cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17882/91064
title: Historical database: French Fishery National Statistics from 1901 to 1979: English Channel crustacean fisheries report

description: The MECANOR² FEAMP project (2020-2023) focused on the eastern English Channel whelk and crustacean trap fisheries. An historical approach has been developped to collect information on three crustacean species’ (lobster, Homarus gammarus, edible crab, Cancer pagurus, and spider crab, Maja brachydactyla) past dynamics. To achieve these objectives the annual reports from the French National Fishery Statistics have been banked to analyse fisheries trends. This banking was adapted by sequences to follow changes in spatial scale and species identification precisions. The following document informs choices that have been made when creating this database to ease its use.
DOI: 10.17882/91023
title: Data applied to automatic method to transform routine otolith images for a standardized otolith database using R

description: Fisheries management is generally based on age structure models. Thus, fish ageing data are collected by experts who analyze and interpret calcified structures (scales, vertebrae, fin rays, otoliths, etc.) according to a visual process. The otolith, in the inner ear of the fish, is the most commonly used calcified structure because it is metabolically inert and historically one of the first proxies developed. It contains information throughout the whole life of the fish and provides age structure data for stock assessments of all commercial species. The traditional human reading method to determine age is very time-consuming. Automated image analysis can be a low-cost alternative method, however, the first step is the transformation of routinely taken otolith images into standardized images within a database to apply machine learning techniques on the ageing data. Otolith shape, resulting from the synthesis of genetic heritage and environmental effects, is a useful tool to identify stock units, therefore a database of standardized images could be used for this aim. Using the routinely measured otolith data of plaice (Pleuronectes platessa; Linnaeus, 1758) and striped red mullet (Mullus surmuletus; Linnaeus, 1758) in the eastern English Channel and north-east Arctic cod (Gadus morhua; Linnaeus, 1758), a greyscale images matrix was generated from the raw images in different formats. Contour detection was then applied to identify broken otoliths, the orientation of each otolith, and the number of otoliths per image. To finalize this standardization process, all images were resized and binarized. Several mathematical morphology tools were developed from these new images to align and to orient the images, placing the otoliths in the same layout for each image. For this study, we used three databases from two different laboratories using three species (cod, plaice and striped red mullet). This method was approved to these three species and could be applied for others species for age determination and stock identification.
DOI: 10.17882/90901
title: Bern3D-LPX simulations with the adaptive emission reduction approach (AERA)

description: The files provide the model output from Bern3D-LPX forced with the Adaptive Emission Reduction Approach (AERA) that are presented in Terhaar et al. (2022). The AERA allows to develop time series of CO2 forcing equivalent emissions that allow the global warming to converge to a given temperature target. The simulations here include the standard simulations as well as the simulations with (i) variying non-CO2 radiative agent trajectories, (ii) using GWP-100 instead of CO2 forcing equivalent emissions, as well as (iii) various roubstness tests of the AERA. The simulations demonstrate that the AERA works robustly and that it can be used for policy decisions. Each simulations follows the same name structure: The file names follow this structure: AXX_YYYY_Z AXX describes the model configuration, the first number stands for diapycnal mixing (1=1e-4 m2 s-1, 2 =2e-5 m2 s-1, 3=1e-4 m2 s-1), the second for the feedback parameter lambda in Bern3D (1=0.1 W m-2 K-1, 2=-0.3 W m-2 K-1, 3=-0.7 W m-2 K-1). YYYY describes the run and the interannual variability. The first two digits are without a special meaning and just give the run numbers, the standard is ‘11’. The third number is the phasing of the superimposed inter-annual variability (1=0 years, 2=50 years, 3 = 25 years, 4=75 years) and the third says if the variability is added (0) or subtracted (1). Z is the temperature target: 1 is 1.5°C, 2 is 2.0°C and 4 is 1.75°C until 2050 and 1.5°C in 2100. For more information, please read through the associated publication and GitHub repository (https://github.com/Jete90/AERA).
DOI: 10.17882/90833
title: Activity and consistency of a marine gastropod behaviour, Haliotis tuberculata, is strongly modified in the absence of a shelter

description: Objective : The presence of a shelter is often not included in enclosure housing of experimental animals, especially in mollusc. The objective of this experiment was (1) to study how the presence of a shelter would affect the activity and foraging behaviour; (2) to evaluate if the consistency of individual behaviour over time would alter in the presence or absence of this shelter, in a marine gastropod, Haliotis tuberculata. Methodology : A total of 48 adult european abalone were placed individually in holding aquaria, where half of the aquaria contained crevices to shelter in, and the other half had no shelter. After gently detaching them with a spatula, a reflective tag was glued with cyanoacrylate gel. One abalone was placed in the middle of each aquarium. All tanks were continuously videotaped for 7 days using a digital camera linked to a 24h-recording device. Algae Palmaria palmata was provided ad libitum in the open area. The videos were analysed at 16 times normal speed and slowed to four times when necessary. This procedure was repeated 4 times in total (n = 12 abalone per repetition) during a one-month experiment. The following variables were calculated: total time spent moving and feeding, and number of movement and feeding bouts for each day and night period, and per day. A feeding bout corresponds to the presence of an abalone less than 2 cm from the algae with small movements of the algae observed. If an abalone initiated a movement for at least 2-min, and then came back to the algae, it was considered as another feeding bout. Results : There was a strong diurnal rhythm of abalone movement during this experiment. When an abalone began moving, it was usually to feed. Significant individual consistency was observed in locomotion as well as in foraging behaviour. However, the absence of a shelter in the experimental set-up it nearly tripled the time spent moving and doubled the number of moving bouts per day. In addition, it reduced the consistency of individual differences in foraging behaviour. Conclusion : This experiment highlights that it is important to include a shelter in the housing set-up if the species uses one in its ecological niche, including for mollusc species. The higher locomotion probably indicated a reduction of animal welfare with increased motivation to seek a refuge.
DOI: 10.17882/90776
title: observations on a flow through a contraction and over a bottom elevation in the Aegean Sea – East Mediterranean

description: A CTD/ADCP/surface-drifter survey in fall 2004 reveals the behavior of a mesoscale unidirectional flow coming from the Cretan sea in the south with depths ~1000 m and entering a channel-like area of the Cycladic shelf in the north that forms a contraction leading to a bottom elevation (sill depth ~100 m) and then a return into the Cretan Sea in the lee-side of the sill.
DOI: 10.17882/90671
title: Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryotes community structure along MIAU oceanographic cruise

description: Flow cytometry is one of the standard methods for abundance determinations of prokaryotes, picophytoplankton and viruses in aquatic environment; it is a very popular tool based on the simplicity of the protocols and the fast processing of samples. In a regular oceanographic cruise these abundance measures are collected through a Niskin bottle following a sample plan of stations spatially divided by e.g. kilometers. Nevertheless, precisely for its simplicity and velocity, flow-cytometry is a perfect tool for continuous measurements. Here we test the use of a continuous automated sampling machine (OC-300) connected to a flow-cytometer (Accuri-C6) to estimate abundance, relative size and phenotypic diversity of prokaryotes in marine surface waters every 15 min for 5 days during a short Mediterranean cruise. Sea-water was taken by a faucet linked to a continuum pump (5 m depth). Once taken the sample, the Oncyt-300 stains it and sends it to the flow-cytometer. Through this method we achieved a fine-grain scale view of microbial community composition both during space and during time. It is worth to highlight that it was also possible to keep measuring during a storm, a common event during a cruise, taking advantage of the entire duration of the cruise. The measured features (abundance and size) were associated with metadata (temperature, salinity, conductivity, etc) also taken in continuous and used to study the effect of the environment on microbial community structure. The dataset produced (which included the optical properties of every single cell measured) it is also perfectly tailored for application of cytometric fingerprinting which is used to understand how phenotypic diversity, based on populations with common optical properties, varies along space and time. The OC-300 has previously been used in bioreactors and culture experiment but this is the first time it is applied to the marine environment directly in MIAU oceanographic cruise. Due to its high-resolution, we foresee great potentiality to this application both, to cover large sampling areas and to in situ monitor day-night cycles.
DOI: 10.17882/90509
title: Chlorophyl-a datasets collected at the Rabnabad channel, upstream area of BoB (Bangladesh) from March 3rd to 6th 2022

description: These datasets were derived from the water samples obtained at the Rabnabad channel, which is located in the Bay of Bengal's upstream region. From March 3rd to 6th 2022, a detailed field survey was conducted. Chlorophyll – a (chl-a) measurements were taken from 32 water samples collected from eight different locations. The sampling was carried out with the help of the Payra Port's vessel 'SAGOR JATRA-1.' Water samples were collected from various depths using a Niskin sampler of HYDRO-BIOS with a non-metallic interior. To obtain in-situ data, water samples were tested in the laboratory according to conventional procedures. In this channel, a large community relies on fishing as a means of their livelihood. Understanding the chlorophyll status in this region is crucial because it forms the basis of the food web and serves as an indicator of primary production, which in turn influences secondary output. In order to isolate the pigments from this murky upstream location, a trustworthy extraction technique need to be identified.
DOI: 10.17882/90241
title: Analyses of the composite yield per recruit model CYPR14: Input parameters, R scripts, and outputs for the application species

description: Growth parameters, R scripts, and analysis outputs that were the basis of the paper Munyandorero –Analyses of the composite yield per recruit model CYPR14 for inferring plausible fishing mortality targets of fish in the tropics, are provided for the application species, Lake Tanganyika’s Lates stappersii and Lake Victoria’s Lates niloticus. The file “ReadMe.txt” found in the “Rprogs” folder may be of interest for an analysist who would run the various R scripts. For further methodological information, please refer to the full paper published at Aquatic Living Resources.
DOI: 10.17882/90028
title: Piecewise trends and discontinuities in GNSS and SATTG time series

description: This dataset contains estimates of piecewise trends and discontinuities in vertical land motion (VLM) time series. The time series are based on two techniques, the Global Navigation Satellite System (GNSS) and differences of satellite altimetry and tide gauge measurements (SATTG). SATTG data are based on monthly PSMSL tide gauge observations (Permanent Service for Mean Sea Level, Holgate et al. [2013]) and multi-mission satellite altimetry from DGFI-TUM. The coastal along-track altimetry SLA data feature latest corrections and adjustments, as well as coastal retracking (using the ALES retracker (Passaro et al., 2014)). The GNSS time series are obtained from the Nevada Geodetic Laboratory (NGL) of the University of Nevada (Blewitt et al. [2016], http://geodesy.unr.edu). This dataset contains information of piecewise trends, uncertainties, as well as discontinuity epochs and sizes in 606 SATTG and 381 GNSS time series. These parameters are estimated with a Bayesian change point detection method (DiscoTimeS), as described in ‘Bayesian modelling of piecewise trends and discontinuities to improve the estimation of coastal vertical land motion’.
DOI: 10.17882/90025
title: Bathymetry data from the R/V Ramon Margalef echosounder (2013)

description: In the framework of the R/V R. Margalef (Spanish Institute of Oceanography, IEO-CSIC) field works and alongtrack navigation, a continuous singlebeam echosounder was used in order to measure the depth along its trajectory. These data were mainly held around Spanish territorial waters. During the ship trajectory, the echosounder was receiving and integrating bathymetry data and GPS position. All the data recorded were checked for quality control in a semi-automatic standard procedure and stored in MEDAR/MEDATLAS-SDN format.
DOI: 10.17882/90016
title: Hauling data for fyke net in crayfish fisheries

description: This dataset consists of hauling data for fyke net in Turkish crayfish fisheries. The experiment was designed by covered-codend method. Shared dataset includes hauling data for commercial and newly-designed fyke nets by different seasons.
DOI: 10.17882/89892
title: Reconstruction of land-sea DTMs at several geological periods: Example of the Mozambique Channel and Madagascar

description: We present here the methodology used to reconstruct six paleobathymetric and paleotopographic grids for six periods of age (~70, 66-60, ~45, 36-30, ~20, 12-5 Ma) based on the compilation of published onshore and offshore structural and sedimentary data. We provide xyz format (WGS84, z in metres) of the reconstructed geometry of the Mozambique Channel as well as the paleo-elevations of the East Africa and Madagascar landscapes. The compilation is beneficial both to the scientific community working in sedimentation, tectonics and for oceanographic modelling.
DOI: 10.17882/89718
title: Telemetry data obtained from Fastloc GPS/GSM tracking of 14 harbour seals (Phoca vitulina) captured in Baie des Veys in 2020 and 2021

description: Tracking data of 14 harbour seals were obtained from the deployment of Fastloc GPS/GSM tags developed by the Sea Mammal Research Unit (UK). Full tag description is available at: http://www.smru.st-andrews.ac.uk/Instrumentation/GPSPhoneTag/. The tags include a wet-dry sensor from which haulout events are recorded, a pressure sensor providing detailed dive data, as well as a Fastloc GPS recording irregular locations when the seal is not underwater. Data is stored onboard and transmitted via the GSM network when the seal is in the reception range. The data provided here are the individual GPS locations of the seals fitted with these tags for an average duration of 102 days.
DOI: 10.17882/89715
title: Telemetry data obtained from Fastloc GPS/GSM tracking of 15 harbour seals (Phoca vitulina) and 12 grey seals (Halichoerus grypus), captured in Baie de Somme in 2019

description: Tracking data of 15 harbour seals and 12 grey seals were obtained from the deployment of Fastloc GPS/GSM tags developed by the Sea Mammal Research Unit (UK). Full tag description is available at: http://www.smru.st-andrews.ac.uk/Instrumentation/GPSPhoneTag/. The tags include a wet-dry sensor from which haulout events are recorded, a pressure sensor providing detailed dive data, as well as a Fastloc GPS recording irregular locations when the seal is not underwater. Data is stored onboard and transmitted via the GSM network when the seal is in the reception range. The data provided here are the individual GPS locations of the seals fitted with these tags for an average duration of 106 days.
DOI: 10.17882/89642
title: Hydrographic data from the south-bound Drake 2006 section

description: An hydrographic section with closely spaced stations (12 nm distance) was performed across the Drake Passage during the DRAKE 2006, ANT-XIII/3 cruise on board RV Polarstern on her way south from Punta Arenas to Jubany station (King-George Island). The section acquired during 16 - 26 January 2006 follows ground track #104 of Jason altimetry satellite. Thus, the section runs parallel to the Shackleton Fracture Zone and crosses the Yaghan Basin and the Ona Basin. The data set comprises the 51 full-depth CTD stations of the south-bound section. The data were obtained with a Sea-Bird Electronics SBE 9/11+ with a 24 Hz sampling frequency. At the end of the cruise, the CTD sensors were sent to Sea-Bird Company for calibration. Conductivity and temperature sensor drifts were negligible (respectively, less than 10–5 S m−1 per year and less than 310–4 K per year). Salinity derived from the CTD measurements was compared with the salinity of samples taken from the water bottles, measured by Guildline-Autosal-8400 salinometer that was adjusted to IAPSO Standard Seawater. The data quality for salinity is better than ±0.002 and for temperature better than ±0.001 K. The data processed with Sea-Bird processing software have a vertical resolution of 0.1 m.
DOI: 10.17882/89630
title: Spatial distribution of megabenthic communities and associated diversity in Cap de Creus continental shelf and submarine canyon (NW Mediterranean)

description: In 2014, the continental shelf and submarine canyon off Cap de Creus (NW Mediterranean) were included in the Site of Community Importance (SCI) “South-West Gulf of Lions canyons system” of the Natura 2000 Network of protected areas. Before the declaration of the SCI (2007-2103), 60 underwater video transects were performed in the area by means of ROVs and a manned submersible, covering more than 30 km of seafloor. Based on the annotation of the video images, we identified the main invertebrate megabenthic communities dwelling from the shelf (70 m depth) down to the bottom of the canyon head (400 m depth). The results of the multivariate analyses indicated that this marine area hosted several benthic communities dominated by suspension- and filter-feeding species, including octocoral gardens, soft-coral assemblages, crinoid fields, sponge grounds and cold-water corals. This dataset includes (1) the geographical location of the benthic communities identified in the video footage, as determined by the clustering analysis, (2) the intra-community diversity associated to the benthic communities, provided as the number of megafauna species identified in each sampling unit and the exponential of Shannon, and (3) the spatial distribution of the benthic communities mapped by means of the Random Forest classification algorithm. This dataset is related to the article “Diversity, structure and spatial distribution of megabenthic communities in Cap de Creus continental shelf and submarine canyon (NW Mediterranean)” submitted to Progress in Oceanography by Dominguez-Carrió et al., which contains further information on how the data were obtained and processed.
DOI: 10.17882/89623
title: Geochemistry of benthic foraminifera grown under different carbonate system conditions

description: Insights into past marine carbon cycling and water mass properties can be obtained through controlled laboratory experiments with accurate seawater carbonate system (C-system) manipulations. Here, we explored the use of strontium/calcium ratio (Sr/Ca) of the calcite shells of benthic foraminifera as a potential seawater C-system proxy through a controlled growth experiment with two deep-sea species (Bulimina marginata and Cassidulina laevigata) and one intertidal species (Ammonia T6). To this aim, we decoupled carbonate chemistry in controlled growth experiments, i.e., changing pH at constant dissolved inorganic carbon (DIC) and changing DIC at constant pH. Four climatic chambers were used with different controlled concentrations of atmospheric pCO2 (180 ppm, 410 ppm, 1000 ppm, 1500 ppm). Our results demonstrated that low pH conditions (7.56-7.73) did not influence the survival and growth rates of the three species. However, low DIC conditions (879 µmol kg-1) negatively affected B. marginata and C. laevigata through low growth rate, whereas no effect was observed for Ammonia T6. Our results also showed a significant positive correlation between Sr/Ca and the C-system (DIC - bicarbonate ion concentration) for Ammonia T6 and B. marginata. For these two species, the regression models were coherent with published data (existing so far only for Ammonia T6) and showed overall similar slopes but different intercepts, implying species-specific effect. Furthermore, the Sr/Ca - C-system relationship was not impacted by ontogenetic trends between chamber stages, which is a considerable advantage for paleo-applications. However, no correlation with any of the C-system parameters was observed for Sr/Ca in C. laevigata. This might imply either a strong species-specific effect and/or a low tolerance to laboratory conditions leading to physiological stress, thereby impacting the Sr incorporation into the calcite lattice.
DOI: 10.17882/89590
title: Data for "Identifying priority areas to manage mobile bottom fishing on seabed carbon in the UK"

description: Associated data and R code for the paper Epstein & Roberts 2022 - Identifying priority areas to manage mobile bottom fishing on seabed carbon in the UK. This repository contains the primary output data from a desk-based investigation of seabed sediment organic carbon (OC) and mobile demeresal fishing in the UKEEZ. Best available published datasets were combined to produce unified maps of predicted seabed OC stocks, mean annual mobile bottom fishing disturbance, mean value of fish landed by mobile bottom fishing, and mean annual cummulative disturbance to seabed carbon from mobile bottom fishing. This data was combined with modeling of estimated fishing displacement to idenitfy priority areas for managmement and/or future research. For further methodological information please refer to the full paper published at PLOS Climate.
DOI: 10.17882/89557
title: Isotopic ratios of fish sampled around Mediterranean artificial reefs

description: This dataset gather replicated measurement of isotopic ratios measured for 32 fish species sampled in summer and winter 2010 around artificial reefs deployed in the Prado Bay in Marseille (43.27397N, 43.257969S, 5.371262E, 5.325944O).