eDNA Metabarcoding of Mangrove Fish Assemblages in Siargao dataset

This dataset provides the first eDNA metabarcoding survey of mangrove-associated fish communities from seven sites across the Siargao Islands Protected Landscape and Seascape (SIPLAS), a UNESCO Biosphere Reserve in the Philippines. It contains 12S rRNA mitochondrial amplicon sequence variants (ASVs) taxonomically annotated to the finest level possible using BLASTn and previously established identity thresholds. Our dataset provides annotations at the species-level, followed by their corresponding gene sequences and ecological descriptors (e.g., conservation status, habitat preference, and trophic structure). Additional metadata such as salinity, temperature, clarifies station location, and alpha and beta diversity metrics across spatial scales is also provided. Ultimately, the structure of this data is ideally suited for biodiversity assessments, ecological modeling, indicator species analysis, and reference library development in tropical coastal ecosystems. Standard legal and ethical protocols were adhered to (e.g., field decontamination, negative controls to minimize contamination, etc.). Study based on data collection does not directly harm or handle any vertebrates. Reuse potential: long-term monitoring programs, habitat restoration evaluations, integration into global marine DNA barcode databases. Adherence to FAIR Data Principles • Alignment to national and international conservation objectives, including (but not limited to) UN Sustainable Development Goal 14 (Life Below Water).Environmental DNA (eDNA) was sampled from 14 mangrove stations across 7 coastal sites in Siargao Island, Philippines under neap tide conditions to reduce the potential for tidal variation in the collected samples. Paired 1-liter surface water samples were filtered through 0.22 μm Sterivex filters at each station and processed following stringent decontamination procedures to avoid cross-site contamination. Environmental variables—salinity and temperature—were measured in situ using a multiparameter probe (calibrated probes). DNA extraction was performed using the Qiagen DNEasy PowerWater kit, and the fish 12S rRNA region was PCR amplified twice using the MiFish-U2, MiFish-U and MiFish-E-v2 primers and KAPA HiFi HotStart ReadyMix (Roche). Amplicons were sequenced on 160 bp paired-end reads on an Illumina iSeq 100 platform. Raw sequences were processed with QIIME2 and DADA2 for denoising and chimera removal, then clustered with VSEARCH to obtain high-resolution amplicons sequence variants (ASVs). Taxonomic assignments were performed through BLASTn against GenBank with identity thresholds from species to class levels. PERMANOVA, beta dispersion test, distance-based redundancy analysis (dbRDA), and indicator species analysis were utilized in downstream analyses to calculate alpha and beta diversities. The resulting dataset of ASVs was supplemented with ecological traits and conservation information from FishBase, IUCN and literature.