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.

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.

Estimates of body sizes at maturation and at sex change, and the spawning seasonality and sex ratio of the endemic Hawaiian grouper (Hyporthodus quernus, F. Epinephelidae)

A case study of the reproductive biology of the endemic Hawaiian grouper or hapu’upu’u (Hyporthodus quernus) is presented as a model for comprehensive future studies of economically important epinephelid groupers. Specimens were collected throughout multiple years (1978–81, 1992–93, and 2005–08) from most reefs and banks of the Northwestern Hawaiian Islands. The absence of small males, presence of atretic oocytes and brown bodies in testes of mature males, and both developed ovarian and testicular tissues in the gonads of five transitional fish provided evidence of protogynous hermaphroditism. No small mature males were collected, indicating that Hawaiian grouper are monandrous (all males are sex-changed females). Complementary microscopic criteria also were used to assign reproductive stage and estimate median body sizes (L50) at female sexual maturity and at adult sex change from female to male. The L50 at maturation and at sex change was 580 ±8 (95% confidence interval [CI]) mm total length (TL) and 895 ±20 mm TL, respectively. The adult sex ratio was strongly female biased (6:1). Spawning seasonality was described by using gonadosomatic indices. Females began ripening in the fall and remained ripe through April. A February–June main spawning period that followed peak ripening was deduced from the proportion of females whose ovaries contained hydrated oocytes, postovulatory follicles, or both. Testes weights were not affected by season; average testes weight was only about 0.2% of body weight—an order of magnitude smaller than that for ovaries that peaked at 1–3% of body weight. The species’ reproductive life history is discussed in relation to its management.

Sensitivity of angler benefit estimates from a model of recreational demand to the definition of the substitute sites considered by the angler

Fishery managers are mandated to understand the effects that environmental damage, fishery regulations, and habitat improvement projects have on the net benefits that recreational anglers derive from their sport. Since 1994, the National Marine Fisheries Service (NMFS) has worked to develop a consistent method for estimating net benefits through site choice models of recreational trip demand. In estimating net benefits with these models, there is a tradeoff between computational efficiency and angler behavior in reality. This article examines this tradeoff by considering the sensitivity of angler-welfare estimates for an increase in striped bass (Morone saxatalis) angling quality across choice sets with five travel distance cutoffs and compares those estimates to a model with an unrestricted choice set. This article shows that 95% confidence intervals for welfare estimates of an increase in the striped bass catch and keep rate overlap for all distance-based choice sets specified here.

Precision estimates and suggested sample sizes for length-frequency data

For most fisheries applications, the shape of a length-frequency distribution is much more important than its mean length or variance. This makes it difficult to evaluate at which point a sample size is adequate. By estimating the coefficient of variation of the counts in each length class and taking a weighted mean of these, a measure of precision was obtained that takes the precision in all length classes into account. The precision estimates were closely associated with the ratio of the sample size to the number of size classes in each sample. As a rule-of-thumb, a minimum sample size of 10 times the number of length classes in the sample is suggested because the precision deteriorates rapidly for smaller sample sizes. In absence of such a rule-of-thumb, samplers have previously under-estimated the required sample size for samples with large fish, while over-sampling small fish of the same species.

The use of multibeam sonar mapping techniques to refine population estimates of the endangered white abalone (Haliotis sorenseni)

Multibeam sonar mapping techniques provide detailed benthic habitat information that can be combined with the data on species-specific habitat preferences to provide highly accurate calculations of populations in a particular area. The amount of suitable habitat available for the endangered white abalone (Haliotis sorenseni) was quantified to aid in obtaining an accurate estimate of the number of remaining individuals at two offshore banks and one island site off the coast of southern California. Habitat was mapped by using multibeam sonar survey techniques and categorized by using rugosity and topographic position analysis. Abalone densities were evaluated by using a remotely operated vehicle and video transect methods. The total amount of suitable habitat at these three sites was far greater than that previously estimated. Therefore, although present estimates of white abalone densities are several orders of magnitude lower than historic estimates, the total population is likely larger than previously reported because of the additional amount of habitat surveyed in this study.

Estimates of commercial longline selectivity for Pacific halibut (Hippoglossus stenolepis) from multiple marking experiments

The term “selectivity” refers to the relationship between the size (or age) of a fish and its vulnerability to a given kind of fishing gear. A selectivity schedule, along with other parameters, is normally estimated in the course of fitting a stock assessment model, and the estimated schedule can have a large effect on both the estimate of present stock abundance and the choice of an appropriate harvest rate. The form of the relationship is usually not known and not well determined by the data, and equally good model fits can often be obtained with different plausible specifications of selectivity. Choosing among the model fits and associated abundance estimates in this situation is problematic (Sigler, 1999; Sullivan et al., 19

Parameter estimates for fishes of the upper Paraná river floodplain and Itaipu reservoir (Brazil)

Estimates of the growth (K), natural mortality (M), consumption/biomass (Q/B) rate and trophic level (TL) for 35 species in the upper Paraná river floodplain and the Itaipu reservoir (interconnected ecosystems) are presented. A compilation of these biological statistics is made for comparison purposes and some general trends are briefly discussed.

Reference area as a factor affecting potential yield estimates of coral reef fishes

A compilation of 48 estimates of Caribbean and Pacific coral reef fish catches, ranging from 0.1 to 23.7 t km super(-2) year super(-1), obtained from coral reef areas ranging from 0.1 to nearly 4-10 super(5) km super(2), are used to show that observed catches, and hence potential yield estimates, depend strongly on the reference area. The implications for coral reef fisheries assessments are discussed.

Mapeamento de difusão no reconhecimento e reconstrução de sinais

Em muitas representações de objetos ou sistemas físicos se faz necessário a utilização de técnicas de redução de dimensionalidade que possibilitam a análise dos dados em baixas dimensões, capturando os parâmetros essenciais associados ao problema. No contexto de aprendizagem de máquina esta redução se destina primordialmente à clusterização, reconhecimento e reconstrução de sinais. Esta tese faz uma análise meticulosa destes tópicos e suas conexões que se encontram em verdadeira ebulição na literatura, sendo o mapeamento de difusão o foco principal deste trabalho. Tal método é construído a partir de um grafo onde os vértices são os sinais (dados do problema) e o peso das arestas é estabelecido a partir do núcleo gaussiano da equação do calor. Além disso, um processo de Markov é estabelecido o que permite a visualização do problema em diferentes escalas conforme variação de um determinado parâmetro t: Um outro parâmetro de escala, Є, para o núcleo gaussiano é avaliado com cuidado relacionando-o com a dinâmica de Markov de forma a poder aprender a variedade que eventualmente seja o suporte do dados. Nesta tese é proposto o reconhecimento de imagens digitais envolvendo transformações de rotação e variação de iluminação. Também o problema da reconstrução de sinais é atacado com a proposta de pré-imagem utilizando-se da otimização de uma função custo com um parâmetro regularizador, γ, que leva em conta também o conjunto de dados iniciais.