scholarly journals DELTA MODEL APPROACH FOR CPUE STANDARDIZATION OF SWORDFISH (Xiphias gladius Linnaeus, 1978) CAUGHT BY INDONESIAN LONGLINE FLEET IN THE EASTERN INDIAN OCEAN

2017 ◽  
Vol 23 (1) ◽  
pp. 7
Author(s):  
Irwan Jatmiko ◽  
Humber Andrade ◽  
Budi Nugraha
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Fishery Management ◽  
Stock Assessment ◽  
Short Branch ◽  
Abundance Indices ◽  
Configuration Data ◽  
Catch Rates ◽  
Proportional Decrease ◽  
Model Approach

Relative abundance indices as calculated based on commercial catches are the input data to run stock assessment models to gather useful information for decision making in fishery management. A Generalized Linear Model (GLM) was used to calculate relative abundance indices and effect of longline fishing gear configuration. Data were collected by a scientific observer program from August 2005 to November 2013. Most of the boats monitored were based in the Benoa Port, Bali. Catches are often equal to zero because swordfish is a bycatch for Indonesian longline fleets. Therefore, a hurdle model and a binomial distribution was used to model the proportion of positive catch rates, while a gamma distribution were used to model the positive longline sets. Correlations between the proportion of positive sets and year () and quarter () were weak. However, linear correlation between the proportion of positive sets and the length of branch lines () and number of hooks between floats () were negative and significant. The probability of success is higher for surface longline with small number of hooks and short branch lines. Models with year in interactions as random effects did not converge. Models with year in interactions as fixed effects did converge, but the estimation of standard errors of year coefficients were high. Meaningful estimations were obtained only when using the simplest model, in which year is not in interactions. The low proportional decrease of deviance indicates that most of the variability of catch rates of swordfish caught by Indonesian longline boats are not related to year, quarter, number of hooks between floats and the length of branch lines. Other variables and information, like the daytime while the longlines deployed in the water (day or night), type of bait, size and type of hooks, and if the fishermen use light-sticks to attract the fish, are necessary to better understand the catch rate, and improve the estimations of the relative abundance indices.

scholarly journals A Standardized Abundance Index from Fishery Independent Data: A Case Study of Swordfish (Xiphias Gladius) from Indonesian Tuna Longline Fishery

2020 ◽  
Vol 147 ◽  
pp. 02016
Author(s):  
Bram Setyadji ◽  
Zulkarnaen Fahmi
Keyword(s):  
Relative Abundance ◽  
Fishery Management ◽  
Negative Binomial ◽  
Stock Assessment ◽  
Information Criterion ◽  
Catch Per Unit Effort ◽  
Hurdle Models ◽  
Abundance Indices ◽  
Longline Fisheries ◽  
Tuna Longline

Most varieties of the billfish caught in the Indian Ocean are either swordfish or Indo-Pacific sailfish. Swordfish is mostly considered as by-catch from tuna longline fisheries, except for South African, Spanish and Portuguese fleets. Despite of its importance, little are known about their abundance. Relative abundance indices are the input data for stock assessment analyses that provide useful information for decision making and fishery management. In this paper, a Generalized Linear Model (GLM) was utilized to systematize the catch-per-unit-effort (CPUE) and to estimate relative abundance indices based on the Indonesian longline dataset. The data was collected by scientific observers from August 2005 to December 2016. Conventional models for counting data were used, but zero-inflated and hurdle models also considered, due to the high number of zero-catchper-set. Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) were applied to select the best models among all those evaluated. Both AIC and BIC suggested that the simple negative binomial (NB) model is the best option. The trends were relatively similar to the nominal series, but with smoother peaks. In general, there was a tendency of positive trends in the last decade, with the series varying throughout the period.

scholarly journals Integrating spatial synchrony/asynchrony of population distribution into stock assessment models: a spatial hierarchical Bayesian statistical catch-at-age approach

2016 ◽  
Vol 73 (7) ◽  
pp. 1725-1738 ◽  
Author(s):  
Yan Jiao ◽  
Rob O'Reilly ◽  
Eric Smith ◽  
Don Orth ◽  
Keyword(s):  
Relative Abundance ◽  
Bayesian Model ◽  
Population Distribution ◽  
Stock Assessment ◽  
Spatial Models ◽  
Reference Points ◽  
Hierarchical Bayesian ◽  
Hierarchical Bayesian Model ◽  
Spatial Synchrony ◽  
Abundance Indices

Abstract In many marine fisheries assessments, population abundance indices from surveys collected by different states and agencies do not always agree with each other. This phenomenon is often due to the spatial synchrony/asynchrony. Those indices that are asynchronous may result in discrepancies in the assessment of temporal trends. In addition, commonly employed stock assessment models, such as the statistical catch-at-age (SCA) models, do not account for spatial synchrony/asynchrony associated with spatial autocorrelation, dispersal, and environmental noise. This limits the value of statistical inference on key parameters associated with population dynamics and management reference points. To address this problem, a set of geospatial analyses of relative abundance indices is proposed to model the indices from different surveys using spatial hierarchical Bayesian models. This approach allows better integration of different surveys with spatial synchrony and asynchrony. We used Atlantic weakfish (Cynoscion regalis) as an example for which there are state-wide surveys and expansive coastal surveys. We further compared the performance of the proposed spatially structured hierarchical Bayesian SCA models with a commonly used Bayesian SCA model that assumes relative abundance indices are spatially independent. Three spatial models developed to mimic different potential spatial patterns were compared. The random effect spatially structured hierarchical Bayesian model was found to be better than the commonly used SCA model and the other two spatial models. A simulation study was conducted to evaluate the uncertainty resulting from model selection and the robustness of the recommended model. The spatially structured hierarchical Bayesian model was shown to be able to integrate different survey indices with/without spatial synchrony. It is suggested as a useful tool when there are surveys with different spatial characteristics that need to be combined in a fisheries stock assessment.

scholarly journals Non-linearity in stock–recruitment relationships of Atlantic cod: insights from a multi-model approach

2019 ◽  
Vol 77 (4) ◽  
pp. 1492-1502 ◽  
Author(s):  
Camilla Sguotti ◽  
Saskia A Otto ◽  
Xochitl Cormon ◽  
Karl M Werner ◽  
Ethan Deyle ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Gadus Morhua ◽  
Fishery Management ◽  
Atlantic Cod ◽  
Stock Assessment ◽  
Fish Stock ◽  
Recovery Potential ◽  
Stock Recruitment ◽  
Model Approach ◽  
Non Parametric

Abstract The stock–recruitment relationship is the basis of any stock prediction and thus fundamental for fishery management. Traditional parametric stock–recruitment models often poorly fit empirical data, nevertheless they are still the rule in fish stock assessment procedures. We here apply a multi-model approach to predict recruitment of 20 Atlantic cod (Gadus morhua) stocks as a function of adult biomass and environmental variables. We compare the traditional Ricker model with two non-parametric approaches: (i) the stochastic cusp model from catastrophe theory and (ii) multivariate simplex projections, based on attractor state-space reconstruction. We show that the performance of each model is contingent on the historical dynamics of individual stocks, and that stocks which experienced abrupt and state-dependent dynamics are best modelled using non-parametric approaches. These dynamics are pervasive in Western stocks highlighting a geographical distinction between cod stocks, which have implications for their recovery potential. Furthermore, the addition of environmental variables always improved the models’ predictive power indicating that they should be considered in stock assessment and management routines. Using our multi-model approach, we demonstrate that we should be more flexible when modelling recruitment and tailor our approaches to the dynamical properties of each individual stock.

scholarly journals Abundance trends of highly migratory species in the Atlantic Ocean: accounting for water temperature profiles

2018 ◽  
Vol 75 (4) ◽  
pp. 1427-1438 ◽  
Author(s):  
Patrick D Lynch ◽  
Kyle W Shertzer ◽  
Enric Cortés ◽  
Robert J Latour
Keyword(s):  
Atlantic Ocean ◽  
Relative Abundance ◽  
Stock Assessment ◽  
Migratory Species ◽  
Column Temperature ◽  
Temperature Regimes ◽  
Abundance Trends ◽  
Pelagic Habitat ◽  
Pelagic Longline Fishery ◽  
Catch Rates

Abstract Relative abundance trends of highly migratory species (HMS) have played a central role in debates over the health of global fisheries. However, such trends have mostly been inferred from fishery catch rates, which can provide misleading signals of relative abundance. While many biases are accounted for through traditional catch rate standardization, pelagic habitat fished is rarely directly considered. Using a method that explicitly accounts for temperature regimes, we analysed data from the US pelagic longline fishery to estimate relative abundance trends for 34 HMS in the Atlantic Ocean from 1987 through 2013. This represents one of the largest studies of HMS abundance trends. Model selection emphasized the importance of accounting for pelagic habitat fished with water column temperature being included in nearly every species’ model, and in extreme cases, a temperature variable explained 50–60% of the total deviance. Our estimated trends represent observations from one fishery only, and a more integrated stock assessment should form the basis for conclusions about stock status overall. Nonetheless, our trends serve as indicators of stock abundance and they suggest that a majority of HMS (71% of analysed species) are either declining in relative abundance or declined initially with no evidence of rebuilding. Conversely, 29% of the species exhibited stable, increasing, or recovering trends; however, these trends were more prevalent among tunas than either billfishes or sharks. By estimating the effects of pelagic habitat on fishery catch rates, our results can be used in combination with ocean temperature trends and forecasts to support bycatch avoidance and other time-area management decisions.

scholarly journals Interpreting catch per unit effort data to assess the status of individual stocks and communities

2006 ◽  
Vol 63 (8) ◽  
pp. 1373-1385 ◽  
Author(s):  
Mark N. Maunder ◽  
John R. Sibert ◽  
Alain Fonteneau ◽  
John Hampton ◽  
Pierre Kleiber ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Stock Assessment ◽  
Limited Information ◽  
Catch Per Unit Effort ◽  
Fish Stocks ◽  
Unit Effort ◽  
Strategy Evaluation ◽  
The Status ◽  
Catch Rates ◽  
Management Advice

AbstractDespite being one of the most common pieces of information used in assessing the status of fish stocks, relative abundance indices based on catch per unit effort (cpue) data are notoriously problematic. Raw cpue is seldom proportional to abundance over a whole exploitation history and an entire geographic range, because numerous factors affect catch rates. One of the most commonly applied fisheries analyses is standardization of cpue data to remove the effect of factors that bias cpue as an index of abundance. Even if cpue is standardized appropriately, the resulting index of relative abundance, in isolation, provides limited information for management advice or about the effect of fishing. In addition, cpue data generally cannot provide information needed to assess and manage communities or ecosystems. We discuss some of the problems associated with the use of cpue data and some methods to assess and provide management advice about fish populations that can help overcome these problems, including integrated stock assessment models, management strategy evaluation, and adaptive management. We also discuss the inappropriateness of using cpue data to evaluate the status of communities. We use tuna stocks in the Pacific Ocean as examples.

scholarly journals THE INFLUENCE OF THE COASTAL CURRENT ON THE ESTIMATION OF RELATIVE ABUNDANCE INDICES IN SMALL-SCALE SHRIMP FISHERY

2021 ◽  
Vol 47 ◽  
pp. e665
Author(s):  
Paulo Victor do Nascimento ARAÚJO ◽  
Alex Barbosa de MORAES ◽  
Flávia LUCENA FRÉDOU ◽  
Fúlvio Aurélio de Morais FREIRE
Keyword(s):  
Relative Abundance ◽  
Stock Assessment ◽  
Northeastern Brazil ◽  
Small Scale ◽  
Coastal Current ◽  
Sampling Effort ◽  
Catch Per Unit Effort ◽  
Abundance Index ◽  
Shrimp Fishery ◽  
Abundance Indices

The aim of this scientific note was to evaluate the influence of the coastal current on the estimation of relative abundance indices for small-scale marine shrimp trawling to indicate the best relative abundance index to be used for stock assessment and conservation. Georeferenced experimental trawls were carried out with standardized equipment and capture time on the coast of Rio Grande do Norte, northeastern Brazil. Drags followed convergent and divergent orientations in relation to the flow of the local coastal current. The results showed that the direction of the coastal current flow directly influences the distances and drag shifts, generating variations in the sampling effort and, consequently, bias when using Catch per Unit Effort (CPUE) as a relative abundance index. Conversely, the adoption of Catch per Unit of Swept Area (CPUA) as an index of relative abundance for shrimp trawling becomes more suitable since the variations in the distances of trawl shifts are perceptible through this index.

scholarly journals Lumpfish (Cyclopterus lumpus) in the Barents Sea: development of biomass and abundance indices, and spatial distribution

2014 ◽  
Vol 71 (9) ◽  
pp. 2398-2402 ◽  
Author(s):  
Elena Eriksen ◽  
Caroline M. F. Durif ◽  
Dmitry Prozorkevich
Keyword(s):  
Fishery Management ◽  
Barents Sea ◽  
Stock Assessment ◽  
Strong Association ◽  
Atlantic Water ◽  
Negative Effects ◽  
Cyclopterus Lumpus ◽  
The Barents Sea ◽  
Abundance Indices ◽  
Annual Biomass

Abstract Little is known about lumpfish (Cyclopterus lumpus) ecology, especially its distribution in the open Barents Sea. This paper describes fluctuations in abundance and biomass indices of lumpfish based on pelagic trawl catches. This long-term monitoring survey has been conducted between August and September since 1980. Investigations show that lumpfish is widely distributed in the pelagic waters of the Barents Sea. Relative biomass and abundance indices were calculated for the period 1980–2012. The mean annual biomass was estimated to be 48 000 t, with a maximum of 143 000 t; the estimated mean annual abundance was 53 million individuals, with a maximum of 132 million individuals. There were more juveniles than adults, with juveniles comprising 40–80% of the total abundance (average 60%). The largest concentrations of both juveniles and adults were in years with warm temperatures. The majority of fish were found in waters of 5–7°C (60% of juveniles) and 4–7°C (70% of adults), indicating a strong association with Atlantic water masses in the Barents Sea. Regulations on the Norwegian and Russian fisheries for prespawning lumpfish are based only on after-the-fact fishery data and, therefore, have been insufficient in preventing negative effects on the lumpfish resource from fishing. Understanding the stock fluctuations and the use of fishery-independent data may improve the precautionary approach to fishery management. The use of lumpfish indices from the scientific surveys in the Barents Sea should be implemented to strengthen the current stock assessment.

Aspects of the fishery, maturation and net selectivity of the wedge sole (Dicologoglossa cuneata) off south-western Iberia: implications for fishery management

2009 ◽  
Vol 90 (7) ◽  
pp. 1465-1474 ◽  
Author(s):  
Miguel Neves Santos ◽  
Pedro Gil Lino
Keyword(s):  
Fishery Management ◽  
River Mouth ◽  
Mesh Size ◽  
Scientific Basis ◽  
Catch Per Unit Effort ◽  
Important Species ◽  
Gill Net ◽  
Catch Rates ◽  
Log Normal ◽  
First Maturity

The wedge sole (Dicologoglossa cuneata, Moreau 1881) is a commercially important species for the artisanal fleet operating off the south-western Iberian Peninsula. During 2004 and 2005 a study was undertaken aiming to provide a scientific basis for management. Data collection included information on aspects of the fishery, spawning season, size at first maturity, tangle and gill-net selectivity. Seven nominal mesh sizes were used (40, 45 and 50 mm tangle nets and 40, 50, 60 and 70 mm gill-nets). Spawning lasts from December to June, with peaks in March and May. Length at first maturity for females was estimated at 18.5 cm. Catch rates decreased sharply with increasing mesh size, with tangle nets providing the highest yields. The log-normal selectivity model provided the best fit for specimens that were wedged. The higher catch-per-unit-effort of the smaller mesh sizes and the modal length of the fitted selectivity curve being below the size-at-maturity for wedge sole, suggests that the 50 mm nominal mesh size tangle net is the most appropriate for ensuring the fishery sustainability. Nevertheless, the minimum legal size should increase to at least 18 cm and a time–area closure should be implemented off the Guadiana River mouth.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P < 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

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