scholarly journals Estimating catch-at-age by combining data from different sources

2005 ◽  
Vol 62 (6) ◽  
pp. 1377-1385 ◽  
Author(s):  
David Hirst ◽  
Geir Storvik ◽  
Magne Aldrin ◽  
Sondre Aanes ◽  
Ragnar Bang Huseby
Keyword(s):  
Gadus Morhua ◽  
Ad Hoc ◽  
Atlantic Cod ◽  
Data Types ◽  
Commercial Fish ◽  
Bayesian Hierarchical ◽  
Length Relationship ◽  
Setting Process ◽  
Combining Data ◽  
Almost All

Estimating the catch-at-age of commercial fish species is an important part of the quota-setting process for many different species and almost all countries with a fishing fleet. Current procedures are usually very time-consuming and somewhat ad hoc, and the estimates have no measure of uncertainty. We previously developed a method for catch-at-age of Norwegian Atlantic cod (Gadus morhua), but this only considered aged fish sampled randomly from random hauls. In most countries, the sampling scheme is not so simple. There are usually a very large number of length-only samples from which the age must be estimated using an age–length relationship, and often some or all of the age samples are collected from data that are first stratified by length. This adds considerably to the difficulties in the estimation. In this paper, we model the three different kinds of data simultaneously using a development of our earlier Bayesian hierarchical model. This enables us to obtain estimates of the catch-at-age with appropriate uncertainty and also to provide advice on how best to sample data in the future. The data types are random samples of age, length, and weight; age and weight stratified by length; and length only.

scholarly journals An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

2016 ◽  
Author(s):  
Ole K. Tørresen ◽  
Bastiaan Star ◽  
Sissel Jentoft ◽  
William B. Reinar ◽  
Harald Grove ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gadus Morhua ◽  
Tandem Repeats ◽  
Atlantic Cod ◽  
Genomic Variation ◽  
Promoter Regions ◽  
Sequencing Technologies ◽  
Combining Data ◽  
Genome Assemblies ◽  
Multiple Assembly

AbstractBackground: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Evaluating the performance of a multispecies statistical catch-at-age model

2013 ◽  
Vol 70 (3) ◽  
pp. 470-484 ◽  
Author(s):  
Kiersten L. Curti ◽  
Jeremy S. Collie ◽  
Christopher M. Legault ◽  
Jason S. Link
Keyword(s):  
Species Interactions ◽  
Input Data ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Model Performance ◽  
Clupea Harengus ◽  
Model Parameters ◽  
Data Types ◽  
Commercial Catch ◽  
Important Species

Predation is a substantial source of mortality that is a function of the abundance of predator and prey species. This source of mortality creates a challenge of incorporating species interactions in statistical catch-at-age models in a way that accounts for the uncertainty in input data, parameters, and results. We developed a statistical, age-structured, multispecies model for three important species in the Georges Bank fish community: Atlantic cod (Gadus morhua), silver hake (Merluccius bilinearis), and Atlantic herring (Clupea harengus). The model was fit to commercial catch, survey, and diet data from 1978 to 2007. The estimated predation rates were high, compared with fishing mortality, and variable with time. The dynamics of the three species can be explained by the interplay between fishing and predation mortality. Monte Carlo simulations were used to evaluate the ability of the model to estimate parameters with known error introduced into each of the data types. The model parameters could be estimated with confidence from input data with error levels similar to those obtained from the model fit to the observed data. This evaluation of model performance should help to move multispecies statistical catch-at-age models from proof of concept to functional tools for ecosystem-based fisheries management.

Large effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence

2010 ◽  
Vol 67 (10) ◽  
pp. 1585-1595 ◽  
Author(s):  
Nina Overgaard Therkildsen ◽  
Einar Eg Nielsen ◽  
Douglas P. Swain ◽  
Jes Søe Pedersen
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Population Decline ◽  
Allelic Diversity ◽  
Estimation Methods ◽  
Effective Population ◽  
Commercial Fish

Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod ( Gadus morhua ) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline.

Nutrient Flex onto the Labrador Shelf from Hudson Strait and its Biological Consequences

1983 ◽  
Vol 40 (10) ◽  
pp. 1692-1701 ◽  
Author(s):  
W. H. Sutcliffe Jr. ◽  
R. H. Loucks ◽  
K. F. Drinkwater ◽  
A. R. Coote
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Population Analysis ◽  
Water Discharge ◽  
Nutrient Supply ◽  
Fish Abundance ◽  
Residual Circulation ◽  
Yearly Variation ◽  
Commercial Fish ◽  
Time Required

Fish abundance, based upon commercial fish catches and numbers offish-feeding birds, is shown to increase southward along the Labrador Shelf from Hudson Strait. Also, yearly abundance of Labrador Atlantic cod (Gadus morhua) using virtual population analysis is shown to be closely correlated with salinity changes at Station 27 off St. John's, Newfoundland. We suggest these observations are related to physical oceanographic events originating within Hudson Strait. Analysis of available data indicates nutrient enrichment of the surface waters through physical mixing in Hudson Strait. These waters are carried by the residual circulation onto the northern Labrador Shelf. Our interpretation of the southward increase in fish abundance is that fish production develops downstream of the area of nutrient injection due to the southward flow of the Labrador Current coupled with the time required for food chain development. The yearly variation of cod is interpreted as arising from the variation of the nutrient supply, which is itself correlated with salinity. The fresh water discharge into Hudson Bay which eventually flows out through Hudson Strait and onto the Labrador Shelf appears to suppress mixing and hence years of higher discharge would tend to decrease the nutrient supply.

Integrated stock mixture analysis for continous and categorical data, with application to genetic–otolith combinations

2010 ◽  
Vol 67 (10) ◽  
pp. 1533-1548 ◽  
Author(s):  
Stephen J. Smith ◽  
Steven E. Campana
Keyword(s):  
Elemental Composition ◽  
Categorical Data ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Data Types ◽  
Allele Frequency Data ◽  
Credible Intervals ◽  
Available Information ◽  
Stock Mixture ◽  
Mixed Groups

Fish populations or stocks often intermix on fishing grounds, thus posing problems for stock assessors or managers attempting to optimize yields and minimize overexploitation of individual stocks. A Bayesian framework is developed here to simultaneously analyse many of the different data types (e.g., otolith elemental composition, nuclear and mitochondrial DNA) that have been used to identify stock origins of fish in mixed groups and thus take maximal advantage of the available information. Elements of this framework include the capability to analyse each data type either separately or in combination for any number of mixed-group samples, Bayesian credible intervals to evaluate the uncertainty associated with the estimated proportion of the original stocks in the mixed groups, and posterior predictive diagnostics to evaluate the assumptions of the underlying models. The framework was used to re-analyse a subset of otolith elemental composition and microsatellite allele frequency data obtained from the same fish from Atlantic cod ( Gadus morhua ) stocks in the Gulf of St. Lawrence, Canada.

Measuring changes in the direction and magnitude of size-selective mortality in a commercial fish population

2002 ◽  
Vol 59 (2) ◽  
pp. 361-371 ◽  
Author(s):  
A F Sinclair ◽  
D P Swain ◽  
J M Hanson
Keyword(s):  
Gadus Morhua ◽  
Slow Growth ◽  
Atlantic Cod ◽  
Fish Population ◽  
Disruptive Selection ◽  
Commercial Fishery ◽  
Fishing Mortality ◽  
Selective Mortality ◽  
Commercial Fish ◽  
Size Selection

A 28-year time series (1971–1998) of backcalculated length-at-age was used to investigate changes in the direction and magnitude of size-selective mortality of prerecruit and adult Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence, Canada. Size selection changed from favouring fast growth in the 1970s to favouring slow growth in the late 1980s and 1990s. There was an intervening period of disruptive selection where fast and slow growth was favoured while intermediate growth rates were selected against. The intensity of size selection declined at the end of the study period following the closure of the commercial fishery. These different forms of selection (positive directional, negative directional, and disruptive selection) can all be accounted for by the sharply dome-shaped curve of fishing mortality against length observed in the fishery.

A Novel Method for Predicting Anisakid Nematode Infection of Atlantic Cod Using Rough Set Theory

2018 ◽  
Vol 81 (3) ◽  
pp. 502-508
Author(s):  
Barbara Wąsikowska ◽  
Ewa Sobecka ◽  
Iwona Bielat ◽  
Monika Legierko ◽  
Beata Więcaszek
Keyword(s):  
Set Theory ◽  
Rough Set ◽  
Fish Species ◽  
Gadus Morhua ◽  
Rough Set Theory ◽  
Atlantic Cod ◽  
Production Chain ◽  
Commercial Fish ◽  
Pseudoterranova Decipiens ◽  
Parasite Infections

ABSTRACT Atlantic cod (Gadus morhua L.) is one of the most important fish species in the fisheries industries of many countries; however, these fish are often infected with parasites. The detection of pathogenic larval nematodes is usually performed in fish processing facilities by visual examination using candling or by digesting muscles in artificial digestive juices, but these methods are both time and labor intensive. This article presents an innovative approach to the analysis of cod parasites from both the Atlantic and Baltic Sea areas through the application of rough set theory, one of the methods of artificial intelligence, for the prediction of food safety in a food production chain. The parasitological examinations were performed focusing on nematode larvae pathogenic to humans, e.g., Anisakis simplex, Contracaecum osculatum, and Pseudoterranova decipiens. The analysis allowed identification of protocols with which it is possible to make preliminary estimates of the quantity and quality of parasites found in cod catches before detailed analyses are performed. The results indicate that the method used can be an effective analytical tool for these types of data. To achieve this goal, a database is needed that contains the patterns intensity of parasite infections and the conditions of commercial fish species in different localities in their distributions.

scholarly journals Continuous light delays sexual maturation and increases growth of Atlantic cod (Gadus morhua L.) in sea cages

2006 ◽  
Vol 63 (2) ◽  
pp. 365-375 ◽  
Author(s):  
G.L. Taranger ◽  
L. Aardal ◽  
T. Hansen ◽  
O.S. Kjesbu
Keyword(s):  
Sexual Maturation ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Gonad Development ◽  
Somatic Growth ◽  
Continuous Light ◽  
Reproductive Investment ◽  
Spawning Season ◽  
Commercial Fish ◽  
Spawning Period

Abstract Prevention of early sexual maturation is essential in Atlantic cod (Gadus morhua) farming because maturity results in reduced growth, affects flesh quality, and may lead to increased mortality. In farmed cod, almost 100% of the fish mature at two years of age and often at a size of 1.5–2 kg. Two pilot experiments were conducted with cod in sea cages at a commercial fish farm in western Norway (60°N) to test the effect of additional continuous light (LL) on the timing of sexual maturation and somatic growth compared with controls under natural light (NL). In the NL groups, 100% maturation was indicated during the natural spawning period from February to April at the age of two years. By contrast, LL treatment from 27 June (15-month-old cod) or 2 September (18-month-old cod) onwards delayed gonad development by three to five months, reduced reproductive investment, and enhanced winter growth compared with the controls. Fish held at NL decreased in body weight during the spawning season (February–April), whereas LL-exposed fish appeared to continue to grow during their spawning season (May–August). LL-treated cod reached mean body weights of 2.90–3.13 kg within 28 months of hatching, whereas the controls reached 2.20–2.42 kg during the same period.

scholarly journals Latent Gaussian models to decide on spatial closures for bycatch management in the Barents Sea shrimp fishery

2016 ◽  
Vol 73 (8) ◽  
pp. 1271-1280 ◽  
Author(s):  
Olav Nikolai Breivik ◽  
Geir Storvik ◽  
Kjell Nedreaas
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Juvenile Fish ◽  
Ratio Estimator ◽  
Bayesian Hierarchical ◽  
Spatiotemporal Model ◽  
Shrimp Fishery ◽  
The Barents Sea ◽  
Simple Ratio

In the Barents Sea and adjacent water, fishing grounds are closed for shrimp fishing by the Norwegian Directorate of Fisheries Monitoring and Surveillance Service (MSS) if the expected number of juvenile fish caught are predicted to exceed a certain limit per kilogram shrimp (Pandalus borealis). Today, a simple ratio estimator, which does not fully utilize all data available, is in use. In this paper, we construct a Bayesian hierarchical spatiotemporal model for improved prediction of the bycatch ratio in the Barents Sea shrimp fishery. More predictable bycatch will be an advantage for the MSS because of more correct decisions and better resource allocation and also for the fishermen because of more predictable fishing grounds. The model assumes that the occurrence of shrimp and juvenile Atlantic cod (Gadus morhua) can be modeled by linked regression models containing several covariates (including 0-group abundance estimates) and random effects modeled as Gaussian fields. Integrated nested Laplace approximations is applied for fast calculation. The method is applied to prediction of the bycatch ratio for Atlantic cod.

Effects of temperature on life history set the sensitivity to fishing in Atlantic cod Gadus morhua

2014 ◽  
Vol 514 ◽  
pp. 217-229 ◽  
Author(s):  
HY Wang ◽  
LW Botsford ◽  
JW White ◽  
MJ Fogarty ◽  
F Juanes ◽  
...  
Keyword(s):  
Life History ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Effects Of Temperature
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