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The potential use of genomic methods in bottom trawl surveys to improve stock assessments in Europe

FRONTIERS IN MARINE SCIENCE (2023)

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Summary: Natural mortality (M), an important parameter in fisheries stock assessment and management, is difficult to estimate and uncertain. This paper reviews various methods to estimate M and suggests that directly estimating M using data and assigning a prior based on empirical methods is the most effective approach.

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Summary: The distribution of age classes is an important parameter for population management and conservation biology. Traditional methods of age estimation in fishes, such as analyzing growth marks in hard structures, are time-consuming and often inaccurate. The development of epigenetic clocks based on DNA methylation provides a new and promising method for age estimation. Epigenetic clocks have been developed for various fish species and have shown potential in improving fisheries management and aiding in the conservation of endangered species. Further research is needed to understand the effects of environmental changes on the accuracy of epigenetic clocks.

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Summary: In this study, we applied the recent close-kin mark-recapture (CKMR) abundance estimation method to thornback ray and drew four practical lessons from the results. CKMR was found to be helpful in identifying metapopulation structure, which could affect abundance estimates and time trends if ignored. We discovered evidence of two distinct local populations of thornback ray with no demographic connectivity. We also found that the composition of the demographic sample and the availability of reasonable age information for potential offspring and the sex of potential parents are crucial for reliable abundance estimation.

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Combined Use of eDNA Metabarcoding and Bottom Trawling for the Assessment of Fish Biodiversity in the Zhoushan Sea

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Summary: This study used environmental DNA metabarcoding and bottom trawl methods to assess fish assemblages in the Zhoushan Sea. The results showed that the eDNA method detected 38.2% more fish species than bottom trawls, and a total of 33 orders, 65 families, and 130 species of fishes were identified using the combined methods. The study also found significant differences in fish community structure between summer and winter, with depth and temperature being the main environmental factors influencing fish distribution. Biodiversity index was higher in summer than in winter. This research provides important data for the long-term management and conservation of coastal biodiversity in the Zhoushan Sea.

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FRONTIERS IN MARINE SCIENCE (2022)

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A cold-water fish striving in a warming ocean: Insights from whole-genome sequencing of the Greenland halibut in the Northwest Atlantic

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Summary: Monitoring marine resource exploitation is crucial in fisheries science and biodiversity conservation, with fishery-dependent data playing an increasingly important role. By using DNA metabarcoding in slush water from fishing nets, the study demonstrates a strong relationship between read counts and species abundances in the catch, showing the potential for this approach to provide valuable information on demersal assemblages and fisheries impact.

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Summary: RADSex is a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data, with visualization and identification of sex-specific markers. By applying RADSex, we uncovered Y chromosome polymorphism in Japanese medaka, identified sex determination systems and sex-specific markers in six out of 15 fish species.

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