ICES. 2020. Working Group on Acoustic and Egg Surveys for Sardine and Anchovy in ICES areas 7, 8 and 9

he Working Group on Acoustic and Egg Surveys (WGACEGG) coordinates pelagic surveys for a number of stocks and provides monitoring for the two major sardine and anchovy stocks in ICES areas 6, 7, 8, and 9. The group evaluated small pelagic fish biomass indices derived from acoustic and Daily Egg Production Method (DEPM) surveys in ICES areas 6, 7, 8 and 9. These indices have been provided to the ICES Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA), the Working Group on Widely Distributed Stocks (WGWIDE) and the Herring Assessment Working Group for the Area South of 62ºN (HAWG) stock assessment group, to serve as fishery-independent input for analytical assessment purposes. DEPM and acoustic indices were derived based on data collected using independent methods. Acoustic- and DEPM-derived biomass indices from quasi-synoptic surveys conducted in the Bay of Biscay in spring were compared, to assess the presence of potential bias and to improve the precision of fish stock biomass estimates. The DEPM-based anchovy biomass index was 22% higher than the acoustic index in 2019. Unusual concentrations of anchovy in Eastern Cantabrian Sea, an area not covered by the acoustic survey, and the presence near the sea surface of actively spawning individuals possibly under-sampled by acoustics in central Bay of Bay had been postulated as potential causes of this discrepancy. No significant difference was found between sardine biomass indices derived from DEPM and acoustics in 2019. The group has updated its database of standard gridded maps covering the European Atlantic area. This initiative continues to inform on the spatial dynamics of various parameters collected during the surveys coordinated under the auspices of the group (fish acoustic densities, anchovy and sardine egg abundance, surface temperature and salinity). Results of an analysis of the time series of gridded maps (anchovy and sardine acoustic density, surface salinity and temperature) showed quantitative changes in the spatial and temporal distribution of anchovy and sardine over the last 15 years, and further define their habitats in European Atlantic waters in spring. The timing and spatial coverage of DEPM and acoustic surveys that will be conducted by group members in 2020 were planned to optimise the monitoring of anchovy and sardine populations and their pelagic environment in the European Atlantic area. The synoptic nature of the survey components has been assessed for each target species. A manual describing the protocols used during the DEPM surveys coordinated by the WGACEGG group was reviewed, and writing of a manual of WGACEGG acoustic surveys continued. Both manuals will be available in 2020. The final results of the 2017 sardine DEPM assessment were endorsed by the group

Preliminary results from the ECOCADIZ 2020-07 Spanish acoustic survey (01 – 14 August 2020)

The present working document summarises a part of the main results obtained from the Spanish (pelagic ecosystem-) acoustic survey conducted by IEO between 01st and 14th August 2020 in the Portuguese and Spanish shelf waters (20-200 m isobaths) off the Gulf of Cadiz (GoC) onboard the R/V Miguel Oliver. The 21 foreseen acoustic transects were sampled. A total of 26 valid fishing hauls were carried out for echo-trace ground-truthing purposes. Four additional night trawls were conducted to collect anchovy hydrated females (DEPM). This working document only provides abundance and biomass estimates for anchovy, sardine and chub mackerel, which are presented without age structure. The distribution of all the mid-sized and small pelagic fish species susceptible of being acoustically assessed is also shown from the mapping of their back-scattering energies. GoC anchovy acoustic estimates in summer 2020 were of 5153 million fish and 44 877 tones, with the bulk of the population occurring in the Spanish waters. The current biomass estimate becomes in the second historical maximum within the time-series. The estimates of sardine abundance and biomass in summer 2020 were 1923 million fish and 50 721 t, estimates close to the historical average, but lower than the values estimated last year and the most recent maxima reached in 2018. A total of 32 854 t and 448 million fish were estimated for Chub mackerel, estimates similar to the most recent ones and very close to the time-series average

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Manuel d'utilisation d'Echobase

User manual of the postgreSQL database EchoBase dedicated to the storage of: i) acoustic, navigation and fishing data of ecosystemic cruises; ii) biomass estimates and population indices derived from these cruises.Manuel d'utilisation de la base de données postgreSQL EchoBase dédiée au stockage : i) des données acoustiques, de navigation et de pêche issues de campagnes écosystémiques ; ii) des résultats d'estimation de biomasse et des indicateurs dérivés des campagnes

WGACEGG2014 EchoR training course

A summary of methodological questions tackled during the EchoR training course given during the joint ICES WGACEGG/MEDIAS working group in Vigo on november, 16th 2014.Synthèse des questions méthodologiques soulevées lors de la formation EchoR donnée lors de la réunion conjointe des groupes CIEM WGACEGG et MEDIAS à Vigo, le 16/11/2014

Effect of Target Strength equation selection on PELGAS anchovy and sardine biomass estimates

Knowledge of the acoustic response of single fish (or Target Strength: TS) is of prime importance for acoustic target classification and abundance estimation. This report investigates the effect of TS~length equation selection on the anchovy and sardine biomass estimates derived from PELGAS acoustic and fishing survey data. We aim at assessing the respective effects of b20 and depth correction terms on anchovy biomass acoustic estimates derived from the PELGAS survey, in order to evaluate the magnitude of a potential non linear effect of fish depth on acoustic biomass estimates. The PELGAS 2012, 2014, 2015 and 2016 survey data are re-analysed using several TS equations with different b20 values and/or depth correction terms to assess the respective effects of each single term on PELGAS anchovy and sardine biomass estimates. Our results confirm that the main TS equation parameter influencing the spring Biscay anchovy and sardine biomass estimations is the b20. In comparison, the Ona (2003)'s depth correction term yields marginal and more or less constant changes in the biomass estimates. The hypothesis of a strong and non linear effect of a depth-correction term in the TS equation used to derive acoustic biomass estimates of anchovy or sardine in the Bay of Biscay is invalidated by these results. The annual depth distributions of anchovies, as estimated based on PELGAS catch and ESDU data, show moderate variability, which does not seem to be related to biomass fluctuations