f0ad76a4-a9d3-4cd7-aaf5-7a1a43dc1e99 ARNAUD HAOND Sophie IFREMER, Laboratoire Halieutique Mediterranee (LHM) 04 99 57 32 61 Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sète France Sophie.Arnaud@ifremer.fr pointOfContact 2025-12-14T17:12:05.611871Z ISO 19115-3 - SEXTANT 1.0 WGS 84 (EPSG:4326) EPSG 8.6 Worlwide Blue shark population genomics data generated through DartSeq 2021-06-21 creation 2021-06-21 publication FR-330-715-368-00032-IFR_BIOINFO_BLUE_SHARK_DARTSEQ Dart Seq data gathered on Blue Shark in the framework of the PSTBS-IO project supported by funding from FAO, CSIRO Oceans and Atmosphere, AZTI Tecnalia, Institut de recherche pour le développement (IRD), and Research Institute for Tuna Fisheries (RITF) and financial assistance of the European Union (GCP/INT/233/EC – Population structure of IOTC species in the Indian Ocean), and POPSIZE project supported by FEAMP (2014-2020 UE N°508/2014), and Institut français de recherche pour l'Exploitation de la mer (Ifremer). IFREMER, Marine Biodiversity Exploitation and Conservation (MARBEC) IFREMER +33 (0)2 98.22.49.16 +33 (0)2 98.22.46.44 IFREMER Centre de Bretagne ZI Pointe du diable CS 10070 PLOUZANE 29280 France sismer@ifremer.fr http://data.ifremer.fr/SISMER web site publisher Nikolic Natacha IRD author Floriaan Devloo-Delva author Diane Bailleul author Ekaterina Noskova author Clément Rougeux author Chrystelle Delord author Philippe Borsa author Cathy Liautard-Haag author Mohamad Hassan IFREMER Mohamad.Hassan@ifremer.fr author Amandine Marie author Pierre Feutry author Peter Grewe author Campbell Davies author Jessica Farley author Daniel Fernando author Sebastian Biton-Porsmoguer author Poisson Francois IFREMER 04 99 57 32 45 04 99 57 32 95 Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sete France Francois.Poisson@ifremer.fr author Denham Parker author Leone Agostino IFREMER Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sete France Agostino.Leone@ifremer.fr author Jorden Aulich author Matt Lansdell author Arnaud-Haond Sophie IFREMER 04 99 57 32 61 04 99 57 32 95 Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex Sete France Sophie.Arnaud@ifremer.fr author https://sextant.ifremer.fr/geonetwork/srv/api/records/f0ad76a4-a9d3-4cd7-aaf5-7a1a43dc1e99/attachments/peau_bleue_Laurent_Ballesta_Andromede_Oceanologie.jpg peau_bleue_©Laurent_Ballesta_Andromede_Oceanologie.jpg Habitats and biotopes GEMET - INSPIRE themes, version 1.0 2018-07-27T14:39:48 publication 2018-07-27 publication geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme /Biological Environment/Bioinformatics Thèmes Sextant 2025-12-09 publication geonetwork.thesaurus.local.theme.sextant-theme Variables ODATIS 2023-10-13 publication geonetwork.thesaurus.local.theme.odatis_variables Bioinformatics ODATIS aggregation parameters and Essential Variable names 2025-07-29 publication geonetwork.thesaurus.external.theme.NVS.OD1 Analysis data Type de jeux de donnée ODATIS 2025-12-09 publication geonetwork.thesaurus.local.theme.type_jeux_donnee Licence Ouverte utf8 -140.00 100.00 -60.00 60.00 https://doi.org/10.12770/f0ad76a4-a9d3-4cd7-aaf5-7a1a43dc1e99 DOI Digital Object Identifier (DOI) https://data-dataref.ifremer.fr/bioinfo/ifremer/marbec/RAD_Blue_Shark/ WWW:DOWNLOAD Lien de téléchargement Lien de téléchargement /home/ref-bioinfo/ifremer/marbec/RAD_Blue_Shark NETWORK:LINK https://doi.org/10.22541/au.165648248.86647399/v1 WWW:LINK-1.0-http--publication-URL Main publication DarT data were produced based on samples gathered at IRD, IFREMER, and CSIRO with the partners associated, and genotyped using DarT protocols and genotyped by CSIRO using DarT protocols. The data to download contain: 1/demultiplexed raw data, 2/data filtered using radiator and exported with different format (genpop, structure etc...), and 3/demographic simulations using FastSimCoal and GADMA. A total of 364 individual DNAs passed the DArT library constructions’ quality checks and genotypes were generated from sequencing runs completed at DArT using a proprietary DArTseq analytical pipeline (DArT-Soft14 version). The DArT toolbox was then used to filter away poor-quality sequences and apply more stringent selection criteria to the barcode region, and generate the final genotypes (Kilian et al. 2012), here called “Raw data”. As detailed in the publication associated to these data (Nikolic et al. 2022, submitted), the data were transformed iteratively (Figure 1) following a sequence of filtering steps using radiator (Gosselin 2018; Gosselin et al. 2020) (see detailed in the publication associated). This resulted in a dataset of SNPs (one SNP per de novo assembled fragment) called “DATA 3” excluding sex-linked marked yet keeping outlier loci. The “DATA 4” was subsequently obtained by removing SNPs detected as outliers and those with minor allele frequencies (MAF) lower than 0.01 using dartR v1.5.5 (Georges et al. 2018). Finally, a dataset “DATA 5” including only the 9 outlier loci detected was also constructed for comparative population genetic analysis. When grouping individuals per geographic regions, the final number of individuals is 312 while a clustering per sampling site led to retain 313 individuals (Figure 1, see also the R Markdown file “2024_04_Blue_shark_markdown.pdf”). The dataset in this web portal contains also the data form to run demographic inferences through GADMA (Noskova et al. 2020) and FastSimCoal (Excoffier et al. 2011) analysis detailed in the associated publication.