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Additional file 1: Table S1. Comparison table of fish taxonomic assignments and reads between Mare-MAGE and NCBI, and the 3 sub-databases for the COI gene. Table S2. Comparison table of number of Fish taxonomic assignments and reads between Mare-MAGE and NCBI, and the 3 sub-databases for the 12s rRNA gene.

This report describes the results obtained by the application of several novel HTS genomic techniques - Close Kin Mark Recapture (CKMR), connectivity, stock substructure, epigenetic age determination by DNA methylation (DNAm), environmental DNA (eDNA), and sex marker search - in the Pilot studies performed by the FishGenome Consortium. To discuss the suitability, potentiality pros and constraints of these novel genomic techniques, to complement and improve current fisheries assessments.

The Joint EIFAAC/ICES/GFCM Working group on eels (WGEEL) met by correspondence and video conference from September 7 – 10 September and 27 September – 4 October in 2021 to assess the state of the European eel and its fisheries, investigate the effects of contaminants on the reproductive capacity of the eel stock, discuss the findings of WKFEA, further identify issues specific to the Mediterranean region and report on any updates to the scientific basis of the advice, new and emerging threats or opportunities. For a better integration of the Mediterranean area, new members joined WGEEL, providing data and support as regional experts. This is considered an important step in a continuous process to identify and address Mediterranean-specific issues and harmonize the efforts of WGEEL and the recent ‘GFCM research Programme on European Eel’. The recruitment of European eel strongly declined from 1980 to 2011. The glass eel recruitment compared to that in 1960–1979 in the “North Sea” index area was 0.6% in 2021 (provisional) and 0.9 % in 2020 (final). In the “Elsewhere Europe” index series it was 5.4 % in 2021 (provisional) and 7.1% in 2020 (final), based on available dataseries. For the yellow eel dataseries, recruitment for 2020 was 16% (final) of the 1960–1979 level; the 2021data collection for yellow eel is ongoing. Time-series from 1980 to 2021 show that recruitment has stopped decreasing in 2011 but the trend thereafter is rather unclear.Preliminary analyses of 160 dataseries on yellow or silver eel abundance show the potential of the yellow and silver eels’ series to improve the stock assessment. A comprehensive framework of analyses of the yellow and silver stocks through these series will, however, require many iterations of data collection, analyses and further data needs.Mortality and biomass indicators have been reviewed and visualized, preparing for a future workshop on the evaluation of eel management plans (WKEMP). Spatial overviews and temporal trends show a lack of data for many regions and no evidence yet of a general improvement in stock status for regions with data. Overall silver eel escapement remains low and mortalities high. Doubts remain about the consistency of indicators across countries. The information provided on data and methods used for assessment are not available or sufficiently detailed to ensure transparency and reproducibility of estimates. These limitations and the incomplete reporting impair the use of these data to inform on the status of the stock at a larger scale.A review on the effects of contaminants (in a broader sense: spawner quality) on the reproductive capacity of eel highlighted this as an important, but a frequently lacking, aspect of stock assessment. Monitoring of silver eel quality should be considered as part of new or existing programmes.WGEEL supports the findings WKFEA and the suggested roadmap and agreed to implement the necessary steps towards achieving it. This implies further exploration and analyses of existing as well as the systematic collection of additional data. Implementation will require concerted data collection and assessment, which will require additional support.In summary, the working group has focused on exploring and analysing the data collected in the WGEEL database for their potential use in stock assessment. This included identifying gaps in the available data, defining data requirements for specific analyses in future and developing procedures for the analysis of these data. Furthermore, the group reviewed the effects of contamination on the reproductive potential of eels and renewed their recommendation to consider these in the assessment of effective spawning-stock biomass.

The Joint EIFAAC/ICES/GFCM Working group on eels (WGEEL) met from September 6–9 and 12–20 September 2022 in Toombridge, Northern Ireland, to provide the scientific basis for the ICES advice on fishing opportunities and conservation aspects for the European eel and address requests from EIFAAC and GFCM.WGEEL assessed the state of the European eel and its fisheries, collated and analysed biometric data, reviewed and summarized available data on eel quality, further identified issues specific to the Mediterranean region, discussed the use of landings data for the assessment (following WKFEA) and reported on any updates to the scientific basis of the advice, new and emerging threats or opportunities.The recruitment of European eel declined markedly from 1980 to 2011. The glass eel recruitment compared to that in 1960–1979 in the “North Sea” index area was 0.5% in 2022 (provisional) and 0.6 % in 2021 (final). In the “Elsewhere Europe” index series it was 9.7 % in 2022 (provisional) and 5.5% in 2021 (final), based on available data series. For the yellow eel data series, recruitment for 2021 was 19% (final) of the 1960–1979 level; the 2022 data collection for yellow eel is ongoing. Time-series from 1980 to 2022 show that glass eel recruitment remains at a very low level.Analyses of data series on yellow or silver eel abundance (162 series analysed) and grouped biometric data were re-run this year and show the potential of the yellow and silver eels’ series to improve the stock assessment. A graphical analysis of the new biometric data integrated in the database, 1.2 million individual data and 4908 grouped data (combining length, weight and age data), was carried out to identify future analyses and information that might be missing. To identify the potential of Length-Based Models for stock assessment, a preliminary overview of the models, the input needed and of the assumptions was realised.A collation and integration of available data relating to eel quality – lipid content, parasites and virus, and contaminants - was carried out and examples of analyses and visualisation presented. A review of recent publications relating to eel quality was carried out. Recommendations for improving submission and harmonisation of relevant data, and using eel quality in the context of stock assessments are proposed.Available landings data was reviewed and scoped with potential methods for their use in the assessment of the European eel in preparation of a workshop foreseen in the WKFEA roadmap. Currently, landings data cannot be included in the assessment but follow up work for their use in a potential spatial assessment approach is recommended.In summary, besides updating recruitment time series, further progress was made in collating and analysing individual biometric data and eliciting there use in future assessment, particularly for a spatial assessment approach. Significant progress was made towards utilizing data on eel quality but its use in the assessment is currently data limited.