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cti_cross_region_taxon This repository provides the data and codes used in the manuscript: Guillem Chust, Ernesto Villarino, Matthew McLean, Nova Mieszkowska, Lisandro Benedetti-Cecchi, Fabio Bulleri, Chiara Ravaglioli, Angel Borja, Iñigo Muxika, José A. Fernandes-Salvador, Leire Ibaibarriaga, Ainhize Uriarte, Marta Revilla, Fernando Villate, Arantza Iriarte, Ibon Uriarte, Soultana Zervoudaki, Jacob Carstensen, Paul J. Somerfield, Ana M. Queirós , Andrea J. McEvoy, Arnaud Auber, Manuel Hidalgo, Marta Coll, Joaquim Garrabou, Daniel Gómez-Gras, Cristina Linares, Francisco Ramírez, Núria Margarit, Mario Lepage, Chloé Dambrine, Jérémy Lobry, Myron A. Peck, Paula de la Barra, Anieke van Leeuwen, Gil Rilov, Erez Yeruham, Anik Brind'Amour, and Martin Lindegren. Cross-basin and cross-taxa patterns of marine community tropicalization and deborealization in warming European seas. Nature Communications Please check the github repo cti_cross_region_taxon for updates. Abstract Ocean warming and acidification, decreases in dissolved oxygen concentrations, and changes in primary production are causing an unprecedented global redistribution of marine life. The identification of underlying ecological processes underpinning marine species turnover, particularly the prevalence of tropicalization over deborealization, has been recently debated in the context of ocean warming. Here, we track changes in the mean thermal affinity of marine communities across European seas by calculating the Community Temperature Index for 65 biodiversity time series collected over four decades and containing 1,817 species from different communities (zooplankton, coastal benthos, pelagic and demersal invertebrates and fish). We show most communities and sites have clearly responded to ongoing ocean warming via abundance increases of warm-water species (tropicalization; 54%) and decreases of cold-water species (deborealization; 18%). Tropicalization dominated Atlantic sites compared to semi-enclosed basins such as the Mediterranean and Baltic Seas, probably due to physical barrier constraints to connectivity and species colonization. Semi-enclosed basins appeared to be particularly vulnerable to ocean warming, experiencing the fastest rates of warming and biodiversity loss through deborealization. Keywords: climate change, community temperature index, CTI, ocean connectivity. Acknowledgements This study has been supported by the European Union's Horizon 2020 research and innovation programme under grant agreement No 869300 (FutureMARES project) (G.C., E.V., J.F-S., M.P., M.Lin., C.D., D.G-G., G.R., L.B., C.R., M.C., F.R., G.R., P.B., M.P., M.Lep., J.L., A.B., N.M., J.G., F.B., L.B.C, A.Q., F.V., A.I., and I.U.), and by the Urban Klima 2050 -- LIFE 18 IPC 000001 project, which has been received funding from European Union's LIFE programme (G.C., E.V., L.I., A.B., A.U., and M.R.). Additional financial support was obtained from the Basque Government (PIBA2020-1-0028 & IT1723-22). We thank the NOAA Climate Prediction Center for providing Sea Temperature data through the NCEP Global Ocean Data Assimilation System (GODAS) www.cpc.ncep.noaa.gov/products/GODAS. We also thank Ocean Biodiversity Information System (OBIS) for providing global occurrences of the biological group studied here. Data from the Basque Country were obtained from the Basque Water Agency (URA) monitoring network, through a Convention with AZTI. M.C., J.G., D.G.-G. and F.R. acknowledge the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). Authors M.H. and M.Lin. are grateful for the support from ICES Working Group on Comparative Ecosystem-based Analyses of Atlantic and Mediterranean marine systems (WGCOMEDA) for this research. This paper is contribution nº xxxx from AZTI, Marine Research, Basque Research and Technology Alliance (BRTA)

The Tara Pacifc expedition (2016–2018) provided an opportunity to investigate calcifcation patterns in extant corals throughout thePacifc Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected fromdiferent environments to assess calcifcation parameters of long-lived reef-building corals. In this study, we compared the calcifcation and carbonate chemistryup-regulation of Diploastrea heliopora and Porites corals from across a range of environments. To this, we analyzed the skeletal geochemistry and growth parameters of 39 colonies of Porites (n=33) and Diploastrea (n=6) collected across the tropical Pacifc Ocean during the Tara Pacifc expedition (2016–2018). Te collected corals represent a suite of cores exposed to various hydrological conditions of seawater temperature (SST: 22.4–29.8 °C), salinity (SSS: 31.5–36.1), and carbonate chemistry (total scale pHsw: 8.01–8.09). Te average chemical composition of the calcifying fuid (pHcf, [CO32−]cf, DICcf, Ωcf) was derived from paired boron isotope (δ11B) and B/Ca analyses of core-top samples corresponding to the last 6 years of growth (2010–2016). Based on these data, we assessed the impact of the ambient seawater properties (SST, salinity, carbonate chemistry) on the cf composition of these slow-growing reef-building genera at the Pacifc basin scale. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2024-04-08.

Current velocities of the upper water column along the cruise track of R/V Meteor cruise M197 were collected by a vessel-mounted 75 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 8.00 m, a blanking distance of 4.00 m, and a total of 100 bins, covering the depth range between 17.0 m and 809.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-0.1521° +/- 0.5577°) and scale factor (1.0055 +/- 0.0082) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 120 s. Velocity quality flagging is based on different threshold criteria: Depth cells with ensemble-averaged percent-good values below 25% are marked as 'bad data'. Depth cells with velocities above 0.8 m/s are flagged as 'bad data'. Depth cells with a root-mean-square deviation between the measured ensemble-average velocity and a cell-wise running-mean velocity above 0.2 m/s are flagged as 'probably bad data'.

Current velocities of the upper water column along the cruise track of R/V Meteor cruise M197 were collected by a vessel-mounted 38 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 16.00 m, a blanking distance of 8.00 m, and a total of 80 bins, covering the depth range between 29.0 m and 1293.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. Single-ping data were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-44.8506° +/- 0.5350°) and scale factor (1.0005 +/- 0.0083) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 120 s. Velocity quality flagging is based on different threshold criteria: Depth cells with ensemble-averaged percent-good values below 25% are marked as 'bad data'. Depth cells with velocities above 0.8 m/s are flagged as 'bad data'. Depth cells with a root-mean-square deviation between the measured ensemble-average velocity and a cell-wise running-mean velocity above 0.2 m/s are flagged as 'probably bad data'.

Raw water column data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 122 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: (i) characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw multibeam bathymetry data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 710 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw multibeam bathymetry data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 122 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: (i) characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw water column data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 710 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.