Roadmap for the implementation of genomic-based approaches in fisheries stock assessment

The Tender contract “FishGenome: Improving cost-efficiency of fisheries research surveys and fish stocks assessments using next-generation genetic sequencing methods” was developed to assess the ability and readiness of several new emerging genomic technologies to enhance fisheries assessments. These assessments are needed to monitor the status of fish stocks and ensure fishing practices that exploit them at sustainable levels. They rely on the collection of data from multiple sources, that include fishery- dependent data -catches, landings, biological information - as well fishery-independent data obtained from research surveys. These surveys provide valuable and systematised information regarding exploited fish populations, marine biodiversity and their environment, and are essential piece in stock assessment and scientific advice. The overall purpose of FishGenome was to evaluate the suitability of three genomic techniques - Close Kin Mark Recapture (CKMR), epigenetic Age Determination by DNA methylation (DNAm) and environmental DNA (eDNA) to estimate various essential parameters for fisheries stock assessments, including absolute abundance, survival, age and biomass. Additionally, it was assessed the potential and ripeness of a fourth genomic technique - restriction site Associated DNA Sequencing (RAD-Seq) - to estimate a series of parameters that are also important to evaluate stocks but have been mostly neglected in fisheries assessments, i.e. fine-scale stock substructure, connectivity and molecular sexing. The results indicated the need and convenience of implementing the genomic sampling into EU-MAP research surveys, as well the high potential of these techniques to contribute to an improved stock assessment of many stocks. On one hand, EU Data collection Framework (EU-DCF) has contributed to improve fisheries management and the implementation of different policies, by harmonising and coordinating the collection of data from the fishery, as well, and more i