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.

本数据集首次对菲律宾联合国教科文组织（UNESCO）生物圈保护区——锡亚高岛保护景观与海景（Siargao Islands Protected Landscape and Seascape, SIPLAS）内7个站点的红树林相关鱼类群落开展了环境DNA宏条形码技术（eDNA metabarcoding）调查。数据集包含12S核糖体核糖核酸（12S rRNA）线粒体扩增子序列变体（amplicon sequence variants, ASVs），这些变体通过BLASTn及已建立的同一性阈值完成了尽可能精细水平的分类学注释。数据集提供物种水平注释，以及对应的基因序列和生态描述符（如保护状态、栖息地偏好、营养结构）；还包含盐度、温度、站点位置说明及不同空间尺度的α和β多样性指标等额外元数据。最终，该数据集的结构极适合热带海岸生态系统的生物多样性评估、生态建模、指示物种分析及参考库构建。研究遵循标准法律与伦理协议（如野外去污、设置阴性对照以减少污染等），数据收集过程未直接伤害或处置任何脊椎动物。复用潜力包括：长期监测项目、栖息地恢复评估、整合至全球海洋DNA条形码数据库。遵循FAIR数据原则 • 符合国家及国际保护目标，包括（但不限于）联合国可持续发展目标14（水下生物）。

环境DNA（environmental DNA, eDNA）样本采集自菲律宾锡亚高岛7个海岸站点的14个红树林监测站，采样于小潮期以降低潮汐变化对样本的潜在影响。每个站点采集1升表层水样并配对过滤，使用0.22 μm Sterivex滤器，后续处理遵循严格去污流程以避免跨站点污染。环境变量（盐度和温度）通过校准的多参数探针现场测量。DNA提取采用Qiagen DNEasy PowerWater试剂盒；鱼类12S rRNA区域使用MiFish-U2、MiFish-U及MiFish-E-v2引物，结合KAPA HiFi HotStart ReadyMix（Roche）进行两次PCR扩增。扩增子在Illumina iSeq 100平台上完成160 bp双端测序。原始序列通过QIIME2和DADA2去噪及嵌合体去除，再经VSEARCH聚类获得高分辨率ASVs。分类学注释通过BLASTn比对GenBank数据库实现，采用从物种到纲水平的同一性阈值。下游分析使用PERMANOVA、β离散度检验、基于距离的冗余分析（distance-based redundancy analysis, dbRDA）及指示物种分析计算α和β多样性。最终的ASVs数据集补充了来自FishBase、IUCN及相关文献的生态特征与保护信息。