eDNA metabarcoding dataset of fish community composition in Qiandao Lake, China, for assessing niche dynamics of invasive Coptodon zillii

1. Background and study objective This dataset supports the research article titled "Multi-dimensional niche partitioning at the invasion front: an eDNA-based study of invasive Coptodon zillii in Qiandao Lake, China". The study aimed to investigate the multi-dimensional spatial niche dynamics of the invasive redbelly tilapia (Coptodon zillii) at its northern invasion front in Qiandao Lake, a large subtropical deep-water reservoir in China, using environmental DNA (eDNA) metabarcoding. Specifically, we quantified niche breadth and niche overlap between C. zillii and co-occurring native fish species across vertical (surface, middle, bottom), horizontal (littoral vs. pelagic), and regional (five lake basins: central, southeastern, southwestern, northeastern, northwestern) dimensions. 2. Sampling design In July 2025 (the breeding season of C. zillii), we established 24 sampling sites across five lake regions, with a 1:1 ratio between littoral and pelagic zones. At each site, water samples were synchronously collected from three layers: surface (0.5 m below surface), middle (50% water depth), and bottom (0.5 m above bottom). Three replicate 2 L water samples were collected per layer (total 6 L per layer), homogenized, and filtered on-site using mixed cellulose acetate membranes (47 mm diameter, 0.45 µm pore size; Whatman, UK). An additional 6 L of sterilized ultrapure water was filtered as an on-site negative control. All membranes were flash-frozen in liquid nitrogen and stored at −80°C until DNA extraction. 3. eDNA metabarcoding and sequencing eDNA was extracted using the Fast DNA Spin Kit (MP Bio, USA). PCR amplification targeted a ~170 bp fragment of the 12S mitochondrial rRNA gene using the MiFish-U primers (Miya et al., 2015): forward 5′-GTCGGTAAAACTCGTGCCAGC-3′ and reverse 5′-CATAGTGGGGTATCTAATCCCAGTTTG-3′, appended with Illumina adapters. Eight PCR replicates per sample were performed to reduce stochasticity. Illumina paired-end sequencing (250 bp, v2 kit) was performed on an Illumina MiSeq platform with a target depth of 10,000 reads per sample. Raw sequencing data were processed using a standard bioinformatics pipeline including Cutadapt (v3.4), DADA2 (v1.20), and taxonomic assignment against MitoFish and GenBank databases. 4. Data usage These raw data can be used for fish community composition analysis, biodiversity assessment, detection of invasive species, and validation of eDNA metabarcoding protocols in large deep-water reservoirs. Researchers may also reuse these data for meta-analyses of freshwater fish eDNA studies or for comparative studies with traditional capture-based fish surveys. 5. Contact information For any questions regarding this dataset, please contact Shoujie Tang ([e-mail]) or Prof. Jinliang Zhao ([e-mail]), Shanghai Ocean University, Shanghai, China.1. 背景与研究目标 本数据集支撑题为《入侵前沿的多维生态位分化：基于环境DNA（eDNA）的中国千岛湖入侵齐氏非鲫（Coptodon zillii）研究》的学术论文。本研究旨在利用环境DNA元条形码技术，探究中国大型亚热带深水水库千岛湖北部入侵前沿的入侵物种红肚罗非鱼（齐氏非鲫，Coptodon zillii）的多维空间生态位动态。具体而言，我们在垂直（表层、中层、底层）、水平（沿岸带与远洋带）以及区域（五个湖盆：中部、东南部、西南部、东北部、西北部）维度上，定量分析齐氏非鲫与伴生本土鱼类的生态位宽度及生态位重叠度。 2. 采样设计 2025年7月（齐氏非鲫的繁殖季），我们在五个湖域布设了24个采样点，沿岸带与远洋带采样点比例为1:1。在每个采样点，同步采集三层水体样本：表层（水面下0.5米）、中层（水体深度的50%处）、底层（离水底0.5米处）。每层采集3个平行2升水体样本（每层总采样量为6升），将样本混匀后，使用混合纤维素乙酸酯滤膜（直径47毫米，孔径0.45微米；Whatman，英国）现场过滤。额外采集6升灭菌超纯水进行过滤，作为现场阴性对照。所有滤膜经液氮速冻后，于-80℃条件下保存，直至DNA提取环节。 3. 环境DNA元条形码与测序 使用Fast DNA Spin试剂盒（MP Bio，美国）提取环境DNA。以MiFish-U引物（Miya等，2015）扩增约170 bp的12S线粒体rRNA基因片段，引物序列为：正向5′-GTCGGTAAAACTCGTGCCAGC-3′、反向5′-CATAGTGGGGTATCTAATCCCAGTTTG-3′，引物末端添加Illumina测序接头。为降低随机误差，每个样本设置8次PCR重复。使用Illumina MiSeq平台进行双端测序（250 bp，v2试剂盒），目标测序深度为每个样本10000条读段。原始测序数据通过标准生物信息学流程进行处理，包括Cutadapt（v3.4）、DADA2（v1.20），并基于MitoFish和GenBank数据库进行物种分类注释。 4. 数据使用范围 本原始数据集可用于鱼类群落组成分析、生物多样性评估、入侵物种检测，以及大型深水水库中环境DNA元条形码技术方案的验证。研究人员还可复用该数据集开展淡水鱼类环境DNA研究的荟萃分析，或与传统捕捞式鱼类调查进行比较研究。 5. 联系方式 若对本数据集有任何疑问，请联系上海海洋大学的唐守杰（[e-mail]）或赵金良教授（[e-mail]），中国上海。