bias is negligible, relative bias estimates using both data from the TSB-JASON formation flight period and data from 48 water level gauges around the entire Great Lakes confirmed the Marblehead results. Global analyses using both the formation flight data and dual-satellite (TSB and JASON) crossovers yield a similar relative bias estimate of 146 ± 59 mm, which agrees well with open ocean absolute calibration results obtained at Harvest, Corsica, and Bass Strait (e.g., Watson et al. 2003). We find that there is a strong dependence of bias estimates on the choice of sea state bias (SSB) models. Results indicate that the invariant JASON instrument bias estimated oceanwide is 71 mm, with additional biases of 76 mm or 28 mm contributed by the choice of Collecte Localisation Satellites (CLS) SSB or Center for Space Research (CSR) SSB model, respectively. Similar analysis in the Great Lakes yields the invariant JASON instrument bias at 19 mm, with the SSB contributed biases at 58 mm or 13 mm, respectively. The reason for the discrepancy is currently unknown and warrants further investigation. Finally, comparison of the TOPEX/POSEIDON mission (1992-2002) data with the Great Lakes water level gauge measurements yields a negligible TOPEX altimeter drift of 0.1 mm/yr.     

Satellite Remote Sensing as a Reconnaissance Tool for Assessing Nautical Chart Adequacy and Completeness

National hydrographic offices need a better means of assessing the adequacy of existing nautical charts in order to plan and prioritize future hydrographic surveys. The ability to derive bathymetry from multispectral satellite imagery is a topic that has received considerable attention in scientific literature. However, published studies have not addressed the ability of satellite-derived bathymetry to meet specific hydrographic survey requirements. Specifically, the bathymetry needs to be referenced to a chart datum and statistical uncertainty estimates of the bathymetry should be provided. Ideally, the procedure should be based on readily-available, low-cost software, tools, and data. This paper describes the development and testing of a procedure using publicly-available, multispectral satellite imagery to map and portray shallow-water bathymetry in a GIS environment for three study sites: Northeast United States, Nigeria, and Belize. Landsat imagery and published algorithms were used to derive estimates of the bathymetry in shallow waters, and uncertainty of the satellite-derived bathymetry was then assessed using a Monte Carlo method. Results indicate that the practical procedures developed in this study are suitable for use by national hydrographic offices.