Kevin R. Piner

A Simulation-Based Method to Determine Model Misspecification: Examples Using Natural Mortality and Population Dynamics Models

Abstract Recent developments in the models used in wildlife and fisheries science have allowed the inclusion of a wider range of data than previously. However, the diagnostics of such complex models have not kept pace. We describe a new diagnostic technique based on simulation analysis. Model misspecification was identified through simulation methods that created a distribution of likely parameter values for a model that was correctly specified. If the actual estimate of that parameter is outside the bounds of the simulated distribution, then the model is probably misspecified. We tested the reliability of the new diagnostic by introducing known-model misspecification into complex fisheries stock assessment models. We then compared the results from this new diagnostic with those of a more tradition fisheries diagnostic, namely, retrospective analysis. The simulation-based diagnostic was shown to identify inisspecification affecting the estimated dynamics more reliably than retrospective analysis.

A Robust Deterministic Model Describing the Bomb Radiocarbon Signal for Use in Fish Age Validation

Abstract The bomb radiocarbon chronometer has become a standard tool for assessing the accuracy of otolith-based fish age estimates. Use of the chronometer depends upon the increase in 14C that occurred due to the atmospheric testing of nuclear weapons in the middle of the 20th century. In previous analyses, a variety of ad hoc methods have been used to compare test chronologies with reference chronologies. This paper proposes a deterministic coupled-functions model that describes bomb radiocarbon chronologies and standardizes and facilitates comparisons within and across species. In this model, a Gaussian pulse of radiocarbon over time is assumed, and dispersion and dilution are described by continuous exponential decay. The model simplifies to the product of a cumulative normal function and an exponential function; despite its simplicity, the model approximates the observed changes in oceanic radiocarbon quite well. It also allows for statistical testing of the timing of increase between different time ...

Isotopic Correlation (δ18O versus δ13C) of Otoliths in Identification of Groundfish Stocks

Abstract The management of many marine fish stocks suffers from a lack of genetic data or insignificant genetic differentiations, particularly for the commercially important groundfish along the U.S. Pacific coast. In this study, we investigated a large number of otoliths of various groundfish species from the coasts of Washington and Oregon and analyzed them for stable oxygen (18O/16O, or δ18O) and carbon isotope ratios (13C/12C, or δ13C). The isotopic results and correlation of δ18O versus δ13C of Pacific hake Merluccius productus, sablefish Anoplopoma fimbria, Pacific halibut Hippoglossus stenolepis, and Pacific cod Gadus macrocephalus indicated that most of the groundfish we examined had two or more spawning stocks or subpopulations; the only tested species that might belong to a single coastwide stock was yelloweye rockfish Sebastes ruberrimus. Compared with genetic methods of stock identification, the isotopic signatures of otoliths have distinct advantages in determining (1) a time series to separa...

Population dynamics and status of striped marlin (Kajikia audax) in the western and central northern Pacific Ocean

AnewunderstandingofthestructureofstripedmarlinstocksinthePacificOceanwasthebasisforestimating the population dynamics in the western and central northern Pacific (1975-2010). Dynamics were estimated using large- scale spatial data and a fully integrated length-based and age-structured model. The model used fishery-dependent catch, size composition and catch per unit effort (CPUE) as likelihood components. Time-varying selectivity patterns were used inthemodellingtoaccount forchangesinfishing practices.Estimatesoffishing intensityshowedapatternofexploitation generally exceeding the levels associated with maximum sustainable yield (MSY). Estimates of spawning biomass and recruitment described a population that was relatively stable near biomass levels associated with MSY until the 1990s, when recruitment declined and biomass levels fell below those associated with MSY. The reduction in recruitment could beexplainedbyalossofspawningbiomassandpotentiallychangesinenvironment.Thefutureprospectsofrebuildingthe stock will depend on the relative importance of the roles maternal biomass and environment play in determining recruitment strength. Additional keywords: environmental versus maternal effects, integrated modelling, time-varying selection.

Sex-structured population dynamics of blue marlin Makaira nigricans in the Pacific Ocean

The population dynamics of the blue marlin Makaira nigricans stock in the Pacific Ocean were estimated for 1971–2011 using a fully integrated length-based, age-, and sex-structured model. Fishery-specific catch, size composition, and catch-per-unit of effort were used in the modeling as likelihood components. Estimated dynamics were consistent with a stock that is fully exploited and stable over the last several years. No significant trends in recruitment were noted; however, female blue marlin were estimated to make up a majority of the catch, and historical exploitation has disproportionately changed the age structure of females relative to males. This result is due to differences in assumed life history and estimated selectivity. Changes to important life history parameters that are responsible for the productivity of the stock would potentially change the interpretation of current stock status.

Simulation of the estimation of ageing bias inside an integrated assessment of canary rockfish using age estimates from a bomb radiocarbon study

The stock of canary rockfish off the west coast of the continental US is currently assessed using an integrated statistical catch-at-age model. The functional form of an ageing bias detected in production ageing (large numbers of ages read for use in stock assessment) from a bomb radiocarbon study with small sample size (n = 16) was estimated externally and used to adjust the age data in the most recent stock assessment. Using simulation methods, the present study evaluated whether integrating the estimation of the ageing bias inside the assessment model would (1) influence the uncertainty in assessment results and (2) improve our ability to differentiate between competing functional forms (linear, linear with intercept and jointed) for specifying the ageing bias. Internal estimation of the ageing bias relationship increased the approximate 95% confidence interval width about the spawning biomass estimate by 1–10% depending on the functional form assumed. The assessment model was not able to reliably distinguish between all competing functional forms of the ageing bias tested, even with increased radiocarbon sample sizes. However, significant under-ageing at the youngest ages was found to be inconsistent with other sources of data in the assessment model. The question of ageing bias form remains important because it had moderate effects on estimates of spawning biomass and assessment model uncertainty.

Effects of age-based movement on the estimation of growth assuming random-at-age or random-at-length data

Simulation methods were used to generate paired data from a simulated population that included the age-based process of movement and the length-based process of gear selection. The age-based process caused bias in the estimates of growth parameters assuming random at length, even when relatively few age classes were affected. Methods that assumed random at age were biased by the subsequent inclusion of the length-based process of gear selection. Additional knowledge of the age structure of the sampled area is needed to ensure an unbiased estimate of the growth parameters when using the length-conditional approach in the presence of age-based movement. Estimates of the variability in the length-at-age relationship were better estimated with the length-conditional than the traditional method even when the assumptions of random at length were violated. Inclusion of paired observations of length and associated age inside the population dynamics model may be the most appropriate way of estimating growth.

Factors influencing the distribution of Kona crabs Ranina ranina (Brachyura: Raninidae) catch rates in the Main Hawaiian Islands

A generalized linear model and commercial catch report data were used to describe spatial and temporal patterns in Kona crab, Ranina ranina Linnaeus, 1758, catch rates in the Main Hawaiian Islands. Three alternative hypotheses regarding factors influencing the temporal and spatial distribution of Kona crabs were evaluated using multi-model inference. Broad-scale island effects explain the spatial distribution of catch rates better than the finer-scale factors of depth and swell exposure. Interdecadal declines in catch rates were noted for islands with high human density, while other islands had stable or increasing catch rates. The interdecadal changes in catch rates may be explained by changes in population abundance and management-induced changes in fishing patterns in the recent period. Kona crab behaviors associated with the reproductive cycle contribute to seasonal variations in observed catch rates.