Biological diversity in New Caledonia-Kanaky : Characterization from freshwater crustaceans, identification of major explicative factors and perpetuation of knowledges for their (re-)use

This dataset contains the data of Coline Royaux’s PhD thesis. Consisting of occurences of freshwater crustaceans in New Caledonia-Kanaky gathered during expeditions from 2016 to 2023 of the program "La Planète Revisitée", of the environmental consulting firm “Ethyc’o” and the association “Vies d’Ô douce”. Several new species have been found. This dataset is used in the article by Royaux et al., 2024; Royaux et al., 2025 and Royaux et al. 2026. Dataset https://doi.org/10.48579/PRO/DGVWPW is a subset of the present datsaset which is Coline Royaux's PhD thesis dataset. Partial COI (Cytochrome Oxidase I) gene of approx. 500 individuals of freshwater crustaceans species has been sequenced with Sanger method. Original AB1 data files for these sequenced are shared along with tabular data files on individuals (containing e.g. sample ID, species and sex identified, NCBI GenBank accession for cleaned sequences and used primers for amplifications), occurences (containing e.g. sample ID, species identified, French Natural History Museum (MNHN) collection ID), samples (containing e.g. sample type, location ID, sampling date, sampler name), locations (containing e.g. other names of the location, coordinates in decimal degrees WGS84) and DNA extractions (containing e.g. extraction date, laboratory operator) and fasta files with all found haplotypes sequences and primer used. DNA extraction (https://dx.doi.org/10.17504/protocols.io.j8nlk4x7wg5r/v1; https://dx.doi.org/10.17504/protocols.io.36wgqnm9ygk5/v1) and PCR (dx.doi.org/10.17504/protocols.io.261ge4y4jv47/v2; https://dx.doi.org/10.17504/protocols.io.n92ld8q57v5b/v1) protocols are available on protocols.io. Sequence cleaning workflow is available on Galaxy at https://usegalaxy.fr/u/coline_royaux/w/sanger1--from-ab1-to-aligned-fasta-imported-from-uploaded-file ; https://usegalaxy.fr/u/coline_royaux/w/sanger1--from-ab1-to-consensus-and-blast-no-final-alignment and history retracing data cleaning steps at https://usegalaxy.fr/u/coline_royaux/h/automatic-boeckella-nc-data-cleaning-1 ; https://usegalaxy.fr/u/coline_royaux/h/boeck-sanger-2024-clean.