Annotating otoliths with a deep generative model

Otoliths are a central information source for fish ecology and stock management, conveying important data about age and other life history for individual fish. Traditionally, interpretation of otoliths has required skilled expert readers, but recently deep learning classification and regression models have been trained to extract fish age from images of otoliths from a variety of species. Despite high accuracy in many cases, the adoption of such models in fisheries management has been slow. One reason may be that the underlying mechanisms the model uses to derive its results from the data are opaque, and this lack of legibility makes it challenging to build sufficient trust in the results. Here, we implement a deep learning model that instead of age predicts the location of annotation marks for each of the annuli. This allows an expert to evaluate the model’s performance in detail. The quality of the annotations was judged by a panel of four expert otolith readers in a double-blinded randomized survey. Using a scale from 1 to 5, the generated marks received an average quality score of 4.22, whereas expert annotations received an average score of 4.33. By counting the marks to determine fish age, we obtained an agreement between expert and model annotations of 64% on our test set, which running the model stochastically increased to 69%. Stochastic sampling yields further benefits, including an explicit measure of the model’s uncertainty, the post hoc likelihood of the different age classes for each otolith, and a set of alternative annotation sequences that highlight the structure of the annuli.publishedVersio

Counting stars: contribution of early career scientists to marine and fisheries sciences

Scientific careers and publishing have radically changed in recent decades creating an increasingly competitive environment for early career scientists (ECS). The lack of quantitative data available on ECS in marine and fisheries sciences prevents direct assessment of the consequences of increased competitiveness. We assessed the contributions of ECS (up to 6 years post first publication) to the field using an indirect approach by investigating the authorships of peer-reviewed articles. We analysed 118461 papers published by 184561 authors in the top 20 marine and fisheries sciences journals over the years 1991–2020. We identified a positive long-term trend in the proportion of scientific articles (co-)authored by ECS. This suggests a growing contribution by ECS to publications in the field. However, the mean proportion of ECS (co-)authors within one publication declined significantly over the study period. Subsequent tests demonstrated that articles with ECS (co-)authors receive fewer citations and that the proportion of ECS (co-)authors on an article has a significant negative effect on the number of citations. We discuss the potential causes of these inequalities and urge systematic support to ECS to achieve more balanced opportunities for funding and publishing between ECS and senior scientists

Growth portfolios buffer climate-linked environmental change in marine systems

Large-scale, climate-induced synchrony in the productivity of fish populations is becoming more pronounced in the world's oceans. As synchrony increases, a population's “portfolio” of responses can be diminished, in turn reducing its resilience to strong perturbation. Here we argue that the costs and benefits of trait synchronization, such as the expression of growth rate, are context dependent. Contrary to prevailing views, synchrony among individuals could actually be beneficial for populations if growth synchrony increases during favorable conditions, and then declines under poor conditions when a broader portfolio of responses could be useful. Importantly, growth synchrony among individuals within populations has seldom been measured, despite well-documented evidence of synchrony across populations. Here, we used century-scale time series of annual otolith growth to test for changes in growth synchronization among individuals within multiple populations of a marine keystone species (Atlantic cod, Gadus morhua). On the basis of 74,662 annual growth increments recorded in 13,749 otoliths, we detected a rising conformity in long-term growth rates within five northeast Atlantic cod populations in response to both favorable growth conditions and a large-scale, multidecadal mode of climate variability similar to the East Atlantic Pattern. The within-population synchrony was distinct from the across-population synchrony commonly reported for large-scale environmental drivers. Climate-linked, among-individual growth synchrony was also identified in other Northeast Atlantic pelagic, deep-sea and bivalve species. We hypothesize that growth synchrony in good years and growth asynchrony in poorer years reflects adaptive trait optimization and bet hedging, respectively, that could confer an unexpected, but pervasive and stabilizing, impact on marine population productivity in response to large-scale environmental change.publishedVersio

Panel-based Assessment of Ecosystem Condition of the North Sea Shelf Ecosystem

The System for Assessment of Ecological Condition, coordinated by the Norwegian Environment Agency, is intended to form the foundation for evidence-based assessments of the ecological condition of Norwegian terrestrial and marine ecosystems not covered by the EU Water Framework Directive. The reference condition is defined as “intact ecosystems”, i.e., a condition that is largely unimpacted by modern industrial anthropogenic activities. An ecosystem in good ecological condition does not deviate substantially from this reference condition in structure, functions or productivity. This report describes the first operational assessment of the ecological condition of the marine shelf ecosystem in the Norwegian sector of the North Sea and Skagerrak. The assessment method employed is the Panel-based Assessment of Ecosystem Condition (PAEC1) and the current assessment has considered to what extent the North Sea and Skagerrak shelf ecosystem deviates from the reference condition2 by evaluating change trajectories.Panel-based Assessment of Ecosystem Condition of the North Sea Shelf EcosystempublishedVersio

Panel-based Assessment of Ecosystem Condition of the North Sea Shelf Ecosystem - Appendices

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International Bottom Trawl Survey Working Group (IBTSWG). ICES Scientific Reports, 04:65

The International Bottom Trawl Survey Working Group (IBTSWG) coordinates fishery-independent bottom trawl surveys in the ICES area in the Northeast Atlantic and the North Sea. These long-term monitoring surveys provide data for stock assessments and facilitate examina-tion of changes in fish distribution and relative abundance. The group also promotes the stand-ardization of fishing gears and methods as well as survey coordination. This report summarizes the national contributions in 2021–2022 and plans for the 2022–2023 surveys coordinated by IBTSWG

Workshop on Raising Data using the RDBES and TAF (WKRDBESRaiseTAF; outputs from 2022 meeting)

41 páginasThe Workshop on Raising Data using the RDBES and TAF (WKRDBES-Raise&TAF) met online (26–30 of September 2022) to evaluate the use of the Regional Database and Estimation System (RDBES) format to reproduce the 2022 InterCatch input and output, identifying a Transparent Assessment Framework (TAF) structure to organize the intermediate steps and to propose standardized output formats. The main outcomes of WKRDBES-Raise&TAF were: · RDBES provides sufficient support for current national estimation protocols. However, some minor issues were reported that hampered an exact reproduction of the estimates. Therefore, adaptations of the data model should not be excluded completely. · All the input to stock assessment that InterCatch currently provides, could be reproduced. The participants started from the current stock extracts that can be downloaded from InterCatch. · A workflow was proposed with a national TAF repository for each country, a stock estimation repository and a stock assessment repository. The intermediate output of those repositories will be stored in an ‘intermediate output database’ and depending on the user role, you will get access to the relevant stages in this workflow. · The following requirements for the standard output formats were defined: they cannot be more restrictive than the InterCatch input and output format; they should present measures of uncertainty and sample sizes (for national estimates) and should have a configurable domain definition (for national estimates). Despite those successful outcomes, the current plan for transition to an operational system was concluded to be too optimistic. WKRDBES-Raise&TAF therefore recommends to the Working Group on Governance of the Regional Database and Estimation System (WGRDBESGOV) to revise the roadmap and allow RDBES to be in a test phase also for 2023. WKRDBES-Raise&TAF felt the need to test the proposed workflow on a small scale and therefore recommends to the WGRDBESGOV to arrange a workshop where two stocks (pok.27.3a46 (Saithe (Pollachius virens) in Subareas 4, 6 and Division 3.a (North Sea, Rockall and West of Scotland, Skagerrak and Kattegat) and wit.27.3a47d (Witch (Glyptocephalus cynoglossus) in Subarea 4 and Divisions 3.a and 7.d (North Sea, Skagerrak and Kattegat, eastern English Channel)) will be set up to go through the whole flow.Peer reviewe

Counting stars: contribution of early career scientists to marine and fisheries sciences

Scientific careers and publishing have radically changed in recent decades creating an increasingly competitive environment for early career scientists (ECS). The lack of quantitative data available on ECS in marine and fisheries sciences prevents direct assessment of the consequences of increased competitiveness. We assessed the contributions of ECS (up to 6 years post first publication) to the field using an indirect approach by investigating the authorships of peer-reviewed articles. We analysed 118461 papers published by 184561 authors in the top 20 marine and fisheries sciences journals over the years 1991–2020. We identified a positive long-term trend in the proportion of scientific articles (co-)authored by ECS. This suggests a growing contribution by ECS to publications in the field. However, the mean proportion of ECS (co-)authors within one publication declined significantly over the study period. Subsequent tests demonstrated that articles with ECS (co-)authors receive fewer citations and that the proportion of ECS (co-)authors on an article has a significant negative effect on the number of citations. We discuss the potential causes of these inequalities and urge systematic support to ECS to achieve more balanced opportunities for funding and publishing between ECS and senior scientists