cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17882/56437
title: Successful recruitment, survival and long-term persistence of eastern oyster and hooked mussel on a subtidal, artificial restoration reef system in Chesapeake Bay

description: Restoration efforts with native eastern oyster, Crassostrea virginica, in Chesapeake Bay and elsewhere have been limited by shell availability, necessitating the use of alternative structures as subtidal reefs, yet these have rarely been evaluated quantitatively. We quantified population structure, density, abundance and biomass of eastern oyster and hooked mussel, Ischadium recurvum, on a concrete modular reef (75 m2 surface area over 5 m2 of river bottom) deployed subtidally at 7 m depth in the Rappahannock River, Virginia during October, 2000. After nearly 5 y (May 2005), we took 120 stratified random samples over the reef. The reef was heavily colonized by 28-168 oysters and 14-2177 mussels m-2 surface area. These densities translate to 1085 oysters and 8617 mussels m-2 river bottom, which are the highest recorded for artificial oyster reefs. Size structure of oysters reflected four year classes, with over half of oysters more than 1 y old and of reproductive age. Oyster biomass (1663 g dry mass m-2 river bottom) and condition index were equally high, whereas parasite prevalence and intensity were low. Oyster density correlated positively in a sigmoid fashion with mussel density up to high densities, then declined. This modular reef is one of the most successful artificial reefs for eastern oyster and hooked mussel restoration, and details features that are conducive for successful settlement, growth and survival in subtidal habitats.
DOI: 10.17882/56395
title: ROCCH SED 2017 data : chemical contaminants levels measured in mediterranean lagoon sediments by the national monitoring network ROCCH in 2017

description: ROCCH, the french monitoring network carried out by Ifremer, surveys chemical contaminants levels in coastal areas through two programmes, mussel watch programme and sediment watch programme. In 1996, 2006, 2012 and 2017, samples were collected in different french mediterranean lagoons for metallic contamination evaluation. In 2017, organic pollutants from the WFD and MSD european directives were analysed too. Data were completed by additional elements of diagnosis like organic matter, total nitrogen and phosphorus concentrations. Chemical contaminant are analysed in whole sediment and co - factors like aluminium and organic carbon are simultaneously measured for normalisation procedures.
DOI: 10.17882/56366
title: SeaExplorer glider SEA028 observations West of Svalbard in July 2017

description: The SeaExplorer glider Sea028 was deployed from the research vessel R/V Lance on the 24 July 2017 at 78.65°N, 9.70°E, on the western slope of Svalbard. The glider was recovered on 7 August 2017 at 79.99°N, 9.51°E. It performed six crossing of the western Svalbard slope. The glider was equipped with a GPCTD (Glider Payload Conductivity Temperature Depth from SeaBird), a dissolved oxygen sensor (Sea Bird SBE43F), and an optical sensor measuring Chlorophyll a (470/695 nm), Colored Dissolved Organic Matter (CDOM, 370/460 nm), and the total particle concentration or backscatter (backscattering at 700 nm) (EcoPuck from Wetlabs). The dataset is composed of the data corrected from the thermal lag and the sensor lag, despiked and interpolated every 1m. The profiles are separated. Please note that the oxygen data are not accurate for the second half of the time series (sensor bias).
DOI: 10.17882/56031
title: Oxygen and Carbon stable isotopes (Globigerina bulloides) and age models of sediment cores RHS-KS65 and RHS-KS67

description: Oxygen and Carbon isotope data (Globigerina bulloides) and age models of sediment cores RHS-KS65 and RHS-KS67.
DOI: 10.17882/56028
title: High-resolution observations of a dual-core anticyclonic eddy in the Algerian Basin (PROTEVS-MED 2016)

description: Mesoscale dynamics in the Mediterranean Sea have been investigated for years and anticyclonic eddies are regularly observed features in the Algerian Basin. In early spring 2016, a field experiment during the ProtevsMed 2016 cruise thoroughly investigated this specific eddy, when it was located near the North Balearic Front, taking high-resolution (Seasoar) hydrological transects, several CTD casts and LADCP measurements. In addition, four drifting buoys were released in the eddy core. These in situ measurements revealed that the vertical structure of this anticyclone was made of two water lenses of very different origins (Atlantic Water above and Western Intermediate Water below) spinning together. In the vicinity of the North Balearic Front, which may act as a dynamical barrier for structures, the eddy interacted with a subsurface anticyclonic eddy made of modal water, which fostered cross-front exchanges generating filaments by stirring. The high-resolution sampling revealed fine scales structures both adjacent to the eddy and within its core. The eddy has been targeted from 21 March to 1 April 2016 taking advantage of a meteorological window. It has been sampled with: - a towed undulating vehicle, the SeaSoar designed and built by Chelsea Instruments; it gets mounted on its sides two Sea-bird SBE-9 (SBE 3 temperature and SBE 4 conductivity sensors) and a Wetlabs Fluorometer of type ChloroA WetStar - CTD casts performed with a Sea-bird SBE-9 (SBE 3 temperature and SBE 4 conductivity sensor) and an RDI 150 kHz current profiler mounted in a general oceanics 12-place rosette, with12l Niskin bottles - drifters with holey-sock positioned at 50 m deep below the expected Ekman layer thickness (remaining in the eddy until mid May).
DOI: 10.17882/55639
title: In situ sea temperature 1km off La Paloma Port (Uruguay) during 2016/2017

description: One year of hourly sea temperature data at 0.5 meters depth 1 kilometer far away from La Paloma Port, in the Atlantic Coast of Uruguay. Measured by a Star-oddi DST-CTD moored in a buoy. From 1 December 2016 to 30 November 2017 located at 34.65ºS, 54.12ºW.
DOI: 10.17882/55576
title: Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L.

description: Among the different sex determination modalities exhibited by fish species, polygenic sex determination (PSD) is supposedly unstable, with genetic and environmental components that may vary between populations exposed/adapted to different environments. European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. We produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). There were less females than males in the progeny, both in the global dataset (32.5%) and within each group of parental origin (from 25.1% for NEM to 39.0% for WEM), with significant variation among populations dams and sires. Sex, body weight (BW) and body length (BL) showed moderate heritability (0.52 ± 0.17, 0.46 ± 0.17, 0.34 ± 0.15, respectively). Sex was genetically correlated with BW and BL (rAsex/BW = 0.69 ± 0.12, rAsex/BL = 0.66 ± 0.13). The weighted genome-wide association study (wGWAS) performed both on the global dataset and within each parental origin, revealed a different genetic architecture of sex determination between Atlantic and Mediterranean populations, with a gradient of similarities from Western to Eastern Mediterranean populations, consistent with the hypothesis of a population-specific evolution of polygenic sex determination systems in different environments.
DOI: 10.17882/55352
title: High angular and spectral directional reflectance dataset of snow and sea-ice

description: This dataset includes the data published in Goyens et al. (2018, DOI:10.1002/2017EA000332). It provides the following parameters for the different ice, snow and ponded ice stations of the GreenEdge Ice Camp 2015: - the hyperspectral (400-1000 nm) Hemispherical Directional Reflectance Factor (HDRF, units: dimensionless) measured with Analytical Spectral Device, Inc. (ASD) over a full hemisphere with 30° angular resolution along zenith and azimuth, - the hyperangular (full hemisphere at 1° angular resolution) multispectral (438, 560 and 628 nm) upwelling irradiance (Lu, units: µW.cm^-2.sr^-1.nm^-1) measured with a circular fish‐eye radiance camera (CE600) (median Lu and coefficient of variation are provided, see Goyens et al. (2018, DOI:10.1002/2017EA000332 for more info about data processing) - the multispectral (at 406.42, 434.48, 442.33, 489.70, 508.43, 560.22 and 624.20 nm) downwelling irradiance (Ed, units: µW.cm^-2.nm^-1) measured with the OCR from Satlantic, - the hyperangular HDRF (units: dimensionless) estimated as PI times the ratio of Lu CE600 to Ed OCR at 438, 560 and 628 nm (median and coefficient of variation are provided, see Goyens et al. (2018, DOI:10.1002/2017EA000332 for data processing), and, - the columnar aerosol optical depth (AOD, units: dimensionless) at 440, 500, 675, 870 and 936 nm estimated from a Handheld 5-channel Sunphotometer Microtops II.
DOI: 10.17882/55020
title: Disentangling the complexity of tropical small-scale fisheries dynamics using supervised Self-Organizing Maps

description: Data serie of small-scale fisheries of San Pedro port, Tabasco, México. These data are kg/fishery trip (lines) by species (common name, columns), by gear type year and month. For reference about gear names and fish common names please look for the paper: Disentangling the complexity of tropical small-scale fisheries dynamics using supervised Self-Organizing Maps. publised in PlosOne
DOI: 10.17882/55008
title: Grotto hydrothermal edifice: abundance and isotopic data from Ocean Networks Canada's Expedition 2015 and 2016: Wiring the Abyss

description: Abundances and isotopic data of inventoried species within tubeworm assemblages of the hydrothermal edifice Grotto (Main Endeavour Field, Juan de Fuca Ridge), during the oceanographic cruises Ocean Networks Canada's Expedition 2015 and 2016: Wiring the Abyss. Six sampling units were collected to represent variate stages of ecological succession on the edifice. Details on the sampling method and analyses are published in Lelièvre et al. 2018 (https://doi.org/10.5194/bg-15-2629-2018).
DOI: 10.17882/54854
title: Global Sea Level Budget Assessment by World Climate Research Programme

description: Global mean sea level is an integral of changes occurring in the climate system in response to unforced climate variability as well as natural and anthropogenic forcing factors. Its temporal evolution allows detecting changes (e.g., acceleration) in one or more components. Study of the sea level budget provides constraints on missing or poorly known contributions, such as the unsurveyed deep ocean or the still uncertain land water component. In the context of the World Climate Research Programme Grand Challenge entitled “Regional Sea Level and Coastal Impacts”, an international effort involving the sea level community worldwide has been recently initiated with the objective of assessing the various data sets used to estimate components of the sea level budget during the altimetry era (1993 to present). These data sets are based on the combination of a broad range of space-based and in situ observations, model estimates and algorithms. Evaluating their quality, quantifying uncertainties and identifying sources of discrepancies between component estimates is extremely useful for various applications in climate research. This effort involves several tens of scientists from about sixty research teams/institutions worldwide (www.wcrp-climate.org/grand-challenges/gc-sea-level). The results presented in this paper are a synthesis of the first assessment performed during 2017-2018. We present estimates of the altimetry-based global mean sea level (average rate of 3.1 +/- 0.3 mm/yr and acceleration of 0.1 mm/yr2 over 1993-present), as well as of the different components of the sea level budget. We further examine closure of the sea level budget, comparing the observed global mean sea level with the sum of components. Ocean thermal expansion, glaciers, Greenland and Antarctica contribute by 42%, 21%, 15% and 8% to the global mean sea level over the 1993-present. We also study the sea level budget over 2005-present, using GRACE-based ocean mass estimates instead of sum of individual mass components. Results show closure of the sea level budget within 0.3 mm/yr. Substantial uncertainty remains for the land water storage component, as shown in examining individual mass contributions to sea level.
DOI: 10.17882/54834
title: Experimental clay-laden density flow velocity and deposit data from the Eurotank laboratory

description: This dataset contains flume experiment data from a series of runs that were performed at the Eurotank laboratory of Utrecht university. It includes velocity data as well as photographs that were taken from the deposits emplaced by the density flows inside the flume. The flume was 3.7 m long, 0.22 m wide, and 0.5 m high with glass side walls. For the experiments, the slope was adjusted to 6, 8, and 9.5 degrees. Before the runs, mixtures composed of 1) sand, silt, clay, and water or, 2) sand, clay, and water, were prepared and stirred for approximately 30 minutes to 2 hours in a 0.45 m3 mixing tank and the flume was filled with tap water. The sediment volume concentration was varied between 9%, 15%, and 21% and contained 2/3 sand and 1/3 clay for the runs without silt and 1/3 sand, 1/3 silt, and 1/3 clay, for the runs including silt. The mixtures were then pumped with a discharge rate of 10 or 15 m3/h into the flume. Velocity data was obtained using two Ultrasonic Doppler Velocity Profiler probes (UVP Duo Mx, 1 MHz) which were placed at 0.7 m and 2.7 m distance from the inlet, at a height of 0.11 m above the bed, and with an abgle of 60 degree to the bed, facing up stream. This dataset was used in Hermidas et al., 2018 to classify clay-rich subaqueous density flow structures.
DOI: 10.17882/54563
title: Benthic biodiversity of the tidal test site of Paimpol-Bréhat assessed by video imagery

description: Marine tidal energy technology is still in its infancy in France and potential environmental impacts on the seabed are virtually unknown. The first French pilot project is currently launched close to Paimpol and the Bréhat Island (Brittany). Environmental monitoring has started in 2012 to assess the baseline of benthic compartment before deployment and the grid-connections of the 4 turbines. The Paimpol-Bréhat tidal site is located on a hard rocky bottom where conventional benthic survey techniques are unsuitable. This paper describes the methodology used to assess the initial state of benthic communities on the turbines and cable deployment area and presents the first results of the mapping and monitoring of the targeted benthic ecosystem.
DOI: 10.17882/54118
title: Biomass and isotopic data for fish community on artificial reefs in the Bay of Marseille

description: This dataset gather (1) fish biomass data on artificial reefs in the bay of Marseille collected during seasonal underwater surveys performed between November 2008 and 2015 and (2) stable isotope ratios for fish species collected also on artificial reefs in the bay of Marseille in summer and winter 2010.
DOI: 10.17882/52864
title: Codes used to study the Crassostrea gigas oyster transcriptome response to Alexandrium exposure

description: R scripts written for differential analysis and regression analysis to investigate the molecular basis of Paralytic Shellfish Toxins load in the oyster Crassostrea gigas exposed to the toxigenic alga Alexandrium minutum. Differentially expressed genes were analyzed with R (version 3.2.3, Gentry et al. (2004) Genome Biol 5:R80) using the packages DESeq2 (version 1.10.0; Love et al. (2014) Genome Biol 15:1-21) and edgeR (version 3.12.0, Robinson et al. (2010) Bioinformatics 26:139-140). Elastic-net regression was run with R using the package glmnet (version 2.0-2, Friedman et al. (2010) J Stat Softw 33:1-22).
DOI: 10.17882/52803
title: Morphological measurements for O. cyanea derived from visual strip transects and commercial catch sampling in Lakshadweep islands, India

description: The data comes from O. cyanea derived from visual strip transects and commercial catch sampling carried out around Agatti and Kavaratti islands (Arabian Sea) during three survey periods between November 2008 and 20 April 2012. Given that octopus fisheries in these islands are constrained by depth owing to the nature of spear-fishing and gleaning techniques (Silas et al., 1985; Appukuttan et al., 187 1989), we surveyed only the lagoon and intertidal areas of the two islands. The depths of the surveyed areas varied from 0.5 to 3 m. Mantle length (ML = dorsal mantle length) was measured using a 1 mm graduated 210 tape and weight (TW = total body weight) was obtained using a spring balance graduated with 50 g intervals.
DOI: 10.17882/52798
title: Historical water level data in the Gironde Estuary

description: Times series of water level at four stations of the Gironde Estuary (Pointe de Grave, Le Marquis, Bordeaux and Cadillac) for the the years 1953, 1971, 1982, 1994, 2005 and 2014. The dataset includes all of the time seris used in the publication: To what extent multidecadal changes in morphology and fluvial discharge impact tide in a convergent (turbid) tidal river (2018), Journal of Geophysical Research: Oceans.
DOI: 10.17882/52522
title: French Marine Economic Data : salt production

description: Salt production in France is documented using structural business statistics published by INSEE National Statistical Institute. This permits to build key figures related to the activity. International benchmarking in terms of production tonnage is based on the US Geological Survey. Both data sets are available online from INSEE and USGS.
DOI: 10.17882/52435
title: Raw data from a wide-angle seismic survey in the Ionian Sea and the eastern Sicily Margin

description: The origin of the Ionian Sea lithosphere and the deep structure of its margins remain a little investigated part of the Mediterranean Sea. To shed light on the plate tectonic setting in this central part of southern Europe, R/V METEOR cruise M111 set out to acquire deep penetrating seismic data in the Ionian Sea. M111 formed the core of an amphibious investigation covering the Ionian Sea and island of Sicily. A total of 153 OBS/OBH deployments using French and German instruments were successfully carried out, in addition to 12 land stations installed on Sicily, which recorded the offshore air gun shots. The aim of this onshore-offshore study is to quantify the deep geometry and architecture of the Calabria subduction zone and Ionian Sea lithosphere and to shed light on the nature of the Ionian Sea crust (oceanic crust vs. thinned continental crust). Investigating the structure of the Ionian crust and lithospheric mantle will contribute to unravel the unknown ocean-continent transition and Tethys margin. Analyzing the tectonic activity and active deformation zones is essential for understanding the subduction processes that underlie the neotectonics of the Calabrian subduction zone and earthquake hazard of the Calabria/Sicily region, especially in the vicinity of local decoupling zones.
DOI: 10.17882/52260
title: Preparing 1967-1986 historical Albacore data for a return to the ICCAT format and database IFREMER Halieutic Information System

description: In 1967, E.Postel, researcher at the OSTPM (Scientific and Technical Office for Maritime Fisheries) set up a data collection system on albacore catches by French fleets. JC Dao and FX Bard continued this work within CNEXO (National Center for the Exploitation of Oceans) and then at IFREMER from 1984. This information was transmitted by fishing professionals via logbooks, on the basis of volunteering (Dao, 1971, Bard, 1977). In 1982, the European Community put in place a mandatory system of declarations of fishing effort and catches via logbooks (EC Regulation No. 2057 in Sanchez and Santurtun, 2013). As a result, the two systems persisted between 1982 and 1986, with European logbooks gradually supplanting logbooks
DOI: 10.17882/51795
title: PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements

description: To date, genome assembly of non-model organisms is usually not at chromosomal level and higly fragmented. This fragmentation is recognized to be, in part, the result of a bad assembly of the transposable elements (TEs) copies, increasing the difficulty to detect and annotate them. In this context, we designed a new bioinformatics pipeline named PiRATE for detect, classify and annotate TEs of non-model organisms. PiRATE combines multiple analysis packages representing all the major approaches for TE detection. The goal is to promote the detection of complete TE sequences of every TE families. The detection of complete TE sequences, bearing recognizable conserved domains or specific motifs, allows to facilitate the classification step. The classification step of PiRATE has been optimized for algal genomes. Each tools used by PiRATE are automated into a stand-alone Galaxy. This PiRATE-Galaxy can be used through a Virtual Machine, which can be download below. This PiRATE-Galaxy is a suitable and flexible platform to study TEs in the genome of every organisms. You can find a tutorial below. Please contact us if you have any issues or comments : berthelier.j [at] laposte.net or gregory.carrier [at] ifremer.fr or you can leave a message on Github: https://github.com/JBerthelier/PiRATE/issues
DOI: 10.17882/51704
title: SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata

description: Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families. Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low Ne due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies.