Role of disease in abundance of a Pacific herring (Clupea pallasi) population

2003 ◽  
Vol 60 (10) ◽  
pp. 1258-1265 ◽  
Author(s):  
Gary D Marty ◽  
Terrance J. Quinn II ◽  
Greg Carpenter ◽  
Theodore R Meyers ◽  
Neil H Willits
Keyword(s):  
Stock Assessment ◽  
Assessment Model ◽  
Fish Mortality ◽  
Viral Hemorrhagic Septicemia Virus ◽  
Pacific Herring ◽  
Population Abundance ◽  
Total N ◽  
Clupea Pallasi ◽  
The Pacific ◽  
Age Structured

Disease significantly affects population abundance of Pacific herring (Clupea pallasi). Comprehensive epidemiological study of the Pacific herring population of Prince William Sound, Alaska, U.S.A., from 1994 to 2000 included complete necropsy examination of 230–500 fish each spring and 40–160 fish each fall (total n = 2983 fish). Mortality is best estimated, through modifications of an age-structured assessment model, using a disease index that combines the prevalence of viral hemorrhagic septicemia virus (VHSV) with the prevalence of ulcers. Risk factors for an epidemic include poor body condition and abundant recruitment before spawning in the spring. Prevalence of the pathogen Ichthyophonus hoferi increased as fish aged, but changes in I. hoferi prevalence were not related to changes in population abundance. Disease that caused an epidemic in 1998 (VHSV and ulcers) nearly disappeared from the population when changes in abundance were detected by traditional stock assessment methods in 1999. Disease significantly affects recruitment — the two lowest recruitment estimates on record, in 1994 and 1999, followed increased natural mortality of adults in 1993 and 1998.

scholarly journals Data conflicts in fishery models: incorporating hydroacoustic data into the Prince William Sound Pacific herring assessment model

2007 ◽  
Vol 65 (1) ◽  
pp. 25-43 ◽  
Author(s):  
Peter-John F. Hulson ◽  
Sara E. Miller ◽  
Terrance J. Quinn ◽  
Gary D. Marty ◽  
Steven D. Moffitt ◽  
...  
Keyword(s):  
Large Population ◽  
Population Decline ◽  
Assessment Model ◽  
Pacific Herring ◽  
Prince William Sound ◽  
Clupea Pallasi ◽  
The Pacific ◽  
Age Structured ◽  
Population Indices ◽  
Asa Model

Abstract Hulson, P-J. F., Miller, S. E., Quinn, T. J. II, Marty, G. D., Moffitt, S. D., and Funk, F. 2008. Data conflicts in fishery models: incorporating hydroacoustic data into the Prince William Sound Pacific herring assessment model. – ICES Journal of Marine Science, 65: 25–43. Data conflicts present difficulties in running integrated assessment models as shown by the age-structured assessment (ASA) model for the Pacific herring population in Prince William Sound (PWS), Alaska. After the 1989 “Exxon Valdez” oil spill in PWS, the Pacific herring (Clupea pallasi) ASA model indicated a significant decline in the population, starting in winter 1992. Back-calculated estimates from hydroacoustic abundance surveys that started in 1993 suggested that the ASA model overestimated herring biomass from 1990 to 1992 and that the population decline actually began in 1989. To expose data conflicts, we incorporated the hydroacoustic survey information with all available spawning population indices directly into the age-structured model. In this way, the substantial uncertainty about population parameters from 1989 to 1992 attributable to data conflicts was quantified. Consequently, the magnitude of declines for that period estimated from both linear and ASA models depend on the type of integrated datasets and weighting, particularly with indices of male spawners. Our view is that a major decline started in 1992 when disease affected a large population that was in weakened condition. Other views are consistent with the existing data too.

scholarly journals Stock assessment and projections incorporating discard estimates in some years: an application to the hake stock in ICES Divisions VIIIc and IXa

2010 ◽  
Vol 67 (6) ◽  
pp. 1185-1197 ◽  
Author(s):  
C. Fernández ◽  
S. Cerviño ◽  
N. Pérez ◽  
E. Jardim
Keyword(s):  
Time Series ◽  
Stock Assessment ◽  
Reference Points ◽  
Assessment Model ◽  
Marine Science ◽  
Fishing Mortality ◽  
Change Over Time ◽  
Age Structured ◽  
Available Information ◽  
Over Time

Abstract Fernández, C., Cerviño, S., Pérez, N., and Jardim, E. 2010. Stock assessment and projections incorporating discard estimates in some years: an application to the hake stock in ICES Divisions VIIIc and IXa. – ICES Journal of Marine Science, 67: 1185–1197. A Bayesian age-structured stock assessment model is developed to take into account available information on discards and to handle gaps in the time-series of discard estimates. The model incorporates mortality attributable to discarding, and appropriate assumptions about how this mortality may change over time are made. The result is a stock assessment that accounts for information on discards while, at the same time, producing a complete time-series of discard estimates. The method is applied to the hake stock in ICES Divisions VIIIc and IXa, for which the available data indicate that some 60% of the individuals caught are discarded. The stock is fished by Spain and Portugal, and for each country, there are discard estimates for recent years only. Moreover, the years for which Portuguese estimates are available are only a subset of those with Spanish estimates. Two runs of the model are performed; one assuming zero discards and another incorporating discards. When discards are incorporated, estimated recruitment and fishing mortality for young (discarded) ages increase, resulting in lower values of the biological reference points Fmax and F0.1 and, generally, more optimistic future stock trajectories under F-reduction scenarios.

Expression of viral hemorrhagic septicemia virus in prespawning Pacific herring (Clupea pallasi) exposed to weathered crude oil

1998 ◽  
Vol 55 (10) ◽  
pp. 2300-2309 ◽  
Author(s):  
M G Carls ◽  
G D Marty ◽  
T R Meyers ◽  
R E Thomas ◽  
S D Rice
Keyword(s):  
Crude Oil ◽  
Immune Surveillance ◽  
Inflammatory Cells ◽  
Viral Hemorrhagic Septicemia Virus ◽  
Pacific Herring ◽  
Toxicant Exposure ◽  
Clupea Pallasi ◽  
Viral Hemorrhagic Septicemia ◽  
Unknown Status ◽  
Splenic Thrombosis

Expression of subclinical viral infection in response to toxicant exposure has not previously been reported, but evidence presented herein indicates that activation of viral hemorrhagic septicemia virus (VHSV) may occur in Pacific herring (Clupea pallasi) exposed to crude oil encountered after an oil spill. Decreased incidence of hepatic inflammatory cells as a function of total polynuclear aromatic hydrocarbon (TPAH) concentration was evidence for immunosuppression in exposed fish, and decreased immune surveillance is a possible mechanism by which subclinical VHSV could be reactivated. Adult Pacific herring of unknown status regarding infection by VHSV were captured from the wild and exposed to weathered crude oil for 16-18 days. TPAH concentration in tissue, VHSV prevalence, and mortality were correlated with dose. Histopathologic lesions were significantly correlated with TPAH concentration and prevalence of VHSV, but not gender or length. Significant lesions included increased hepatocellular necrosis, splenic thrombosis, and decreased inflammation in the liver.

scholarly journals Looking in the rear-view mirror: bias and retrospective patterns in integrated, age-structured stock assessment models

2014 ◽  
Vol 72 (1) ◽  
pp. 99-110 ◽  
Author(s):  
Felipe Hurtado-Ferro ◽  
Cody S. Szuwalski ◽  
Juan L. Valero ◽  
Sean C. Anderson ◽  
Curry J. Cunningham ◽  
...  
Keyword(s):  
Life Histories ◽  
Temporal Change ◽  
Stock Assessment ◽  
Model Misspecification ◽  
Assessment Model ◽  
Time Varying ◽  
Simulation Framework ◽  
Zero Values ◽  
Age Structured ◽  
Management Advice

Abstract Retrospective patterns are systematic changes in estimates of population size, or other assessment model-derived quantities, that occur as additional years of data are added to, or removed from, a stock assessment. These patterns are an insidious problem, and can lead to severe errors when providing management advice. Here, we use a simulation framework to show that temporal changes in selectivity, natural mortality, and growth can induce retrospective patterns in integrated, age-structured models. We explore the potential effects on retrospective patterns of catch history patterns, as well as model misspecification due to not accounting for time-varying biological parameters and selectivity. We show that non-zero values for Mohn’s ρ (a common measure for retrospective patterns) can be generated even where there is no model misspecification, but the magnitude of Mohn’s ρ tends to be lower when the model is not misspecified. The magnitude and sign of Mohn’s ρ differed among life histories, with different life histories reacting differently from each type of temporal change. The value of Mohn’s ρ is not related to either the sign or magnitude of bias in the estimate of terminal year biomass. We propose a rule of thumb for values of Mohn’s ρ which can be used to determine whether a stock assessment shows a retrospective pattern.

Performance of a fisheries catch-at-age model (Stock Synthesis) in data-limited situations

2011 ◽  
Vol 62 (8) ◽  
pp. 927 ◽  
Author(s):  
Chantell R. Wetzel ◽  
André E. Punt
Keyword(s):  
Stock Assessment ◽  
Estimation Method ◽  
Assessment Method ◽  
Assessment Model ◽  
Limited Data ◽  
Composition Data ◽  
Spawning Stock ◽  
Age Model ◽  
Age Structured ◽  
The Impact

Limited data are a common challenge posed to fisheries stock assessment. A simulation framework was applied to examine the impact of limited data and data type on the performance of a widely used catch-at-age stock-assessment method (Stock Synthesis). The estimation method provided negatively biased estimates of current spawning-stock biomass (SSB) relative to the unfished level (final depletion) when only recent survey indices were available. Estimation of quantities of management interest (unfished SSB, virgin recruitment, target fishing mortality and final depletion) improved substantially even when only minimal-length-composition data from the survey were available. However, the estimates of some quantities (final depletion and unfished SSB) remained biased (either positively or negatively) even in the scenarios with the most data (length compositions, age compositions and survey indices). The probability of overestimating yield at the target SSB relative to the true such yield was ~50%, a risk-neutral result, for all the scenarios that included length-composition data. Our results highlight the importance of length-composition data for the performance of an age-structured assessment model, and are encouraging for the assessment of data-limited stocks.

Comparison of the performance of age-structured models with few survey indices

2018 ◽  
Vol 75 (6) ◽  
pp. 2016-2024
Author(s):  
Hiroshi Okamura ◽  
Yuuho Yamashita ◽  
Momoko Ichinokawa ◽  
Shota Nishijima
Keyword(s):  
Stock Assessment ◽  
Population Analysis ◽  
Assessment Model ◽  
Sufficient Information ◽  
Abundance Estimates ◽  
Virtual Population ◽  
Stock Biomass ◽  
Abundance Indices ◽  
Spawning Stock ◽  
Age Structured

Abstract Age-structured models have played an important role in fisheries stock assessment. Although virtual population analysis (VPA) was once the most widely used stock assessment model for when catch-at-age information is available, (hierarchical) statistical catch-at-age analysis (SCAA) is about to take that position. However, the estimation performance of different age-structured models has not been evaluated sufficiently, especially in cases where there are few available abundance indices. We examined the performance of VPA and SCAA using simulation data in which only the abundance indices of spawning stock biomass and recruitment were available. The simulation demonstrated that VPA with the ridge penalty selected by minimizing retrospective bias provided near-unbiased abundance estimates without catch-at-age error and moderately biased estimates with catch-at-age error, whereas SCAA with random-walk selectivity suffered from problems in estimating parameters and population states. Without sufficient information on abundance trends, naïvely using SCAA with many random effects should be done cautiously, and comparing results from various age-structured models via simulation tests will be informative in selecting an appropriate stock assessment model.

Analytical reference points for age-structured models: application to data-poor fisheries

2009 ◽  
Vol 67 (1) ◽  
pp. 165-175 ◽  
Author(s):  
Elizabeth N. Brooks ◽  
Joseph E. Powers ◽  
Enric Cortés
Keyword(s):  
Stock Assessment ◽  
Meta Analysis ◽  
Reproductive Rate ◽  
Biological Data ◽  
Reference Points ◽  
Assessment Model ◽  
Shark Species ◽  
Stock Status ◽  
Age Structured ◽  
Analytical Reference

AbstractBrooks, E. N., Powers, J. E., and Cortés, E. 2010. Analytical reference points for age-structured models: application to data-poor fisheries. – ICES Journal of Marine Science, 67: 165–175. Analytical solutions for biological reference points are derived in terms of maximum lifetime reproductive rate. This rate can be calculated directly from biological parameters of maturity, fecundity, and natural mortality or a distribution for this rate can be derived from appropriate metadata. Minimal data needs and assumptions for determining stock status are discussed. The derivations lead to a re-parameterization of the common stock–recruit relationships, Beverton–Holt and Ricker, in terms of spawning potential ratio. Often, parameters in stock–recruit relationships are restricted by tight prior distributions or are fixed based on a hypothesized level of stock resilience. Fixing those parameters is equivalent to specifying the biological reference points. An ability to directly calculate reference points from biological data, or a meta-analysis, without need of a full assessment model or fisheries data, makes the method an attractive option for data-poor fisheries. The derivations reveal an explicit link between the biological characteristics of a species and appropriate management. Predicted stock status for a suite of shark species was compared with recent stock assessment results, and the method successfully identified whether each stock was overfished.

Comparison of the frequentist properties of Bayes and the maximum likelihood estimators in an age-structured fish stock assessment model

2002 ◽  
Vol 59 (1) ◽  
pp. 136-143 ◽  
Author(s):  
Anders Nielsen ◽  
Peter Lewy
Keyword(s):  
Maximum Likelihood ◽  
Stock Assessment ◽  
Process Variations ◽  
Bayes Estimator ◽  
Assessment Model ◽  
Fish Stock ◽  
The North ◽  
The North Sea ◽  
Age Structured ◽  
Fish Stock Assessment

A simulation study was carried out for a separable fish stock assessment model including commercial and survey catch-at-age and effort data. All catches are considered stochastic variables subject to sampling and process variations. The results showed that the Bayes estimator of spawning biomass is a useful but slightly biased estimator for which the frequentist variance can be estimated by the posterior variance. Comparisons further show that the Bayes estimator is better than the maximum likelihood in the sense that it is less biased and, surprisingly, has a much lesser variance. The catch simulations were based on the North Sea plaice (Pleuronectes platessa) stock and fishery data.

scholarly journals Two egg-derived molecules in sperm motility initiation and fertilization in the Pacific herring (Clupea pallasi)

2008 ◽  
Vol 52 (5-6) ◽  
pp. 743-752 ◽  
Author(s):  
Gary N. Cherr ◽  
Masaaki Morisawa ◽  
Carol A. Vines ◽  
Kaoru Yoshida ◽  
Edmund H. Smith ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Pacific Herring ◽  
Clupea Pallasi ◽  
The Pacific
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