cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17882/76429
title: Stable isotope ratios of eastern Mediterranean deep cold seep fauna (MEDECO cruise Napoli & Amsterdam mud volcanoes, 2007)

description: During the 2007 MEDECO cruise of RV Pourquoi Pas ? (Sarrazin & Pierre, 2007), https://doi.org/10.17600/7030090), biomass-dominant fauna was sampled in two deep-sea cold seep ecosystems: the Napoli and Amsterdam mud volcanoes (Eastern Mediterranean, depth range: 1939 - 2152 m). Stable isotope ratios of carbon, nitrogen and/or sulfur were measured in 129 samples belonging to 28 taxa, as well as surrounding sediments. Samples were identified, dissected in a cold room and frozen at -20°C on board, then brought back to the laboratory for further processing. Analytical measurements were performed at Iso-Analytical Limited laboratories, Crewe, United Kingdom (http://www.iso-analytical.co.uk/index.html). This data underlies the following paper: Carlier A., Ritt B., Rodrigues C.F., Sarrazin J., Olu K., Grall J. & Clavier J. (2010): Heterogeneous energetic pathways and carbon sources on deep eastern Mediterranean cold seep communities. Marine Biology 157 (11), 2545–2565 (2010), https://doi.org/10.1007/s00227-010-1518-1, https://archimer.ifremer.fr/doc/00016/12684/ The dataset consists of two files: one containing the data itself, and one describing all used terms (measurements or metadata).
DOI: 10.17882/76414
title: Seismic profiles from Limpopo Magma-rich transform margin

description: The continental rifted margins of Mozambique provide an excellent example of continental passive margins with a significant structural variability associated to magmatism and inheritance. Despite accumulated knowledge in this area, the tectonic structure and nature of the crust from Mozambique margins, especially the Limpopo transform margin are still poorly known. Here, we use high-resolution seismic reflection dataset and wells from industry topropose a structural interpretation of this area and a new conceptual model of oblique/hyper oblique margin. Our results indicate first that the Limpopo transform margin limits a continental crust westward, with deep Karoo grabens, from an oceanic crust domain eastward. Such fault controlled volcano-sedimentary basins result from two main tectonic events: a first E-W extension trend during the Permo-Trias (T1) followed by an NNW-SSE trending during the Jurassic (T2), oblique to the margin direction as attested by the presence of flower structures. The onset of oceanic spreading occurred then after ca. M25 (i.e. 156 Ma), triggering the uplift and erosion of the proximal parts of the margin as well as the formation of several other magmatic infilling (T3). This margin may be thus considered as magma-rich transform margin. Our new conceptual model from the onset of the rifted margin to the seafloor spreading shows a complex evolution where transtensional deformation contributes significantly to the distribution of magma generated. Such extensional pattern which is made of syn-transfer and - transform faults forming pull-apart structures becomes more important with time.
DOI: 10.17882/76328
title: Processed data from the Ocean Observatory Initiative array in the Argentine Basin

description: The Argentine Basin array was part of the National Science Foundation’s (NSF) Ocean Observatories Initiative (OOI; http://www.oceanobservatories.org). The Argentine Basin (AB) array was deployed and maintained at 42°S 42°W, in international waters. Moorings were deployed for the first time in March 2015. The mooring site was then visited in three other opportunities: October 2015, September 2016 and January 2018. Moorings were recovered and redeployed at the same position in 2015 and 2016 . January 2018 was the end of operations in the Argentine Basin with the final mooring recovery. In addition, in each expedition CTD casts with water sampling at the mooring sites were performed for instrument calibration and data verification. This data set include 3 years of processed temperature and salinity data from Ocean Observatory Initiative Argentine Basin from the three deployments (d1,d2 and d3). Users are referred to the data processing report for further details on the data treatment.
DOI: 10.17882/76298
title: Wide-angle seismic velocity models from the Grenada Basin

description: The Grenada back-arc basin is located between the Aves Ridge, which hosted the remnant Early Paleogene “Great Caribbean Arc”, and the Eocene to Present Lesser Antilles Arc. Several earlier studies have proposed different modes of back-arc opening for this basin, including N-S and E-W directions. The main aim of this study is to constrain the circumstances leading to the early opening of the basin. Three combined wide-angle and reflection seismic profiles were acquired in the Grenada basin. The final velocity models from forward and gravity modeling image variations in thickness and velocity structure of the sedimentary and crustal layers. The sedimentary cover has a variable thickness between one kilometer on top of the ridges to ~10 km in the basin. North of Guadeloupe Island, the crust is ~20 km thick without significant changes between the Aves Ridge, the Eocene and present Lesser Antilles volcanic arc. South of Guadeloupe Island the Grenada basin is underlain by a 6.5-7 km thick oceanic crust of mainly magmatic origin over a width of ~80 km. Here,the western flank of the Lesser Antilles Arc, the crust is 17.5-km thick. The velocity structure of the Lesser Antilles Arc is typical of volcanic arcs or oceanic plateaus. West of the basin, the crust thickens to 25 km at Aves Ridge in a 80-100 km wide arc-ocean transition zone. The fact that this transition zone is narrow suggests that opening might have proceeded in a direction oblique to the main convergence. Opening probaly was accompanied by moderate volcanism.
DOI: 10.17882/76103
title: DNA barcoding campaign in a fish market in the Northern Red Sea provides clues for cryptic speciation and fishing form close geographical areas or bottle-necked populations

description: Herein, a pilot, random sampling trial was carried out to characterize and assess some genetic population parameters for fish species in the landings reaching the market in Suez city, Egypt. The Samples were DNA barcoded using the mitochondrial cytochrome oxidase subunit 1 mitochondrial gene (COI). DNA barcoding could characterize 9 species belonging to 7 different families and 3 orders. These species were Coris aygula, Papilloculiceps longiceps, Priacanthus sagittarious, Gerres longirostris, Alepes djedaba, Psettodes erumei, Cheilinus trilobatus, Calotomus viridescens, and Pardachirus marmoratus. Moderate haplotype, yet low genetic, diversities could be identifies in the first six species. This might be secondary to their fishing from bottlenecked populations, or from areas that do not hinder the genetic flow. Also, possible cryptic speciation could be detected in P. sagittarius, P. erumei and G. longirostris. The current study pointed to the power of DNA barcoding as a tool for identifying the state of biodiversity in fished populations, and the taxonomic richness of Red Sea fish-based markets.
DOI: 10.17882/75983
title: Data on growth during very early life stages of European sea bass (Dicentrarchus labrax L.)

description: The European sea bass (Dicentrarchus labrax) displays female-biased sexual size dimorphism early in development. To generate this dataset, we produced an experimental population by artificial fertilization and followed a rearing-temperature protocol (~16 °C from hatching to 112 days post-hatching, dph; ~20 °C from 117 to 358 dph) targeting a roughly balanced sex ratio. The fish were tagged with microchips between 61 and 96 dph in five tagging trials of 50 fish each; individual standard length (SL) was recorded through repeated biometric measurements performed between 83 to 110 dph via image analyses. Body weight (BW) was modelled using the traits measured on the digital pictures (i.e. SL, area, height, perimeter and volume). At 117 dph, the fish were tagged with microtags and regularly measured for SL and BW until 335 dph. The experiment ended at 358 dph with the sexing of the fish. The present datasets include the sex and the repeated biometric measurements of body weight, standard length and daily growth coefficient (DGC) of the animals between 83 to 335 dph.
DOI: 10.17882/75810
title: Growth and transgenerational acclimatization of juvenile Pocillopora damicornis

description: Global carbon emissions and associated increase in ocean temperatures are understood to be the main driving force in the degradation of coral reefs. Elevated temperatures impact various life stages of scleractinian corals, from the free-floating planulae of brooding corals to older, sexually viable individuals. With global warming, questions have arisen over whether organismal adaptation will be enough to keep up with the pace of environmental change. Researchers have pursued investigations of whether or not rapid acclimatization, through transgenerational plasticity, can help protect populations until genetic adaptation occurs. Acclimatization in corals has been widely studied in all life stages of corals, with the important exception of recently settled juveniles. In this study, I built upon past research by exposing adult Pocillopora damicornis colonies to elevated (28.5ºC) or ambient (25.5ºC) temperatures and examining the settlement ability and growth of their planulae ex situ. Juveniles from preconditioned parents fared better in higher temperatures compared to their naïve counterparts. Lunar timing of planula release between treatments peaked at different times in the lunar cycle. Peak planula release occurred on lunar day 23 for prestressed corals and on lunar day 7 for corals from ambient temperature seawaters. While future projects should follow up on these preliminary trials with in situ experiments to assess this phenomenon in the field, this study represents an important step in understanding how corals may be able to acclimatize and eventually adapt to climate change.
DOI: 10.17882/75706
title: Realised niche and suitability index of toxic phytoplankton species. Dataset

description: Understanding the spatial and temporal preferences of toxic phytoplankton species is of paramount importance in managing and predicting harmful events in aquatic ecosystems. In this study we address the realised niche of the species Alexandrium minutum, Pseudo-nitzschia fraudulenta and P. australis. We used them to highlight distribution patterns at different scales and determine possible drivers. To achieve this, we have developed original procedures coupling niche theory and habitat suitability modelling using abundance data in four consecutive steps: 1) Estimate the realised niche applying kernel functions. 2) Assess differences between the species’ niche as a whole and at the local level. 3) Develop habitat and temporal suitability models using niche overlap procedures. 4) Explore species temporal and spatial distributions to highlight possible drivers. Data used are species abundance and environmental variables collected over 27 years (1988-2014) and include 139 coastal water sampling sites along the French Atlantic coast. Results show that A. minutum and P. australis niches are very different, although both species have preference for warmer months. They both respond to decadal summer NAO but in the opposite way. P. fraudulenta realised niche lies in between the two other species niches. It also prefers warmer months but does not respond to decadal summer NAO. The Brittany peninsula is now classified as an area of prevalence for the three species. The methodology used here will allow to anticipate species distribution in the event of future environmental challenges resulting from climate change scenarios.
DOI: 10.17882/75703
title: Observation of deep near-inertial waves using PDS-CPIES in the western Arctic Ocean

description: Notable spatial and temporal variability of near-inertial waves in the western Arctic Ocean is observed from direct deep current measurements. The deep current is about 50 m above the bottom. The current-meter measures a speed range of 0 to 300 cm/s with direction using an Aanderaa Data Instruments Doppler current sensor. All current data is acquired through pop-up data shuttle (PDS); AES2, AES5, AES6 : 1 year, AES3: 2 year, AES1 and AES4: no available data). After removing the four major semidiurnal tides from the current measurements, a third-order Butterworth phase-preserving band-pass filter with cutoff frequency at 0.9–1.1f is applied to extract NIW signals. Bouyancy frequency (N) is calculated from the CTD data casted from RV Araon and RV Sikuliaq.
DOI: 10.17882/75696
title: Genotyping of 4 European sea bass families with the DlabCHIP SNPs genotyping array

description: Four experimental backcross full-sib families (378, 454, 291 and 211 individuals) were produced by in vitro fertilization at Ifremer (Palavas-les-Flots, France). All 1334 individuals were genotyped with a ThermoFisher AxiomTM Sea Bass 57k SNP DlabChip at the genotyping platform Gentyane (INRAE, Clermont-Ferrand, France). SNP calling was done using ThermoFisher software AxiomAnalysisSuiteTM. Preliminary quality controls were applied with threshold values of 95% for SNP call rate and 90% for sample call rate.
DOI: 10.17882/75680
title: Axiom DlabCHIP, a 57K SNPs genotyping array for European sea bass (Dicentrarchus labrax): array design and genetic map

description: We describe the development and characterization of the first high-density single nucleotide polymorphism (SNP) genotyping array for the European sea bass (Dicentrarchus labrax). This Axiom® sea bass Genotyping Array includes 56730 markers and is available in 384 format. To design this array, SNPs were selected from ~2.6 million SNPs identified through whole-genome resequencing of 8 parents-offspring trios generated by experimental crossing of wild sea bass by Duranton et al. 2018. From this database, only SNPs located more than 30bp away from another known variant were selected in order to ensure a high probe specificity. The final set of variants were chosen to cover the whole genome (including ungrouped scaffolds), but with a variable density of SNPs depending on the estimated local nucleotide diversity (π) reported by Tine et al. (2014). This strategy aimed at increasing the density of SNPs within chromosome regions displaying a higher recombination rate. A genetic map was created with LepMap3 (Rastas, 2017). ThermoFisher AxiomTM Sea Bass 57k SNP DlabChip genotypes of 4 backcross families (including 378, 454, 291 and 211 individuals) were merged with another sea bass dataset composed of 880 individuals from 94 sires mated with 39 dams in three partial factorial designs. The resulting data set included 2232 individuals genotyped for 51179 markers. We ran the recommended procedure of LepMap3 with custom settings: 1% segregation distortion for Filtering2, a LOD score of 50 as well as a subset of 25% of the markers for SeparateChromosomes2, and LOD score of 30 for JoinSingles2All. We obtained a genetic map with 50001 markers mapped on 24 linkage groups (LG) inferred as 24 chromosomes.
DOI: 10.17882/75643
title: Trapped low frequency waves on the Northern Israeli continental shelf

description: Time series of sea level measurements from different instruments deployed around the Haifa Bay area are analyzed. All observations indicate the existence of persistent low frequency oscillations with periods corresponding to approximately one hour and half-an-hour. These oscillations are persistent throughout most of the year and reached maximal wave heights of around 30 cm, a comparable value to tidal variations, making these oscillations an important factor in determining the average sea level elevation. The work identifies the phenomenon as resonant trapped waves which are normal modes of the continental shelf extending from Haifa promontory to Achziv Canyon. Their temporal and spatial characteristics are learned through field measurement data analysis, wavelet analysis, numerical simulations and exploration of an analytic solution. Finally, possible mechanisms for the generation of these waves are discussed.
DOI: 10.17882/75444
title: Biological dataset for Pagrus pagrus fished along Southern Brazil

description: The data were obtained from a regular sampling program of industrial fisheries landings in Rio Grande, southern Brazil. The dataset presented is composed of: - Fishing gear with landing date, minimum and maximum depth of the catches in ech fishing trip.. - Individual fish parameters of length, total weight, total, sex, age, maturity stage, gonad weight, gonadosomatic indices and allometric condition factor. - Type of the scales border and classification of the readability of the growth rings. During dock sampling, total length (TL), measured from the tip of the snout to the midpoint of the upper and lower limbs of the caudal fin, was recorded in mm, total weght. (TW) in grams, and sexed: (1) male, (2) female, (3) undetermined and (4) hermaphrodite. Specimens were classified from macroscopic examination as hermaphrodites when both testicular and ovarian tissues were present in the gonads and as males or females when all or most of the tissue was testicular or ovarian, respectively. Maturity stages were determined macroscopically with a seven-point scale: (1) virginal immature, (2) developing virginal, (3) developing, (4) advanced development, (5) running, (6) partly spent and (7) recovering. Gonads were weighted in grams (GW) and the average gonadosomatic indices were calculated as GSI = 100(GW/TW) . Allometric condition factors (K) were calculated as K = TW/TLb, where b is the coefficient of the weight-length relationship. For age determination, scales collected from behind the pectoral fin insertion. The readability of growth rings on the scales were classified as “well-marked”, “faint or absent” and “unreadable”. The position of the last ring relative to the posterior border of the scales were classified a (1) recently formed near the border, or (2) more distant of the border.
DOI: 10.17882/75434
title: Effect of temperature on the unimodal size scaling of phytoplankton growth

description: Contrary to predictions of fundamental laws in biology, there are evidences that phytoplankton growth rates peak at intermediate cell sizes. However, it is still unknown if this pattern may result from the effect of experimental temperature. Here we test whether temperature affects the unimodal size scaling pattern of phytoplankton growth by 1) growing Synechococcus sp., Ostreococcus tauri, Micromonas commoda and Pavlova lutheri at 18℃ and 25℃, and 2) using thermal response curves available in the literature to estimate the growth rate at 25ºC as well as the maximum growth rate at optimal temperature for 22 species assayed previously at 18ºC. We also assess the sensitivity of growth rate estimates to the metric employed for measuring standing stocks, by calculating growth rates based on in vivo fluorescence, chlorophyll a concentration, cell abundance and biomass (particulate organic carbon and nitrogen content). Our results show that the unimodal size scaling pattern of phytoplankton growth, with a peak at intermediate cell sizes, is observed at 18℃, 25℃ and at the optimal temperature for growth, and that it prevails irrespective of the standing-stock metric used. The unimodal size scaling pattern of phytoplankton growth is supported by two independent field observations reported in the literature: i) a positive relationship between cell size and metabolic rate in the picophytoplankton size range and ii) the dominance of intermediate-size cells in nutrient-rich waters during blooms.
DOI: 10.17882/75415
title: nifH gene copy numbers of UCYN-A1, Trichodesmium and GammaA in the North Pacific Ocean

description: This dataset contains nifH gene copy numbers of three major marine diazotrophs (i.e. UCYN-A1, Trichodesmium and GammaA) in the surface layer of 519 stations in the North Pacific Ocean. The observation was conducted along 37 trans-Pacific transects between Japan and North America during 2014-2016 as part of the ship-of-opportunity observation operated by the Japanese National Institute for Environmental Studies (NIES). The detailed information of the observation is available at http://nc2.soop.jp/. The nifH gene copy numbers were estimated with quantitative PCR. Additionally, the sampling dates, locations, and physicochemical parameters of each stations are also included in this dataset.
DOI: 10.17882/75397
title: Bottom Water Temperature collected in Real-Time from Commercial Fishing Gear in Gulf of Maine and Southern New England Shelf

description: Dataset contains bottom temperature data from both fixed and mobile gear types (e.g. traps, trawlers, scallopers, long-liners) in the Gulf of Maine and the South New England Bight. The time series begins in 2015 and runs in real-time until today. The water depths range from 1- 900 meters. The variability associated with tidal, wind, seasonal, and inter-annual processes can be depicted at nearly all sites in this multi-year time series. This data was collected as part of the Environmental Monitors on Lobster Traps (eMOLT) project - a non-profit collaboration of industry, science and academics devoted to the monitoring of the physical environment of the Gulf of Maine and the Southern New England Shelf.
DOI: 10.17882/75396
title: Oceanographic data from fishing vessels

description: Data collected using compact IoT CTD and TD sensors mounted to commercial fishing gears. Dataset contains data from both fixed and mobile gear types. Vessels range from small scale vessels run by one person to factory trawlers. Temperature OEM accuracy is 0.05 °C or better. Automated QC procedures are in place, based upon the Argo program.
DOI: 10.17882/75394
title: Water Temperature collected from Trawl fishing vessels in Gulf of Maine and Southern New England Shelf

description: Dataset contains bottom temperature data from trawlers in the Gulf of Maine and the South New England Bight. These are ~one mile binned-averaged hourly ocean bottom temperatures obtained with thermistors attached to commercial fishing trawls. The Vemco Minilog instrument used in most cases is accurate to 0.2 degC. Since this is not reporting fast enough (90 seconds) to resolve the vertical structure, only the bottom values are reported here. The water depths range from 7- 456 meters. The variability associated with tidal, wind, seasonal, and inter-annual processes can be depicted at nearly all sites in this multi-year time series. This data was collected as part of the Environmental Monitors on Lobster Traps (eMOLT) project - a non-profit collaboration of industry, science and academics devoted to the monitoring of the physical environment of the Gulf of Maine and the Southern New England Shelf.
DOI: 10.17882/75373
title: Experimental investigation of the marine growth effect on the hydrodynamical behavior of a submarine cable under current and wave conditions

description: This document describes the experimental set-up of OMDYN2 and LEHERO-MG projects. The study seeks to quantify the impact of biofouing on the dynamic behavior of an underwater power cable by analysing the hydrodynamic coefficients, such as drag and added mass coefficients. Experiments carried out in the wave and current basin of IFREMER, located at Boulogne-sur-mer, allowed us to compare the dynamics of cylinder with or without roughness. The roughness studied concerns realistic marine growth and has therefore significantly bigger dimensions (like mussels) than roughness studied in the research literature on the subject. Tests are conducted using current only then horizontal oscillating movements and finally the combination of both.