Rapport final ONF

Whole genome pooled sequencing of individuals from 4 populations and 3 different color phenotype in order to uncover the genetic variants linked to color expression in the pearl oyster P. margaritifera.

Analysis of tuna stomach contents

'''This product has been archived''' '''DEFINITION''' Estimates of Ocean Heat Content (OHC) are obtained from integrated differences of the measured temperature and a climatology along a vertical profile in the ocean (von Schuckmann et al., 2018). The regional OHC values are then averaged from 60°S-60°N aiming i) to obtain the mean OHC as expressed in Joules per meter square (J/m2) to monitor the large-scale variability and change. ii) to monitor the amount of energy in the form of heat stored in the ocean (i.e. the change of OHC in time), expressed in Watt per square meter (W/m2). Ocean heat content is one of the six Global Climate Indicators recommended by the World Meterological Organisation for Sustainable Development Goal 13 implementation (WMO, 2017). '''CONTEXT''' Knowing how much and where heat energy is stored and released in the ocean is essential for understanding the contemporary Earth system state, variability and change, as the ocean shapes our perspectives for the future (von Schuckmann et al., 2020). Variations in OHC can induce changes in ocean stratification, currents, sea ice and ice shelfs (IPCC, 2019; 2021); they set time scales and dominate Earth system adjustments to climate variability and change (Hansen et al., 2011); they are a key player in ocean-atmosphere interactions and sea level change (WCRP, 2018) and they can impact marine ecosystems and human livelihoods (IPCC, 2019). '''CMEMS KEY FINDINGS''' Since the year 2005, the near-surface (0-300m) near-global (60°S-60°N) ocean warms at a rate of 0.4 ± 0.1 W/m2. Note: The key findings will be updated annually in November, in line with OMI evolutions. '''DOI (product):''' https://doi.org/10.48670/moi-00233

EMODnet Chemistry aims to provide access to marine chemistry data sets and derived data products concerning eutrophication, acidity and contaminants. The chemicals chosen reflect importance to the Marine Strategy Framework Directive (MSFD). ITS-90 water temperature and Water body salinity variables have been also included (as-is) to complete the Eutrophication and Acidity data. If you use these variables for calculations, please refer to SeaDataNet for having the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets . This aggregated dataset contains all unrestricted EMODnet Chemistry data on Eutrophication and Acidity (14 parameters with quality flag indicators), and covers the Mediterranean Sea with 67271 CDI records (60876 Vertical profiles and 6395 Time series). Vertical profiles temporal range is from 1911-08-17 to 2017-10-25. Time series temporal range is from 1974-06-04 to 2015-12-22. Data were aggregated and quality controlled by 'Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC)' from Greece. Regional datasets concerning eutrophication and acidity are automatically harvested and resulting collections are aggregated and quality controlled using ODV Software and following a common methodology for all Sea Regions ( https://doi.org/10.6092/9f75ad8a-ca32-4a72-bf69-167119b2cc12). When not present in original data, Water body nitrate plus nitrite was calculated by summing up the Nitrates and Nitrites. Same procedure was applied for Water body dissolved inorganic nitrogen (DIN) which was calculated by summing up the Nitrates, Nitrites and Ammonium. Parameter names are based on P35, EMODnet Chemistry aggregated parameter names vocabulary, which is available at: https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/P35/. Detailed documentation is available at: https://doi.org/10.6092/ec8207ef-ed81-4ee5-bf48-e26ff16bf02e The aggregated dataset can be downloaded as ODV spreadsheet, which is composed of metadata header followed by tab separated values. This worksheet can be imported to ODV Software for visualisation (More information can be found at: https://www.seadatanet.org/Software/ODV ). The original datasets can be searched and downloaded from EMODnet Chemistry Download Service: https://emodnet-chemistry.maris.nl/search

'''DEFINITION''' The trend map is derived from version 5 of the global climate-quality chlorophyll time series produced by the ESA Ocean Colour Climate Change Initiative (ESA OC-CCI, Sathyendranath et al. 2019; Jackson 2020) and distributed by CMEMS. The trend detection method is based on the Census-I algorithm as described by Vantrepotte et al. (2009), where the time series is decomposed as a fixed seasonal cycle plus a linear trend component plus a residual component. The linear trend is expressed in % year -1, and its level of significance (p) calculated using a t-test. Only significant trends (p < 0.05) are included. '''CONTEXT''' Phytoplankton are key actors in the carbon cycle and, as such, recognised as an Essential Climate Variable (ECV). Chlorophyll concentration is the most widely used measure of the concentration of phytoplankton present in the ocean. Drivers for chlorophyll variability range from small-scale seasonal cycles to long-term climate oscillations and, most importantly, anthropogenic climate change. Due to such diverse factors, the detection of climate signals requires a long-term time series of consistent, well-calibrated, climate-quality data record. Furthermore, chlorophyll analysis also demands the use of robust statistical temporal decomposition techniques, in order to separate the long-term signal from the seasonal component of the time series. '''CMEMS KEY FINDINGS''' The average global trend for the 1997-2021 period was 0.51% per year, with a maximum value of 25% per year and a minimum value of -6.1% per year. Positive trends are pronounced in the high latitudes of both northern and southern hemispheres. The significant increases in chlorophyll reported in 2016-2017 (Sathyendranath et al., 2018b) for the Atlantic and Pacific oceans at high latitudes appear to be plateauing after the 2021 extension. The negative trends shown in equatorial waters in 2020 appear to be remain consistent in 2021. '''DOI (product):''' https://doi.org/10.48670/moi-00230

'''This product has been archived''' '''DEFINITION''' The linear change of zonal mean subsurface temperature over the period 1993-2019 at each grid point (in depth and latitude) is evaluated to obtain a global mean depth-latitude plot of subsurface temperature trend, expressed in °C. The linear change is computed using the slope of the linear regression at each grid point scaled by the number of time steps (27 years, 1993-2019). A multi-product approach is used, meaning that the linear change is first computed for 5 different zonal mean temperature estimates. The average linear change is then computed, as well as the standard deviation between the five linear change computations. The evaluation method relies in the study of the consistency in between the 5 different estimates, which provides a qualitative estimate of the robustness of the indicator. See Mulet et al. (2018) for more details. '''CONTEXT''' Large-scale temperature variations in the upper layers are mainly related to the heat exchange with the atmosphere and surrounding oceanic regions, while the deeper ocean temperature in the main thermocline and below varies due to many dynamical forcing mechanisms (Bindoff et al., 2019). Together with ocean acidification and deoxygenation (IPCC, 2019), ocean warming can lead to dramatic changes in ecosystem assemblages, biodiversity, population extinctions, coral bleaching and infectious disease, change in behavior (including reproduction), as well as redistribution of habitat (e.g. Gattuso et al., 2015, Molinos et al., 2016, Ramirez et al., 2017). Ocean warming also intensifies tropical cyclones (Hoegh-Guldberg et al., 2018; Trenberth et al., 2018; Sun et al., 2017). '''CMEMS KEY FINDINGS''' The results show an overall ocean warming of the upper global ocean over the period 1993-2019, particularly in the upper 300m depth. In some areas, this warming signal reaches down to about 800m depth such as for example in the Southern Ocean south of 40°S. In other areas, the signal-to-noise ratio in the deeper ocean layers is less than two, i.e. the different products used for the ensemble mean show weak agreement. However, interannual-to-decadal fluctuations are superposed on the warming signal, and can interfere with the warming trend. For example, in the subpolar North Atlantic decadal variations such as the so called ‘cold event’ prevail (Dubois et al., 2018; Gourrion et al., 2018), and the cumulative trend over a quarter of a decade does not exceed twice the noise level below about 100m depth. Note: The key findings will be updated annually in November, in line with OMI evolutions. '''DOI (product):''' https://doi.org/10.48670/moi-00244

'''DEFINITION''' Estimates of Arctic sea ice extent are obtained from the surface of oceans grid cells that have at least 15% sea ice concentration. These values are cumulated in the entire Northern Hemisphere (excluding ice lakes) and from 1993 up to the year 2019 aiming to: i) obtain the Arctic sea ice extent as expressed in millions of km square (106 km2) to monitor both the large-scale variability and mean state and change. ii) to monitor the change in sea ice extent as expressed in millions of km squared per decade (106 km2/decade), or in sea ice extent loss since the beginning of the time series as expressed in percent per decade (%/decade; reference period being the first date of the key figure b) dot-dashed trend line, Vaughan et al., 2013). These trends are calculated in three ways, i.e. (i) from the annual mean values; (ii) from the March values (winter ice loss); (iii) from September values (summer ice loss). The Arctic sea ice extent used here is based on the “multi-product” (GLOBAL_MULTIYEAR_PHY_ENS_001_031) approach as introduced in the second issue of the Ocean State Report (CMEMS OSR, 2017). Five global products have been used to build the ensemble mean, and its associated ensemble spread. '''CONTEXT''' Sea ice is frozen seawater that floats on the ocean surface. This large blanket of millions of square kilometers insulates the relatively warm ocean waters from the cold polar atmosphere. The seasonal cycle of the sea ice, forming and melting with the polar seasons, impacts both human activities and biological habitat. Knowing how and how much the sea ice cover is changing is essential for monitoring the health of the Earth as sea ice is one of the highest sensitive natural environments. Variations in sea ice cover can induce changes in ocean stratification, in global and regional sea level rates and modify the key rule played by the cold poles in the Earth engine (IPCC, 2019). The sea ice cover is monitored here in terms of sea ice extent quantity. More details and full scientific evaluations can be found in the CMEMS Ocean State Report (Samuelsen et al., 2016; Samuelsen et al., 2018). '''CMEMS KEY FINDINGS''' Since the year 1993 to 2023 the Arctic sea ice extent has decreased significantly at an annual rate of -0.57*106 km2 per decade. This represents an amount of -4.8 % per decade of Arctic sea ice extent loss over the period 1993 to 2023. Over the period 1993 to 2018, summer (September) sea ice extent loss amounts to -1.18*106 km2/decade (September values), which corresponds to -14.85% per decade. Winter (March) sea ice extent loss amounts to -0.57*106 km2/decade, which corresponds to -3.42% per decade. These values slightly exceed the estimates given in the AR5 IPCC assessment report (estimate up to the year 2012) as a consequence of continuing Northern Hemisphere sea ice extent loss. Main change in the mean seasonal cycle is characterized by less and less presence of sea ice during summertime with time. Note: The key findings will be updated annually in November, in line with OMI evolutions. '''DOI (product):''' https://doi.org/10.48670/moi-00190

'''DEFINITION''' Variations of the Mediterranean Outflow Water at 1000 m depth are monitored through area-averaged salinity anomalies in specifically defined boxes. The salinity data are extracted from several CMEMS products and averaged in the corresponding monitoring domain: * IBI-MYP: IBI_MULTIYEAR_PHY_005_002 * IBI-NRT: IBI_ANALYSISFORECAST_PHYS_005_001 * GLO-MYP: GLOBAL_REANALYSIS_PHY_001_030 * CORA: INSITU_GLO_TS_REP_OBSERVATIONS_013_002_b * ARMOR: MULTIOBS_GLO_PHY_TSUV_3D_MYNRT_015_012 The anomalies of salinity have been computed relative to the monthly climatology obtained from IBI-MYP. Outcomes from diverse products are combined to deliver a unique multi-product result. Multi-year products (IBI-MYP, GLO,MYP, CORA, and ARMOR) are used to show an ensemble mean and the standard deviation of members in the covered period. The IBI-NRT short-range product is not included in the ensemble, but used to provide the deterministic analysis of salinity anomalies in the most recent year. '''CONTEXT''' The Mediterranean Outflow Water is a saline and warm water mass generated from the mixing processes of the North Atlantic Central Water and the Mediterranean waters overflowing the Gibraltar sill (Daniault et al., 1994). The resulting water mass is accumulated in an area west of the Iberian Peninsula (Daniault et al., 1994) and spreads into the North Atlantic following advective pathways (Holliday et al. 2003; Lozier and Stewart 2008, de Pascual-Collar et al., 2019). The importance of the heat and salt transport promoted by the Mediterranean Outflow Water flow has implications beyond the boundaries of the Iberia-Biscay-Ireland domain (Reid 1979, Paillet et al. 1998, van Aken 2000). For example, (i) it contributes substantially to the salinity of the Norwegian Current (Reid 1979), (ii) the mixing processes with the Labrador Sea Water promotes a salt transport into the inner North Atlantic (Talley and MacCartney, 1982; van Aken, 2000), and (iii) the deep anti-cyclonic Meddies developed in the African slope is a cause of the large-scale westward penetration of Mediterranean salt (Iorga and Lozier, 1999). Several studies have demonstrated that the core of Mediterranean Outflow Water is affected by inter-annual variability. This variability is mainly caused by a shift of the MOW dominant northward-westward pathways (Bozec et al. 2011), it is correlated with the North Atlantic Oscillation (Bozec et al. 2011) and leads to the displacement of the boundaries of the water core (de Pascual-Collar et al., 2019). The variability of the advective pathways of MOW is an oceanographic process that conditions the destination of the Mediterranean salt transport in the North Atlantic. Therefore, monitoring the Mediterranean Outflow Water variability becomes decisive to have a proper understanding of the climate system and its evolution (e.g. Bozec et al. 2011, Pascual-Collar et al. 2019). The CMEMS IBI-OMI_WMHE_mow product is aimed to monitor the inter-annual variability of the Mediterranean Outflow Water in the North Atlantic. The objective is the establishment of a long-term monitoring program to observe the variability and trends of the Mediterranean water mass in the IBI regional seas. To do that, the salinity anomaly is monitored in key areas selected to represent the main reservoir and the three main advective spreading pathways. More details and a full scientific evaluation can be found in the CMEMS Ocean State report Pascual et al., 2018 and de Pascual-Collar et al. 2019. '''CMEMS KEY FINDINGS''' The absence of long-term trends in the monitoring domain Reservoir (b) suggests the steadiness of water mass properties involved on the formation of Mediterranean Outflow Water. Results obtained in monitoring box North (c) present an alternance of periods with positive and negative anomalies. The last negative period started in 2016 reaching up to the present. Such negative events are linked to the decrease of the northward pathway of Mediterranean Outflow Water (Bozec et al., 2011), which appears to return to steady conditions in 2020 and 2021. Results for box West (d) reveal a cycle of negative (2015-2017) and positive (2017 up to the present) anomalies. The positive anomalies of salinity in this region are correlated with an increase of the westward transport of salinity into the inner North Atlantic (de Pascual-Collar et al., 2019), which appear to be maintained for years 2020-2021. Results in monitoring boxes North and West are consistent with independent studies (Bozec et al., 2011; and de Pascual-Collar et al., 2019), suggesting a westward displacement of Mediterranean Outflow Water and the consequent contraction of the northern boundary. Note: The key findings will be updated annually in November, in line with OMI evolutions. '''DOI (product):''' https://doi.org/10.48670/moi-00258

EMODnet (European Marine Observation and Data Network) is the long term marine data initiative supported by the European Commission since 2009 to ensure that European marine data will become easily accessible, interoperable, and free on restrictions on use. EMODnet Chemistry provides access to standardized, harmonized and validated chemical data collections for water quality evaluation at a regional scale, as defined by the Marine Strategy Framework Directive (MSFD). The data portal has adopted and adapted SeaDataNet standards and services, establishing interoperability between the data sets from the many different providers (more than 60 in EMODnet Chemistry network). Concentration maps of nutrients, chlorophyll-a and dissolved oxygen are computed on a standard grid, providing information at a regular time interval, per season and over several vertical layers, including the deepest one. Dedicated OGC standard services for browsing, viewing and downloading chemistry observation, data and data products for the European waters have been developed, and are actively maintained and monitored.