Cities at Sea: Coastal Urbanization Generates Local Biodiversity Hotspots but Homogenizes Marine Fish Communities Regionally (metabarcoding raw data 1/5)

This dataset is associated to the following publication: Macé, B., Delrieu-Trottin, E., Mouillot, D., Valentini, A., Bruno, M., Velez, L., Avouac, A., Deter, J., Bockel, T., Orblin, M., Boissery, P., Le Roux, G., & Manel, S. (2026). Cities at Sea: Coastal Urbanization Generates Local Biodiversity Hotspots but Homogenizes Marine Fish Communities Regionally. Global Change Biology, 32(6), e70965. https://doi.org/10.1111/gcb.70965 It contains the raw eDNA metabarcoding data (part 1/5): the all_samples.csv file records the corresponding sample for each position of the sequencing plate, and the .fastq files are the raw NGS eDNA sequencing outputs. Methods DNA extraction, amplification, and sequencing were conducted following a previously described protocol (Pichot et al., 2025). Briefly, two independent extractions per sample were carried out alongside negative extraction controls to monitor potential contamination using the NucleoSpin® Soil kit (Macherey-Nagel, Germany), and the two extracts per sample were pooled. PCR amplifications were performed using the teleo primer pair (Valentini et al., 2016), targeting a ~60 bp fragment of the 12S mitochondrial DNA region in fish (teleosts and elasmobranchs). Twelve PCR replicates per sample were run, each with a unique eight nucleotide tag for downstream identification (identical tag for both the forward and the reverse primer). Negative PCR controls were analyzed in parallel. Amplified products were quantified, purified, and pooled to reach a theoretical depth of 1,000,000 reads per sample before library preparation. High-throughput sequencing libraries were prepared using the TruSeq® DNA PCR-Free kit (Illumina, USA) and sequenced on a NextSeq® 1000 (Illumina) using a P1 or P2 kit (Illumina). References Pichot, F., Manel, S., Velez, L., Juhel, J.-B., Ballesta, L., Boissery, P., Bruno, M., Cancemi, M., Holon, F., Riutort, J.-J., Schultz, M., Tomasi, N., Valentini, A., Adam, O., Deter, J., & Mouillot, D. (2025). Mesophotic protected habitats as refugia for the most at-risk elasmobranch species. Biological Conservation, 310, 111371. https://doi.org/10.1016/j.biocon.2025.111371 Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428