Monthly Archives: November 2019

Thinking about the methods & climate-dependencies in time-varying biological reference points: a case study with summer flounder.

Thinking about the methods & climate-dependencies in time-varying biological reference points: a case study with summer flounder.

Cecilia O’Leary
December 3rd, 2019 9:00 AM (PST): FSH 203

Fisheries managers use biological reference points (BRPs) as targets or limits on fishing and biomass to maintain productive levels of fish stock biomass. There are multiple ways to calculate BRPs when biological parameters are time-varying. Using summer flounder (Paralichthys dentatus) as a case study, we investigated time-varying approaches in concert with climate-linked population models to understand the impact of environmentally-driven variability in natural mortality, recruitment, and size-at-age on two commonly-used BRPs (B_0(t) and F_35%(t) ). We used two approaches to calculate time-varying BRPs: dynamic-BRP and moving-average-BRP. We quantified the variability and uncertainty of different climate dependencies and estimation approaches, attributed BRP variation to variation in life-history processes, and evaluated how using different approaches impacts estimates of stock status. Results indicate that the dynamic BRP approach using the climate-linked natural mortality model produced the least variable reference points compared to others calculated. Summer flounder stock status depended on the estimation approach and climate model used. These results emphasize that understanding climate dependencies is important for summer flounder reference points and perhaps other species, and careful consideration is warranted when considering what time-varying approach to use, ideally based upon simulation studies within a proposed set of management procedures.

Maia Sosa Kapur coauthors JABBA-Select paper in Fisheries Research

Current grad student Maia Sosa Kapur, along with Puntlab alum Jim Thorson and a host of international collaborators released a new paper presenting an extention of the JABBA model in Fisheries Research. (This link will be open-access for the next 45 days). JABBA-Select is an extension of the JABBA model, which Maia co-developed, which implementes Bayesian surplus production model to account for differential impacts of selective fishing. JABBA-Select incorporates life history parameters and fisheries’ selectivity and distinguishes between exploitable biomass and spawning biomass, enabling more direct comparison with age-structured model results. Simulation-testing experiments showed that JABBA-Select performs at least as well as, and often better than, age-structured production models for data-moderate stock assessment cases. JABBA-Select is freely available online on the global open-source platform GitHub here.

 

CAPAM Next Generation Stock Assessment Models

This week, André and Maia Sosa Kapur (graduate student) journeyed to Wellington, New Zealand to attend the CAPAM Workshop in Next Generation Stock Assessment Models. André delivered a keynote talk, and Maia’s coauthor presented an upcoming diagnostics project. Lively discussions about the goals, requirements and objectives for the future assessment model(s) build to manage fisheries were had. André cautioned against the development of an “uber” model controlled by only one or a few scientists, and the group as a whole agreed that modularity and speed are important considerations in the new development. Other highlights included the revelation of the SIMULATE() function within TMB. A special issue of Fisheries Research following the workshop is forthcoming in 2020.

 

Evaluating the impacts of fixing or estimating natural mortality, across life histories and data availability.

Evaluating the impacts of fixing or estimating natural mortality, across life histories and data availability.

Claudio A. Castillo Jordan

November 12th, 2019 9:00 AM (PST): FSH 203

In integrated, age-structured stock assessment model, common practice gives us two alternatives on how to use natural mortality. First, to use a value coming from an indirect method and not estimate it. Second, natural mortality is estimated in the model simultaneously with other parameters. We used simulation testing with models simplified from real stock assessments to generate simulated data, using the ss3sim framework. The operating model “truth” included various levels of complexity, such as sex- and age-specific, and time-varying M.  Simulated data sets were used to investigate the bias and uncertainty in estimates of natural mortality and management quantities when assuming and estimating various levels of complexity of M in stock assessments, as well as the data sources that inform natural mortality by varying the type and amount of data available to the model. Given a large number of assessment models available and the range of data, life histories, and other characteristics that they cover, the results were evaluated to determine what characteristics are essential to be able to reliably estimate natural mortality. The uncertainty in the estimates of M was contrasted with the variation in the different indirect methods to evaluate in what context estimation of M inside the stock assessment model is an improvement over the indirect methods and in which cases it is worse. This study provides information about the overall uncertainty in management quantities given the uncertainty in M.

Combining fishery-independent and -dependent catch observations in a single index of abundance by allowing for spatially varying catchability 

Combining fishery-independent and -dependent catch observations in a single index of abundance by allowing for spatially varying catchability 

John Best, Jim Thorson, Rick Methot, Andre Punt

October 29th, 2019 9:00 AM (PST): FSH 203


For fisheries where both fishery-independent and -dependent catch observations are available, spatiotemporally standardized indices of abundance currently use only the fishery-independent data because it is difficult to reliably standardize fishery-dependent observations. There may be an order of magnitude more fishery-dependent observations than fishery-independent observations, representing a currently unused source of information. Integrating these two types of data into a single index of abundance may increase precision, but the fishery-dependent observations would need to be standardized carefully to avoid unacceptable levels of additional bias. One approach to standardizing fishery-dependent observations in a spatiotemporal standardization model would include spatial and/or spatiotemporal random effects on catchability. A model that allows this will be presented along with preliminary simulation study results.

Brazilian fishery stock assessment and management: current status and challenges

Brazilian fishery stock assessment and management: current status and challenges

Flávia Lucena Frédou – Universidade Federal Rural de Pernambuco (Recife – Brazil)

November 5th, 2019 9:00 AM (PST): FSH 203

There is a large diversity of species and fishing gear/methods in Brazilian marine waters, given the long coast (more than 7000 km long), with different environments and a multispecies and multifleet fishery. Most of the industrial fishing fleet is concentrated in Southern Brazil, while most of the small-scale fisheries (SSF) is concentrated in the north and northeast regions (Bertrand et al., 2018), where the activity is extremely important in terms of food security and employment (over 90% of jobs in the fishery sector concentrates). Based on a multi-year Brazilian research Program REVIZEE (Avaliação do Potencial Sustentável da Zona Econômica Exclusiva do Brasil), created by the Brazilian Government in compliance with the United Nations Convention of the Law of the Sea, by the early 2000s, Brazilian fisheries far exceeded sustainable target levels in the main portion and the majority of stocks were either fully (23%) or over-exploited (33%) (MMA, 2006). Moreover, Brazilian Fisheries Statistics have not been reported since 2007, when the existing system was gradually dismantled and not replaced. Hence, the assessment and the management of the Brazilian fishery resources have been a great challenge for scientists and government.  After the Program REVIZEE ended, stocks have never been re-assessed at a national level. However, specific initiatives were established in order to assess the sustainability and conservation of some fishery resources. More recently (2010 – 2014), Brazilian aquatic resources have  been evaluated according to the IUCN Red List categories at a regional scale, in a process  leaded by the ICMBio (Instituto Chico Mendes de Conservação da Biodiversidade, Ministério do Meio Ambiente, Brazil). The red list, published in 2014 (Portaria 445), enumerated 475 aquatic species as threatened. Moreover, research initiatives funded by the Fishery and Aquaculture Secretary (Ministry of Agriculture) and CNPq (National Research Council) are in place in order to evaluate the main fishery resources of the country. This talk will review the initiatives of the Brazilian Government in assessing its stocks and the current challenge given the diversity and the data-limited nature of the national fisheries.