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

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

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

Decadal stability in top predator habitat preferences in the Bay of Biscay

Most oceanographic systems, especially shelf ecosystems, are characterised by interannual variability in the timing, extent and intensity of their seasonal patterns. Such interannual variations have important consequences on top predator habitat preferences. Capitalising on oceanographic surveys performed every spring since 2004 in the Bay of Biscay (BoB), this study explored interannual variations in habitat preferences exhibited by five mobile top predator species: bottlenose and common dolphins, auks, fulmars and northern gannets. We expected to find species with similar habitat preferences every year or species exhibiting important variability in their habitat preferences. First, we identified with a Principal Component Analysis (PCA) three different habitats of varying extent depending on year: river plumes, central shelf waters and shelf edge. Second, the Principal Components were used to explore the habitat preferences of predators through Generalized Additive Models. We fitted two kinds of models, using and not using the year as an interaction term, to test whether habitat preferences changed across years. Our results showed a range of habitat strategies based on the specificity and stability of species preferences. Species exhibiting narrower habitat preferences also exhibited stronger stability in their preferences among years while the species with wider habitat preferences exhibited higher variability among years. The target habitats differed across studied species, with bottlenose dolphins targeting the shelf edge exclusively, auks preferring river plumes, fulmars exhibiting a gradual preference from the shelf edge to river plumes and gannets being present in any of the three habitats. In contrast, the habitat preferences of common dolphins, the most sighted cetacean species in the BoB, could not be reliably inferred

Overview of recent progress in fisheries acoustics made by Ifremer with examples from the Bay of Biscay

This paper provides an overview of the progress Ifremer has made recently in fisheries acoustics and the study of small pelagic fish by: i) pushing observation frontiers using a range of platforms including an autonomous underwater vehicle, AUV, ii) developing measuring instruments and methods and iii) studying fish distributions. Presently, information from several frequencies of single-beam echosounders is routinely collected together with data from the ME70 multibeam echosounder. For onboard data acquisition control the HERMES software was developed. The new MOVIES 3D software includes modules for simultaneous realistic 3D visualisation and post-processing such as bottom detection, school extraction and calculation of descriptors and integration of all acoustic data. Several data analysis methods are being developed and some initial results are presented. Finally, results on the spatial distribution of small pelagic fish schools in the Bay of Biscay illustrate the role that acoustics can play, and are already playing, in the implementation of an ecosystem approach to fisheries

Structure and functioning of the Bay of Biscay ecosystem: A trophic modelling approach

Characterizing the structure and functioning of marine ecosystems requires a deep understanding of the dynamics of its populations and the biotic interactions among them. To this end, we developed a mass-balanced food-web model of a regional sea in the Northeast Atlantic, the Bay of Biscay (BoB), considering one of the most important anthropogenic disturbance in the area, the fishing pressure. The food-web model was performed for the whole BoB region for the first time. The model represents the ecosystems in the early 2000s, encompassing 120433 km2 between 0 and 1000 m depth. The model was composed of 52 functional groups, ranging from primary producers to top predators, and considering both Spanish and French fishing fleets. Input data included biomass obtained locally from bottom trawl and acoustic surveys, data from stock assessment, official fishery statistics, published and unpublished data on stomach content analyses and the use of empirical equations to estimate consumption and production rates. Our results highlight the importance of the pelagic domain, since the main trophic flows are determined by the interaction between phytoplankton, zooplankton and forage fishes. The role of the detritivore pathway was also relevant due to the relatively high abundance of detritivores organisms and the large percentage of primary production flowing to the detritus. Forage fish have resulted to be a key compartment fostering the connectivity between the benthic and pelagic domains. Pelagic sharks, dolphins, anglerfish, large hake and large demersal fishes were identified as potential keystone functional groups in the BoB model. The results also showed an intense exploitation by fisheries in early 2000s. Different strategies between Spanish and French fleets were also found. French fleets were mainly focussed on low trophic level forage fish (e.g., sardine and anchovy) and had larger impacts on higher trophic levels, while Spanish fleets mostly focussed on higher trophic level forage fishes (e.g., mackerel, horse mackerel and blue whiting) but also targeting sardine and anchovy; and displayed lower impacts on higher trophic levels. Overall, our model demonstrates the importance of combining data sources from different countries to regionally address the sought-after implementation of the ecosystem-based management approach