Kristin Privitera-Johnson^1
1SAFS
January 24, 2017 3:30 (PST): FSH 203

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Fishery removal of fish population, catch, is important information used in conducting stock assessments.  However, groundfish, especially rockfish, landings were recorded in broad market categories historically.  Partitioning landings into single species category has relied on analysts, which caused the landing history changes from assessment to assessment depending on assumptions made by the analysts.  This has increased uncertainty among assessments.  In 2008, a major effort to reconstruct historical landings was initiated in response to the Pacific Fishery Management Council’s call to compile the best estimates of catch history early in the development of Pacific Coast groundfish fisheries. For Washington state, databases have been developed for raw landings, historical trawl logbooks and species composition data.  As part of the whole catch reconstruction project, this work explores a method for quantifying uncertainties in the catch estimates based on species composition data collected by department staff since the early 1960’s.

Kristin Privitera-Johnson
¹SAFS
January 24, 2017 3:300 (PST): FSH 203

Evaluating Uncertainties in Historical Groundfish Landing for Washington Coastal Commercial Fisheries

Fishery removal of fish population, catch, is important information used in conducting stock assessments.  However, groundfish, especially rockfish, landings were recorded in broad market categories historically.  Partitioning landings into single species category has relied on analysts, which caused the landing history changes from assessment to assessment depending on assumptions made by the analysts.  This has increased uncertainty among assessments.  In 2008, a major effort to reconstruct historical landings was initiated in response to the Pacific Fishery Management Council’s call to compile the best estimates of catch history early in the development of Pacific Coast groundfish fisheries. For Washington state, databases have been developed for raw landings, historical trawl logbooks and species composition data.  As part of the whole catch reconstruction project, this work explores a method for quantifying uncertainties in the catch estimates based on species composition data collected by department staff since the early 1960’s.

Merrill Rudd¹ and Dr. James Thorson^1
1SAFS
January 17, 2017 2:30 (PST): FSH 203

Development and application of a length-based, integrated mixed effects (LIME) assessment method for data-limited fisheries

Length measurements are often the easiest type of data to reliably collect. Existing stock assessment methods that primarily rely on length composition or mean length of the catch make the assumption that the population is in equilibrium (i.e. fishing mortality and recruitment are not changing over time) to make inferences on fishing pressure and stock status. There are many situations in which this equilibrium condition could be violated. We developed a length-based integrated mixed effects (LIME) method to account for variability in recruitment and fishing mortality using at least one year of length composition data and assumptions about biological parameters to make inferences on stock status. I will review the simulation testing of this method against several scenarios of life history, fishing mortality, and recruitment, as well as violations of model assumptions to identify strengths and weaknesses. I will also present progress and obstacles in the application of the LIME method for Kenyan coral reef fisheries.

Dr. James Thorson^1
1SAFS
November 29, 2016 9:00 (PST): FSH 203

A hands-on discussion and tutorial for using FishStats to estimate spatio-temporal abundance indices, distribution shifts, and range expansion in 2017 stock assessments

Collaborators and I have been developing, testing, and documenting spatio-temporal models and software for single- and multi-species analysis of fishery and/or survey data.  R packages for implementing these models are now publicly available and documented through www.FishStats.org, a spatio-temporal toolbox for fisheries science.

In this Think Tank, I will present a small number of slides (<15 total) to recap recent model developments and applications.  I will then lead a discussion of different applications for which FishStats could be useful in 2017 stock assessments, e.g., estimating survey indices, standardizing fishery catch rates, estimating distribution shifts or range expansion/contraction, or identifying multispecies associations.  With input from attendees, I will then provide a semi-structured, hands-on demonstration of how different modelling goals can be achieved.

I encourage attendees to bring a laptop and to install a recent version of R (e.g., 3.3.1) and appropriate Rtools (if using a windows OS).  Attendees will install other necessary software (including INLA and TMB) as we go through tutorials together.

Samuel Johnson^1  
1  Simon Fraser University

November 22, 2016 9:00 (PST): FSH 203

I am interested in finding the conditions that favour joint stock assessments for multiple flatfish species using hierarchical models. Hierarchical multi-level modeling approaches are being increasingly applied in stock asssessment to share information across stocks and species. These so-called “Robin Hood” approaches borrow information from data-rich to potentially improve assessments for data poor species; however, little research exists to demonstrate the boundary conditions where hierarchical approaches outperform single species models. In this talk, I present a hierarchical surplus production modeling approach for a multi-species flatfish complex in British Columbia, Canada. If applicable, the hierarchical modeling approach could help provide more up-to-date assessments for species last assessed in the 1990s!

Christine Stawitz^1
1SAFS
November 08, 2016 9:00 (PST): FSH 203

How do changing somatic growth rates affect estimation of management quantities in fisheries stock assessments, and can such growth changes be detected?

A substantial body of work suggests that somatic growth in marine fish is plastic, and thus growth rates may change substantially in response to both extrinsic (i.e. climate) and intrinsic (i.e. competition) factors. Additionally, such changes in somatic growth rate may substantially affect population dynamics of marine fish. However, these changes in growth rate are not incorporated into many fisheries stock assessment models and, consequently, management advice. Growth rate changes are difficult to incorporate in management models, since such models are already highly parameterized and often contain temporal variation in observational parameters which are confounded with somatic growth parameters, such as fisheries selectivity. In this analysis, we evaluate the detectability of temporal changes in somatic growth and how such changes may impact fisheries management quantities. We examine these questions using a simulation framework, employing an operating and estimation model closely modeled on stock assessment models for North Pacific groundfish and the Stock Synthesis 3 (SS3) program. Simulated variation in population processes, including growth, recruitment, and fishing, is derived directly from empirical estimates. We test, first, if regime-like growth shifts can be detected using realistic quantities of time series data. We find regime-like patterns in growth rates are not detectable in population models without many decades of high-quality composition data, even when process error is low. Secondly, we find such changes, while difficult to detect, can introduce substantial bias into management reference points, particularly current depletion levels. This suggests more work is needed to increase estimability of temporal growth changes and incorporate them into fisheries stock assessment models.

Peter Kuriyama^1 
1SAFS
October 11, 2016 9:00 (PST): FSH 203

Resolving issues of hook saturation, hook competition, and fixed-site design in the Southern California hook-and-line survey

The Southern California hook-and-line survey has been conducted by the Northwest Fisheries Science Center since 2004 to monitor the untrawlable habitat of the Southern California Bight. Data from the survey have been used in stock assessments and supporting research for a number of shelf rockfish species, such as bocaccio (Sebastes pauicispinis) and vermilion rockfish (S. miniatus). However, an index of abundance estimated from hook-and-line data may be biased due to the fixed-site design of the survey and issues with hook saturation and hook competition. Here, I will present empirical results from the hook-and-line data and results of a simulation study exploring the biases associated with aspects of the survey. Bocaccio are the most sampled species in the survey, and sites with low catch rates of bocaccio have high catch rates of vermilion rockfish. Preliminary results from the simulations indicate that hook saturation causes estimates of abundance to be negatively biased at large population sizes. Additionally, hook competition leads to positively biased indices of abundance, and weighting catch rates by site leads to the least biased index of abundance. These results identify methods of incorporating hook-and-line data from untrawlable habitat into stock assessments and identify biases that are applicable to general hook-and-line survey methods.

Paul Dolder^{1
1 MARES Doctoral Programme on Marine Ecosystem Health and Conservation}
October 04, 2016 9:00 (PST): FSH 203

Progressing scientific advice and management of mixed demersal fisheries in
Europe

In Europe, scientific advice for managing multi-gear, multi-country mixed
fisheries is rapidly developing. Reforms to the EU’s Common Fisheries Policy
have given priority to the development and implementation of fishery-based
management plans and emphasize the importance of understanding how technical
interactions impede effective management of all stocks caught in mixed
fisheries. Modelling approaches which i) characterize these interactions and,
ii) can simulate a range of management options to contrast their bio-economic
impact, are gaining prominence. In this talk I’ll give an overview of the
developments happening within the EU and the ICES frameworks and highlight how
my PhD research aims to improve our ability to understand fleet behavioural
dynamics in mixed fisheries so that managers can better evaluate different
management options.

Dr. Gwladys Lambert^1
1AFSC
May 31, 2016 9:00 (PST): FSH 105

Optimizing otoliths sampling design in fishery-independent surveys for stock assessments

The sampling design of composition data can have a major impact on our perception of the stock status and the estimated reference points for management. Composition data as sampled from bottom trawl surveys are famously clustered which creates major challenges when it comes to estimating length and age composition of the population of interest and in particular with respect to effective sample size/data weighting in stock assessment models. Here I present the approach I have been exploring in order to prepare a simulation framework to compare otoliths sampling strategies and their impact on stock assessment outputs. First I will talk about the questionnaires I have designed as part of the Otolith Sampling Size Working Group that aimed at informing the development of an operating model. Then I will discuss the implications of removing age data in data rich stock assessments based on a couple of examples and I will show some early simulation work using Stock Synthesis and developments from the R package ss3sim. Ss3sim developments include the addition of an option to test for the effect of ageing error on stock assessment outputs. The main focus will be on another option I have been experimenting with which aimed at simulating the sampling of clustered length data (that resemble real survey data) from random or length-stratified sampling in order to investigate the effect of different sampling strategies on the effective sample size estimated in stock assessments. I will also briefly talk about the Stock Synthesis model for GOA Pacific Ocean Perch I have been working on in order to use in the simulations described above.

Dr. William T. Stockhausen^1
1AFSC
May 24, 2016 9:00 (PST): FSH 105

Coupled biophysical/individual-based models: can they inform recruitment, stock assessment and/or fishery management? DisMELS lessons from the GOAIERP

One of the key hypotheses underlying NPRB’s recent Gulf of Alaska (GOA) Integrated Ecosystem Research Project (IERP) was that year-class strength for the five commercially- and ecologically-important groundfish stocks at the focus of the project was determined by success or failure in running the early life, pelagic “gauntlet” from adult spawning areas to young-of-the-year nursery areas. As part of the multi-institution, multidisciplinary effort to address this hypothesis for pollock, Pacific cod, arrowtooth flounder, sablefish, and Pacific ocean perch, a group of modelers (including the author) constructed early life, coupled biophysical/individual-based models (CBP-IBMs) for each stock. For marine species with pelagic early life stages, CBP-IBMs provide one of the best approaches to synthesizing disparate information on individual life stages (e.g., eggs, larvae) and environmental variability into an integrated picture of early life processes. Among our goals for these models was to be able to improve current stock assessments and enhance fishery management by identifying the critical drivers of recruitment variability and hindcasting (or potentially forecasting) recent trends in recruitment for the five focal species. In regard to identifying critical drivers of recruitment variability, I think we can say that variability in physical transport, i.e. where young-of-the-year end up, is less important to recruitment variability than what happens along the way. However, in regard to predicting recruitment variability itself, we were certainly not terribly successful—except perhaps for pollock, the most data-informed of all the IBMs. As an extended introduction, I’ll briefly 1) introduce the concepts behind CBP-IBMs; 2) discuss DisMELS (the Dispersal Model for Early Life Stages), a framework for creating and running CBP-IBMs; and 3) review the five species-specific IBMs created for the GOAIERP. Then I’ll discuss results from the models and what they tell us about early life processes in the GOA. Finally, I’ll present a couple of practical suggestions for some “best practices” using these types of models.