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Collection of rasters and social ecological indicators for Zone Atelier Armorique
No full textOpen, world wide rasters (biogeoregions, land surface temperature, normalised difference vegetation index, population density and land cover) are cropped with respect to the polygon of the Zone Atelier Environmental Urban so as to compute indicators. This dataset contains the shapefile, rasters for variables BIOG (biogeoregion), LSTD (land surface temperature day), LSTN (land surface temperature night), NDVI (normalized difference vegetation index), GPW4 (population density), and LC (land cover) cropped with respect to the shapefile, and social ecological indicators for these variables computed as averages or quantiles
GICIM Data from Perou and Equateur
No full textThose data are selected from the fish collection database GICIM.
The file include all the data from the fish collection including freshwater and marine fishes from Equateur and Perou
Land cover maps of the Haut Vicdessos valley (Pyrenees, France) from 1942 until 2008
No full textLand cover maps made using visual interpretation from panchromatic aerial photographs segmented and classified using e-cognition.
The geometric quality of the map is identical to that of the ortophotoplan of the corresponding year. Raster data have also been converted to vector data
Locomotor performance and morphological measurements in Xenopus laevis individuals.
No full textThis dataset includes locomotor performance and morphological measurements of Xenopus laevis individuals. Locomotor performance data result from locomotor experiments (swimming speed; jump force; maximal distance covered, swim or jump). Morphological measurements were assessed using a calliper. More information are available in the article "Does aquatic performance predict terrestrial performance: a case study with an aquatic frog, Xenopus laevis." Araspin et al., 2023, Journal of Experimental Biology
Exon-capture sequencing data of Turridae
No full textThis is the exon-capture data for the study "Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea)" (Molecular Phylogenetics and Evolution, https://doi.org/10.1016/j.ympev.2023.107969). This datasets consists in raw sequence Illumina reads (please check the M&M of the study for detailed protocol) and a table for sample/species name conversion
Campagne acoustique Roscoff Juin 2023
No full textLe projet ACaPELA (ACoustique PELagique) est un projet porté par le MNHN (Station marine de Dinard) et réalisé en collaboration avec l’IRD (UMR LEMAR) et PatriNat (OFB-CNRS-MNHN). Ce projet R&D a pour objectif de développer et valider la méthodologie de surveillance DCSMM pour l’évaluation de l’état écologique des populations et peuplements de poissons et céphalopodes (PCs) des milieux pélagiques côtiers, c’est-à-dire les espèces pélagiques ou bentho-pélagiques fréquentant la colonne d’eau (le pelagos) dans les zones dont la bathymétrie est comprise entre 0 et 40 m (zones dites côtières). Les protocoles d’échantillonnages proposés consistent à combiner l’utilisation de deux technologies d’acoustiques actives complémentaires, orientées verticalement : un sondeur large bande (Simrad EK80, 70, 120 et 200 kHz) et un sonar multifaisceaux (Simrad M3, 500 kHz). Cette campagne a été réalisée dans le cadre du projet ACaPELA, en Juin 2023, à bord du bateau de station Néomysis. Cette campagne a permis de réaliser des radiales acoustiques en baie de Morlaix, au départ de Roscoff, avec un focus sur les zones de petits fonds et le gradient côte-large. Ces enregistrements ont été complétés avec des enregistrements CTD (Conductivity-Depth-Temperature) à des points clefs identifiés au préalables
Nutrient concentrations in whole mesopelagic and ground fish from two campaigns (2005, 2010) in the Kerguelen area, southern Indian Ocean
No full textThe dataset contains dry weight nutrient concentrations (20 nutrients, calcium Ca, phosphorus P, sodium Na, potassium K, magnesium Mg, strontium Sr, iron Fe, zinc Zn, copper Cu, manganese Mn, selenium Se, arsenic As, nickel Ni, cobalt Co, molybdenum Mo, chromium Cr, cadmium Cd, vanadium V, silver Ag, lead Pb) measured on 264 individuals belonging to 34 forage fish species were collected during two ship-based sampling campaigns on and around the Kerguelen Plateau. The first sampling campaign took place on the eastern slope waters of the Kerguelen Islands (49°05’–49°20’S, 71°15’–72°15’E) on the 25 m-long La Curieuse vessel in January 2005, and aimed to sample the mesopelagic fauna. Fishing operations were carried out at night, with an International Young Gadoid Pelagic Trawl (IYGPT) with 12 m x 7 m opening and 10 mm cod-end mesh deployed for 30-min at constant speed, at depth varying from 50 to 425 m (Cherel et al. 2010, Duhamel et al. 2000). Most samples caught during this campaign (n = 167) were myctophids (n = 119). The second sampling campaign (named ’Poker 2’) took place from August to October 2010 on the 77 m-long trawler FV Austral. It focused on the demersal fauna and yielded the remaining 97 fish samples. Two hundred stations from shelf and deepsea habitats were sampled during 30-min day trawling operations using a bottom trawl (35 m headline/39 m footrope, reference: G2035013 from Le Drezen: www.ledrezen.com) with a 40 mm cod-end mesh (Duhamel et al. 2017). For both campaigns, fish were sorted on board after initial identification and then kept frozen at -20°C until processing. Identification was again confirmed before sample processing relying on fish external features using published guides (Hulley 1981) and our own reference collection. In 2021-2022, each fish was thawed, rinsed with ultrapure water, measured, weighed and ground in the laboratory in a clean and contamination-free setting before being stored at -20°C. All material was carefully rinsed with ultrapure water and ethanol between samples to avoid contamination. Samples were then freeze-dried for a minimum of 72 hours and ground to a fine powder until analysis. Total concentrations of major constitutive chemical elements in biological tissues (P, Ca, K, Na, Mg) were determined by inductively coupled plasma atomic emission spectrometry (ICP-OES, Vista-Pro Varian). Aliquots of samples (∼250 mg dry mass of homogenised powder) were digested using a 6:2 (v/v) mixture with nitric acid (HNO3 69%, Trace Metal Grade®, FisherScientific) and hydrochloric acid (HCl, 34%, Trace Metal Grade®, FisherScientific). Acidic digestion of the samples was performed over-night at room temperature and then in a microwave oven (START-D, Milestone). Finally, the digestats were diluted to 50 mL with ultrapure water before analyses with ICP-OES. Total concentrations of essential trace nutrients (As, Co, Cu, Fe, Mn, Ni, Se, Zn) were determined by inductively coupled plasma mass spectrometry (ICP-MS, ICAP-Qc ThermoFisher). Aliquots of samples (∼200 mg dry mass of homogenised powder) were placed in Teflon bombs and mineralized with a mixture of ultrapure HNO3 acid (PlasmaPure Plus grade, SCP Science®) and ultrapure water using a micro-wave (ETHOS-UP, Milestone). The digests were then diluted to 50 mL with ultrapure water before analyses with ICP-MS. The quality assurance of all metal analyses relied on blank and internal standard controls, and on the accuracy and reproducibility of data relative to the certified reference materials (CRMs) used in each analytical run. The CRMs used were TORT-3 (lobster hepatopancreas, National Research Council of Canada/NRCC) and DOLT-5 (dogfish liver, NRCC). Blank values were systematically below the detection limits, and CRM values concurred with certified concentrations and recovery rates ranged between 75% and 116% depending on the nutrients and the CRMs (they are provided in the dataset)
"An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla"
No full text[ENGLISH BELOW] Ce jeu de données est utilisé pour reproduire les analyses de l'article "An approximate likelihood..." et contient l'archive du matériel nécessaire. Les données brutes correspondent à 4 lots d'arbres phylogénétiques de mammifères téléchargés depuis les bases de données OrthoMam v10 (https://orthomam.mbb.cnrs.fr/) et UCSC Genome Browser (https://genome.ucsc.edu/). Les requêtes OrthoMam ont été passées manuellement en sélectionnant le type "exon" et en ne mettant aucun filtre sur les champs "relative evolutionary rate", "%GC3", "alpha shape", et "alignment length". La requête UCSC a été passée via le script ape_non_coding/download_all.bash
This dataset is used to reproduce the analyses in manuscript "An approximate likelihood...." and contains the archive of the necessary material. Raw data consist in 4 sets of phylogenetic trees downloaded from the OrthoMam v10 (https://orthomam.mbb.cnrs.fr/) and UCSC Genome Browser (https://genome.ucsc.edu/) databases. The OrthoMam database was queried manually, selecting type = "exon" and setting no filter on fields "relative evolutionary rate", "%GC3", "alpha shape", et "alignment length". The UCSC query was passed via script ape_non_coding/download_all.bas
Spatially extensive and temporally continuous three REVEALS pollen-based vegetation reconstructions in Europe over the Holocene.
No full textFossil pollen records are the best empirical data to provide natural (climate-induced) and anthropogenic (human-induced) past vegetation composition (H. H. Birks, 2008; H. J. B. Birks & Willis, 2008; Gaillard et al., 2010, 2018; Willis & Birks, 2006). Nevertheless, pollen percentages have a no-linear relationship with vegetation abundances due to plant species-specific differences in pollen production, dispersal, and deposition (Prentice, 1986; Sugita, 2007). These intertaxonomic differences are corrected by ‘Regional Estimates of VEgetation Abundance from Large Sites’ (REVEALS) model, taking into account two important parameters: relative pollen productivity and fall speed of pollen to infer plant cover. Currently REVEALS model is the most appropriate method to reconstruct plant cover at a regional spatial scale of ca. 100 x 100 km and it allows to transform pollen data from large lakes, but can also produce regional vegetation cover estimates from multiple small-sized sites (Fyfe et al., 2013; Mazier et al., 2012; Sugita, 2007; Trondman et al., 2015a).
REVEALS estimates of the abundance of 31 and 46 taxa, 10 plant functional types (PFTs), and 3 land-cover types (LCTs) were produced for Europe at a 1˚x1˚ spatial scale for 25 consecutive time windows from 11.7 ka calibrated years BP (i.e. before present (1950)) to present as part of the TERRANOVA project (H2020-MSCA-ITN-2018) grant agreement No 813904. This is the third generation (version march 2022) of REVEALS reconstructions in Europe, it was used a total number of 1607 pollen records from pollen databases/archives and individual authors (see TERRANOVA_metadata.xlsx and TERRANOVA_contributors.xlsx), and for the references related to the pollen records (see TERRANOVA_metadata_list_references.pdf). The first generation was published in Trondman et al., 2015 and Gaillard, 2019, and the second generation (Fyfe, Ralph M; Githumbi, Esther; Trondmann, Anna-Kari; Mazier, Florence; Nielsen, Anne Birgitte; Poska, Anneli; Sugita, Shinya; Woodbridge, Jessie; LandClimII contributors; Gaillard, Marie-JoséFyfe, Ralph M; Githumbi, Esther; Trondmann, Anna-Kari; Mazier, 2022). The REVEALS estimates are based on three RPP-means datasets: i) RPP-means dataset from (Githumbi et al., 2022), RPPs.st1 (31 taxa); ii) a new synthesis proposed in this study inclusive of strictly entomophilous taxa RPPs.st2 (46 taxa); iii) a composed synthesis, RPPs.st3 (31 taxa) derived (Mazier et al., 2012) RPP-means dataset combined with southern RPP studies (Githumbi et al., 2022; Grindean et al., 2019) (see TERRANOVA_RPP.sts_values _FSP_taxa_PFT_LCT.xlsx). All the details information can be found in Serge et al. in prep.
25-grid based estimates at 1°x1° (ca. 100 km x 100 km) across 30°-71° N, 20°W-47°E (north-western, central Europe, Mediterranean area and part of the East until 47°E) were produced. REVEALS results are extracted by time window, producing 25 matrices of mean REVEALS estimates and 25 matrices of corresponding mean SEs for each of RPP taxa and each grid cell. As three RPP-means datasets are tested, 3 REVEALS results are produced per time window (see TERRANOVA_RVresults_march2022.zip). It was used 25 time windows i.e. (-65) to 100 BP, 100 – 350 BP, 350 – 700, 700 – 1200, 1200 -1700 BP and in 500 consecutive time windows from here to 11,700 BP (BP – before present (1950)). The consecutive of 500-year-long time windows ensures that a maximum of the REVEALS reconstructions have low SEs and it is still meaningful for the study of past land-cover changes over several millennia (Githumbi et al., 2022; Li et al., 2023).
All REVEALS estimates and their SEs are given in proportions of the grid cell (the total of all REVEALS estimates sum up to 1). There are 25 files labelled TW.(number of time window).RVestimates.csv and 25 files labelled TW.(number of time window).standarderrors.csv. The RVestimates.csv files contain the REVEALS estimates for each land-cover type (LCT), plant function type (PFT) and taxa which has a unique grid ID and corresponding longitude and latitude. The standard error .csv files contain the standard errors for each land-cover type (LCT), plant function type (PFT) and taxa.
The information about the quality of the REVEALS estimates in each grid cell for each time windows is provided in the TERRANOVA_GC_quality_by_TW.xlsx file. There are 3 categories i.e. 1 is high quality (1 or more large lakes, OR 2 or more sites of any site type), 2 is low quality (only 1 small lake, OR small bog OR large bog) and no data. Extra information about each site is provided in the metadata file.
The third generation of pollen-based REVEALS land cover in Europe over the Holocene provides unique possibilities to explore spatial-temporal changes in past land cover and biodiversity over long time periods, to analyse the dynamic of the vegetation, for conservation ecology in the face of environmental changes
Campagne acoustique Saint Malo Mai 2023
No full textLe projet ACaPELA (ACoustique PELagique) est un projet porté par le MNHN (Station marine de Dinard) et réalisé en collaboration avec l’IRD (UMR LEMAR) et PatriNat (OFB-CNRS-MNHN). Ce projet R&D a pour objectif de développer et valider la méthodologie de surveillance DCSMM pour l’évaluation de l’état écologique des populations et peuplements de poissons et céphalopodes (PCs) des milieux pélagiques côtiers, c’est-à-dire les espèces pélagiques ou bentho-pélagiques fréquentant la colonne d’eau (le pelagos) dans les zones dont la bathymétrie est comprise entre 0 et 40 m (zones dites côtières). Les protocoles d’échantillonnages proposés consistent à combiner l’utilisation de deux technologies d’acoustiques actives complémentaires, orientées verticalement : un sondeur large bande (Simrad EK80, 70, 120 et 200 kHz) et un sonar multifaisceaux (Simrad M3, 500 kHz). Cette campagne a été réalisée dans le cadre du projet ACaPELA, en Mai 2023, à bord du bateau de station semi-rigide Emeraude Explorer. Des stations CTD ont également été réalisées à des points préalablement défini