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# Long-term changes in taxonomic and functional composition of European marine fish communities The GitHub linked repository is here: [European_demersal_fish_assemblages (](https://github.com/auroreRECE/European_demersal_fish_assemblages)DOI [10.5281/zenodo.11190119](https://zenodo.org/doi/10.5281/zenodo.11190119)) ## Overview This project is dedicated to studying the influence of environmental conditions and fishing on the functional and taxonomic structure of a demersal fish community in Europe. This GitHub repository provides the code of the Receveur et al. (2024) publication in Ecography. ## Data files description ### df\_MFA.csv This file contains the coordinates resulting from the Multiple Factor Analysis (MFA): * X : the row numbers ; * ID_unique : a unique ID number corresponding to the trawls ; * Dim.1 : the coordinate of each trawl on the first MFA dimension ; * Dim.2 : the coordinate of each trawl on the second MFA dimension ; * Dim.3 : the coordinate of each trawl on the third MFA dimension ; ### df\_PCA.csv This file contains the coordinates * X : the row numbers ; * ID_unique : a unique ID number corresponding to the trawls ; * Dim.1 : the coordinate of each trawl on the first PCA dimension ; * Dim.2 : the coordinate of each trawl on the second PCA dimension ; * Dim.3 : the coordinate of each trawl on the third PCA dimension ; ### df\_env.csv This file contains the following environmental parameters: * X : the row numbers ; * ID_unique : a unique ID number corresponding to the trawls ; * Year : the Year of each trawl ; * Quarter : the Quarter of each trawl ; * Ecoregion : the Ecoregion where each trawl has been done; * Survey : the name of the Survey ; * x_my_spatial_id : the longitude of the ICES rectangle where the trawl has been done ; * y_my_spatial_id : the latitude of the ICES rectangle where the trawl has been done ; * my_spatial_id : an ID for the ICES rectangle where the trawl has been done ; * depth : the bottom depth (meters) ; * depth_span : the bottom depth variability (maximum depth of the ICES cell - minimum depth) (meters) ; * chloro_mea: the mean chlorophyll-a concentration (mg/m³) ; * mlotst_mea : the mean mixed layer depth (meters) ; * oxy_bottom_mea : the mean bottom dissolved oxygen (umol/l) ; * oxy_surf_mea : the mean surface dissolved oxygen (umol/l) ; * temp_bottom_mea : the mean bottom temperature (°C) ; * temp_surf_mea : the mean surface temperature (°C) ; * curr_surf_mea : the mean surface current strength (m/s) ; * curr_bottom_mea : the mean bottom current strength (m/s) ; * sal_surf_mea : the mean surface salinity (PSU) ; * chloro_std : the standard deviation of chlorophyll-a concentration (mg/m³) ; * mlotst_std : the standard deviation of mixed layer depth (meters) ; * oxy_bottom_std : the standard deviation of bottom dissolved oxygen (umol/l) ; * oxy_surf_std : the standard deviation of surface dissolved oxygen (umol/l) ; * temp_bottom_std : the standard deviation of bottom temperature (°C) ; * temp_surf_std : the standard deviation of surface temperature (°C) ; * curr_surf_std : the standard deviation of surface current strength (m/s) ; * curr_bottom_std : the standard deviation of bottom current strength (m/s) ; * sal_surf_std : the standard deviation of surface salinity (PSU). ## Raw Data sources ### Biological data Trawls content is publicly available for the North East Atlantic (DATRAS database). Mediterranean data (MEDITS database) are available upon request to Maritime Affairs and Fisheries (MARE DATACOLLECTIONFRAMEWORK). The project uses the following surveys: | Survey Code | Survey name | Area | Period | References | | :---------- | :----------------------------------------------------- | :------------------------------------- | :-------: | :--------: | | BITS | Baltic International Trawl Survey | Baltic Sea | 1994-2019 | 4 | | BTS | Beam Trawl Survey | Celtic Sea; English Channel; North Sea | 1997-2019 | 7 | | BTS-VIII | Beam Trawl Survey – Bay of Biscay | Bay of Biscay | 2011-2019 | 7 | | DWS | Deepwater Survey | Irish Sea | 2006-2007 | 8 | | DYFS | Inshore Beam Trawl Survey | Southern North Sea | 2002-2019 | 7 | | EVHOE | French Southern Atlantic Bottom trawl Survey | Bay of Biscay and Celtic Sea | 2003-2019 | 1 | | FR-CGFS | French Channel ground Survey | English Channel | 1997-2019 | 2 | | IE-IAMS | Irish Anglerfish and megrim Survey | Scottish rockall and Irish Sea | 2016-2019 | 2 | | IE-IGFS | Irish Groundfish | Ireland Shelf Sea | 2003-2019 | 2 | | MEDITS | International bottom trawl survey in the Mediterranean | Mediterranean Sea | 1994-2018 | 9 | | NIGFS | Northern Ireland Groundfish Survey | Irish Sea | 2009-2019 | 2 | | NS-IBTS | North Sea International Bottom Trawl Survey | North Sea | 1997-2019 | 2 | | PT-IBTS | Portuguese International Bottom Trawl Survey | Portugal Shelf Sea | 2003-2017 | 2 | | ROCKALL | Scottish Rockall Survey (until 2010) | Rockall plateau | 2003-2009 | 2 | | SCOROC | Scottish Rockall Survey (from 2011) | Scottish plateau | 2011-2019 | 2 | | SCOWCGFS | Scottish West Coast Groundfish Survey | Scottish west coast | 2011-2019 | 2 | | SNS | Sole Net Survey | Southern North Sea | 2002-2019 | 7 | | SP-ARSA | Spanish Gulf of Cadiz Bottom Trawl Survey | Spain | 2003-2019 | 6 | | SP-NORTH | Spanish North Bottom Trawl Survey | North of Spain | 2003-2019 | 2 | | SP-PORC | Spanish Porcupine Bottom Trawl Survey | Irish Sea | 2003-2019 | 5 | | SWC-IBTS | Scottish West Coast International Bottom Trawl Survey | Scotland Shelf Sea | 1999-2010 | 2 | ### Trait data The complete traits data table is available upon request. It is a combination of the publicly available PANGAEA database, Fishbase information, and inference based on the FISHLIFE project. ### Environmental variables The data used are all publicly available on the Copernicus website. ### Fishing data The data used are all publicly available on the Global Fishing Watch website. ## Recommended Citation Please use the following citation: Receveur, A., Leprieur F., Ellingsen K., Keith D., Kleisner K., McLean M., Mérigot B., Mills K., Mouillot D., Rufino M., Trindade-Santos I., Van Hoey G., Albouy C., Auber A. Data for “Long-term changes in taxonomic and functional composition of European marine fish communities.” Dryad Digital Repository. (2024). doi.org/10.5061/dryad.x69p8czsj ## Acknowledgments This research is a product of the MAESTRO group funded by the synthesis center CESAB of the French Foundation for Research on Biodiversity (FRB). We thank France Filière Pêche (FFP) who founded the MAESTRO project. We also warmly thank all those who have contributed in any way to the scientific surveys and data collection/provision (European Institutions and scientists implicated in DATRAS-BTS, MEDITS, and DCF). ## References 1. ICES. The EVHOE survey (France). ICES Documents. (1997). Available at: https://archimer.ifremer.fr/doc/00036/14707/12013.pdf 2. ICES. Manual of the IBTS North Eastern Atlantic Surveys. Series of ICES Survey Protocols SISP 15 (2017). doi:10.17895/ices.pub.3519 3. ICES. Manual for the International Bottom Trawl Surveys Revision VIII. Series of ICES Survey Protocols SISP 10 - IBTS IX. (2015). 4. https://ices-library.figshare.com/articles/report/SISP_7_-*Manual_for_the_Baltic_International_Trawl_Surveys_BITS*/19050986 5. https://gis.ices.dk/geonetwork/srv/api/records/ce94a257-c8b3-44f7-9fd0-6bd7449ce073 6. http://ices.dk/sites/pub/CM%20Doccuments/2002/D/D0302A.pdf 7. https://ices-library.figshare.com/articles/report/SISP_14_-*Manual_for_the_Offshore_Beam_Trawl_Surveys_WGBEAM*/19051328 8. https://gis.ices.dk/geonetwork/srv/api/records/936b4fb7-9baa-4dbc-abd0-b1b7bda16406 9. https://archimer.ifremer.fr/doc/00117/22783/20585.pdf Evidence of large-scale biodiversity degradation in marine ecosystems has been reported worldwide, yet most research has focused on few species of interest or on limited spatiotemporal scales. Here we assessed the spatial and temporal changes in the taxonomic and functional composition of fish communities in European seas over the last 25 years (1994-2019). We then explored how these community changes were linked to environmental gradients and fishing pressure. We show that the spatial variation in fish species composition is more than two times higher than the temporal variation, with a marked spatial continuum in taxonomic composition and a more homogenous pattern in functional composition. The regions warming the fastest are experiencing an increasing dominance and total abundance of r-strategy fish species (lower age of maturity). Conversely, regions warming more slowly show an increasing dominance and total abundance of K-strategy species (high trophic level and late reproduction). Among the considered environmental variables, sea surface temperature, surface salinity, and chlorophyll-a most consistently influenced communities’ spatial patterns, while bottom temperature and oxygen had the most consistent influence on temporal patterns. Changes in communities’ functional composition were more closely related to environmental conditions than taxonomic changes. Our study demonstrates the importance of integrating community-level species traits across multi-decadal scales and across a large region to better capture and understand ecosystem-wide responses and provides a different lens on community dynamics that could be used to support sustainable fisheries management.

Project: GCOS Earth Heat Inventory - A study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory (EHI), and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period from 1960 to present. Summary: The file “GCOS_EHI_1960-2020_Earth_Heat_Inventory_Ocean_Heat_Content_data.nc” contains a consistent long-term Earth system heat inventory over the period 1960-2020. Human-induced atmospheric composition changes cause a radiative imbalance at the top-of-atmosphere which is driving global warming. Understanding the heat gain of the Earth system from this accumulated heat – and particularly how much and where the heat is distributed in the Earth system - is fundamental to understanding how this affects warming oceans, atmosphere and land, rising temperatures and sea level, and loss of grounded and floating ice, which are fundamental concerns for society. This dataset is based on a study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory published in von Schuckmann et al. (2020), and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960-2020. The dataset also contains estimates for global ocean heat content over 1960-2020 for different depth layers, i.e., 0-300m, 0-700m, 700-2000m, 0-2000m, 2000-bottom, which are described in von Schuckmann et al. (2022). This version includes an update of heat storage of global ocean heat content, where one additional product (Li et al., 2022) had been included to the initial estimate. The Earth heat inventory had been updated accordingly, considering also the update for continental heat content (Cuesta-Valero et al., 2023).

The biotechnological development has traditionally focused on the compliance with regulatory demands rather than optimising the processes or analysing their sustainability. This work proposes the combination of available tools for the comprehensive sustainability assessment of a blue biotechnology process based on the cultivation of the microalgae Haematococcus pluvialis. The work aims to include environmental, economic and social dimensions to measure the sustainability of the production of a carotenoid with potential applications in food, nutraceutical, cosmetics and eventually pharmaceutical industries. Electricity for cultivation was identified as the major contributor to the environmental impacts, which depended significantly on the production scale. Social benefits were mainly related to workers and consumers, while the economic assessment suggested a profitable process with a relatively short period to recover the initial investment.

AbstractThe Paris Conference of Parties (COP21) agreement renewed momentum for action against climate change, creating the space for solutions for conservation of the ocean addressing two of its largest threats: climate change and ocean acidification (CCOA). Recent arguments that ocean policies disregard a mature conservation research field and that protected areas cannot address climate change may be oversimplistic at this time when dynamic solutions for the management of changing oceans are needed. We propose a novel approach, based on spatial meta‐analysis of climate impact models, to improve the positioning of marine protected areas to limit CCOA impacts. We do this by estimating the vulnerability of ocean ecosystems to CCOA in a spatially explicit manner and then co‐mapping human activities such as the placement of renewable energy developments and the distribution of marine protected areas. We test this approach in the NE Atlantic considering also how CCOA impacts the base of the food web which supports protected species, an aspect often neglected in conservation studies. We found that, in this case, current regional conservation plans protect areas with low ecosystem‐level vulnerability to CCOA, but disregard how species may redistribute to new, suitable and productive habitats. Under current plans, these areas remain open to commercial extraction and other uses. Here, and worldwide, ocean conservation strategies under CCOA must recognize the long‐term importance of these habitat refuges, and studies such as this one are needed to identify them. Protecting these areas creates adaptive, climate‐ready and ecosystem‐level policy options for conservation, suitable for changing oceans.

Geostatistical techniques were applied and a series of spatial indicators were calculated (occupation, aggregation, location, dispersion, spatial autocorrelation and overlap) to characterize the spatial distributions of European anchovy and sardine during summer. Two ecosystems were compared for this purpose, both located in the Mediterranean Sea: the Strait of Sicily (upwelling area) and the North Aegean Sea (continental shelf area, influenced by freshwater). Although the biomass of anchovy and sardine presented high interannual variability in both areas, the location of the centres of gravity and the main spatial patches of their populations were very similar between years. The size of the patches representing the dominant part of the abundance (80%) was mostly ecosystem- and species-specific. Occupation (area of presence) appears to be shaped by the extent of suitable habitats in each ecosystem whereas aggregation patterns (how the populations are distributed within the area of presence) were species-specific and related to levels of population biomass. In the upwelling area, both species showed consistently higher occupation values compared to the continental shelf area. Certain characteristics of the spatial distribution of sardine (e.g. spreading area, overlapping with anchovy) differed substantially between the two ecosystems. Principal component analysis of geostatistical and spatial indicators revealed that biomass was significantly related to a suite of, rather than single, spatial indicators. At the spatial scale of our study, strong correlations emerged between biomass and the first principal component axis with highly positive loadings for occupation, aggregation and patchiness, independently of species and ecosystem. Overlapping between anchovy and sardine increased with the increase of sardine biomass but decreased with the increase of anchovy. This contrasting pattern was attributed to the location of the respective major patches combined with the specific occupation patterns of the two species. The potential use of spatial indices as auxiliary stock monitoring indicators is discussed.

Crossed effects between climate change and chemical pollutions were identified on community structure and ecosystem functioning. Temperature rising affects the toxic properties of pollutants and the sensitiveness of organisms to chemicals stress. Inversely, chemical exposure may decrease the capacity of organisms to respond to environmental changes. The aim of our study was to assess the individual and crossed effects of temperature rising and pesticide contamination on fish. Goldfish, Carassius auratus, were exposed during 96 h at two temperatures (22 and 32 °C) to a mixture of common pesticides (S-metolachlor, isoproturon, linuron, atrazine-desethyl, aclonifen, pendimethalin, and tebuconazol) at two environmentally relevant concentrations (total concentrations MIX1 = 8.4 μg L(-1) and MIX2 = 42 μg L(-1)). We investigated the sediment reworking behavior, which has a major ecological functional role. We also focused on three physiological traits from the cellular up to the whole individual level showing metabolic status of fish (protein concentration in liver and muscle, hepatosomatic index, and Fulton's condition factor). Individual thermal stress and low concentrations of pesticides decreased the sediment reworking activity of fish and entrained metabolic compensation with global depletion in energy stores. We found that combined chemical and thermal stresses impaired the capacity of fish to set up an efficient adaptive response. Our results strongly suggest that temperature will make fish more sensitive to water contamination by pesticides, raising concerns about wild fish conservation submitted to global changes.

As Earth’s climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.