A multispecies age-structured assessment model for the Gulf of Alaska

2010 ◽  
Vol 67 (7) ◽  
pp. 1135-1148 ◽  
Author(s):  
Kray F. Van Kirk ◽  
Terrance J. Quinn ◽  
Jeremy S. Collie
Keyword(s):  
Total Mortality ◽  
Single Species ◽  
Gulf Of Alaska ◽  
Assessment Model ◽  
Proof Of Concept ◽  
Predation Mortality ◽  
Gadus Macrocephalus ◽  
Arrowtooth Flounder ◽  
Age Structured ◽  
Biological Realism

Predation is the largest source of mortality for marine fish and may be an important process in regulating population size. Recent population models have attempted to quantify predation separately from other sources of natural mortality. Building upon such work, a multispecies age-structured assessment model (MSASA) for the Gulf of Alaska was developed, which included arrowtooth flounder ( Atheresthes stomias ), Pacific cod ( Gadus macrocephalus ), and walleye pollock ( Theragra chalcogramma ). Predation mortality was a flexible function of predator and prey abundances that was fitted to stomach-content data. A proof of concept illustration is presented here, assessing model outputs against a set of single-species models. The MSASA model was able to successfully estimate predation between species and integrate it into total mortality. Significant predation occurred on younger pollock and flounder. Results indicate a significant change in predation over time on pollock as a function of increased arrowtooth flounder abundance. Estimating mortality and other parameters for three species simultaneously is complex, and the advantage of greater biological realism of MSASA comes at the expense of greater uncertainty in parameter estimation.

scholarly journals The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel

2009 ◽  
Vol 66 (3) ◽  
pp. 445-454 ◽  
Author(s):  
H. Moustahfid ◽  
J. S. Link ◽  
W. J. Overholtz ◽  
M. C. Tyrrell
Keyword(s):  
Stock Assessment ◽  
Fish Predation ◽  
Reference Points ◽  
Assessment Model ◽  
Fishing Mortality ◽  
Atlantic Mackerel ◽  
Predation Mortality ◽  
Spawning Stock ◽  
Age Structured ◽  
The Impact

AbstractMoustahfid, H., Link, J. S., Overholtz, W. J., and Tyrrell, M. C. 2009. The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel. – ICES Journal of Marine Science, 66: 445–454. An age-structured assessment programme (ASAP) that explicitly incorporates predation mortality was applied to Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic. Predatory removals were modelled in the same manner as fishing mortality, with a comparable set of time-series, to produce estimates of predation mortality at age and for each year. Results from the analysis showed that incorporating predation into a mackerel stock assessment model notably altered model outputs. When excluding explicitly modelled rates of predation, the model underestimated the magnitude and uncertainty in spawning-stock biomass (SSB) and recruitment. Further, the rates of predation mortality varied across time and were higher for younger fish. Predation mortality was higher than fishing mortality for fish aged 1 year, approximately equal for 2-year-olds, and lower for older fish (3 years and older). Biological reference points for Atlantic mackerel differed considerably when predation mortality was included. For example, SSBMSY was more than twice as high in the model where predation was incorporated than in the fisheries-only model. Although there are several caveats to the predation model outputs, chief of which is that the estimates are conservative because some mackerel predators were excluded, the results demonstrate the feasibility of executing such an approach with an extant tool. The approach presented here ultimately has the advantage of detecting, and upon detection parsing out, the impact of predators relative to fisheries and has the potential to provide useful information to those interested in small pelagic fish and their associated fisheries.

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.

Loss of spawning habitat and prerecruits of Pacific cod during a Gulf of Alaska heatwave

2020 ◽  
Vol 77 (4) ◽  
pp. 644-650 ◽  
Author(s):  
Benjamin J. Laurel ◽  
Lauren A. Rogers
Keyword(s):  
Time Series ◽  
Laboratory Data ◽  
Reproductive Potential ◽  
Gulf Of Alaska ◽  
Spawning Habitat ◽  
Pacific Cod ◽  
Pacific Cod Gadus Macrocephalus ◽  
Gadus Macrocephalus ◽  
Hatch Success ◽  
Negative Impacts

Pacific cod (Gadus macrocephalus) stocks in the Gulf of Alaska experienced steep, unexpected declines following an unprecedented 3-year marine heatwave (i.e., “warm blob”) from 2014 to 2016. We contend that stock reproductive potential was reduced during this period, evidenced by a combination of new laboratory data demonstrating narrow thermal hatch success (3–6 °C), mechanistic-based models of spawning habitat, and correlations with prerecruit time series. With the exception of single-year El Niño events (1998, 2003), the recent 3-year heatwave (2014–2016) and return to similar conditions in 2019 were potentially the most negative impacts on spawning habitat for Pacific cod in the available time series (1994–2019). Continued warming will likely reduce the duration and spatial extent of Pacific cod spawning in the Gulf of Alaska.

scholarly journals strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5768 ◽  
Author(s):  
Camilo Saavedra
Keyword(s):  
Total Mortality ◽  
R Package ◽  
Analytical Framework ◽  
Population Projections ◽  
Sources Of Information ◽  
Mortality Models ◽  
Credible Intervals ◽  
Leslie Matrices ◽  
Age Structured ◽  
Derived Data

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.

scholarly journals Comparing the roles of Pacific halibut and arrowtooth flounder within the Gulf of Alaska ecosystem and fishing economy

2019 ◽  
Author(s):  
James J. Ruzicka ◽  
Stephen Kasperski ◽  
Stephani Zador ◽  
Amber Himes‐Cornell
Keyword(s):  
Gulf Of Alaska ◽  
Pacific Halibut ◽  
Arrowtooth Flounder

Evaluating evidence for alternative natural mortality and process error assumptions using a state-space, age-structured assessment model

2018 ◽  
Vol 75 (5) ◽  
pp. 691-703 ◽  
Author(s):  
Timothy J. Miller ◽  
Saang-Yoon Hyun
Keyword(s):  
State Space ◽  
Gulf Of Maine ◽  
Model Performance ◽  
Simulated Data ◽  
State Space Models ◽  
Assessment Model ◽  
Biomass Estimation ◽  
Natural Mortality ◽  
Space Age ◽  
Age Structured

State-space models explicitly separate uncertainty associated with unobserved, time-varying parameters from that which arises from sampling the population. The statistical aspects of formal state-space models are appealing and these models are becoming more widely used for assessments. However, treating natural mortality as known and constant across ages continues to be common practice. We developed a state-space, age-structured assessment model that allowed different assumptions for natural mortality and the degree of temporal stochasticity in abundance. We fit a suite of models where natural mortality was either age-invariant or an allometric function of mass and interannual transitions of abundance were deterministic or stochastic to observations on Gulf of Maine – Georges Bank Acadian redfish (Sebastes fasciatus). We found that allowing stochasticity in the interannual transition in abundance was important and estimating age-invariant natural mortality was sufficient. A simulation study showed low bias in annual biomass estimation when the estimation and simulation model matched and the Akaike imformation criterion accurately measured relative model performance, but it was important to allow simulated data sets to include the stochasticity in interannual transitions of abundance-at-age.

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.

scholarly journals Growth, mortality, and recruitment signals in age-0 gadids settling in coastal Gulf of Alaska

2016 ◽  
Vol 73 (9) ◽  
pp. 2227-2237 ◽  
Author(s):  
Benjamin J. Laurel ◽  
Brian A. Knoth ◽  
Clifford H. Ryer
Keyword(s):  
Early Life History ◽  
Gulf Of Alaska ◽  
Walleye Pollock ◽  
First Year ◽  
Pacific Cod ◽  
Temperature Dependent ◽  
Gadus Macrocephalus ◽  
Class Strength ◽  
Saffron Cod ◽  
Recruitment Signals

Abstract Age-0 juveniles may be the earliest, reliable indicators of recruitment into commercial marine fisheries, but independent fisheries assessments are usually conducted on older life stages in adult habitats. We used an 8 year juvenile gadid survey along the coast of Kodiak, Alaska to examine annual abundance, growth and mortality in age-0 Pacific cod (Gadus macrocephalus), with comparisons to saffron cod (Eleginus gracilis) and walleye pollock (Gadus chalcogrammus) where possible. Annual abundance of age-0 fish was positively correlated among all three species, suggesting Pacific gadids respond similarly to processes controlling pre-settlement survival and/or delivery to coastal nurseries. In Pacific cod, June temperature was positively correlated with size-at-settlement but post-settlement growth was density- rather than temperature-dependent. Age-0 abundance indices for Pacific and saffron cod predicted the number of age-1 fish the following year (i.e. positive “recruitment signals”), but only in the larger nursery (Anton Larsen Bay) where age-1 gadids were more likely to remain resident after their first year. Recruitment signals for Pacific cod improved with later estimates of age-0 abundance, likely because of high mortality following settlement in July. In contrast, very few age-0 and age-1 walleye pollock were caught across the entire time-series of the survey. Collectively, these data suggest that nearshore surveys may be a tractable means of examining early life history processes and assessing year-class strength in juvenile Pacific and saffron cod, but have relatively low value in understanding the population dynamics of walleye pollock.

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