Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary

# Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary **I. General information** Dataset title: "Data from: eDNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary" Principle investigator: Charlotte Van Driessche ([[e-mail]](mailto:[e-mail])) Co-investigators: Teun Everts, Sabrina Neyrinck, David Halfmaerten, Pieter Verschelde, Jan Breine, Dries Bonte, Rein Brys Data collection data: April, July, September 2021 Geographic location of data collection: Belgium, Flanders (Northern Region) Keywords: biodiversity monitoring, integrated sampling, assay sensitivity, reference database, salinity, seasonal migration Principal funders: Research Foundation Flanders grants for strategic basic research (FWO-SB, grant number 1S23822N to CVD and grant number 1S01822N to TE) and the Research Institute for Nature and Forest As a result of this work, an updated version of the reference database used for metabarcoding was created which can be found here: [https://doi.org/10.5281/zenodo.10422227](https://doi.org/10.5281/zenodo.10422227). **II. Data overview and methodological information** *- Datafile: VanDriessche et al. 2024_ObiTools Count Table_Riaz.xlsx* Creation data file: the 26th of October 2023 The dataset contains eight tab pages. 1\. info_tab: an overview repeating this information but facilitating the use of the Excel file and explaining again the use of all different tabs 2\. raw_table_sorted: sorted raw count table as provided via ObiTools 3\. table_allreps_id100_all: started from raw_table_sorted, but now discarded sequences with <100% identity match with our reference database, as well as sequances with less than 500 reads across all samples. 4\. table_allreps_id100_all_frac: same as tab page 3, but in relative frequencies instead of absolute counts 5\. table_allreps_id100_agglomerate: started from tab page 3, but summed the counts of sequences with the same taxonomic assignment 6\. table_allreps_id100_aggl_frac: same as tab page 5, but in relative frequencies instead of absolute counts 7\. table_allreps_id100_agglomerated_fish: started from tab page 5, but retained only fish species and discarded samples containing <5% fish. 8\. table_allreps_id100_agglomerated_fish_f: same as tab page 7, but in relative frequencies instead of absolute counts Cells containing 'NA' in this file, refer to 'Not Available', for example when a genetic sequence was only identified to genus level and not to species level. Across all tab pages; the same lay-out is used. Column explanations are listed below: ASV: number of the amplicon sequence variant family_name: latin family name genus_name: latin genus name species_name: latin species name familie: Dutch translation of the family name categorie: Dutch translation of the large taxonomic group, e.g. fish full_name: full species name combining the information in column B, C and D sequence: actual sequence used for comparison and match with reference database ASV: same as column A Remainder of the columns include identity codes for the samples. These include: the filtercode + the season and year of sampling + the name of the sampling site + low (E) or high (V) tide + replicate 1 or 2 concurring with the fishing haul + depth level of sampling (o = deep, m = middle, b = surface) + the primer assay used (Riaz or Teleo) + the technical replicate number (1, 2 or 3) example: E2020KRW004_L21_Doel_E1O_Riaz_1 *- Datafile: VanDriessche et al. 2024_ObiTools Count Table_Teleo.xlsx* Creation data file: the 19th of September 2023 The dataset contains eight tab pages. 1\. info_tab: an overview repeating this information but facilitating the use of the Excel file and explaining again the use of all different tabs 2\. raw_table_sorted: sorted raw count table as provided via ObiTools 3\. table_allreps_id100_all: started from raw_table_sorted, but now discarded sequences with <100% identity match with our reference database, as well as sequances with less than 500 reads across all samples. 4\. table_allreps_id100_all_frac: same as tab page 3, but in relative frequencies instead of absolute counts 5\. table_allreps_id100_agglomerate: started from tab page 3, but summed the counts of sequences with the same taxonomic assignment 6\. table_allreps_id100_aggl_frac: same as tab page 5, but in relative frequencies instead of absolute counts 7\. table_allreps_id100_agglomerated_fish: started from tab page 5, but retained only fish species and discarded samples containing <5% fish. 8\. table_allreps_id100_agglomerated_fish_f: same as tab page 7, but in relative frequencies instead of absolute counts Cells containing 'NA' in this file, refer to 'Not Available', for example when a genetic sequence was only identified to genus level and not to species level. Across all tab pages; the same lay-out is used. Column explanations are listed below: ASV: number of the amplicon sequence variant family_name: latin family name genus_name: latin genus name species_name: latin species name familie: Dutch translation of the family name categorie: Dutch translation of the large taxonomic group, e.g. fish full_name: full species name combining the information in column B, C and D sequence: actual sequence used for comparison and match with reference database ASV: same as column A Remainder of the columns include identity codes for the samples. These include: the filtercode + the season and year of sampling + the name of the sampling site + low (E) or high (V) tide + replicate 1 or 2 concurring with the fishing haul + depth level of sampling (o = deep, m = middle, b = surface) + the primer assay used (Riaz or Teleo) + the technical replicate number (1, 2 or 3) example: E2020KRW004_L21_Doel_E1O_Teleo_1 *- Datafile: VanDriessche et al. 2024_Raw Stow.xlsx* Creation data file: the 20th of November 2021 The dataset contains one tab page. 1\. stow_net_raw: raw stow net fishing data in numbers of individuals per species as total catch from the stow nets and as reported also on the vis.inbo dataportal. Column explanations are listed below: Study_site: Doel, Antwerp, Steendorp or Branst Date: Date of sampling Tide: Low or High Season: Spring, Summer or Autumn Remainder of the columns include the latin species names of the species identified morphologically on the fishing vessel. **III. Sharing access and information** This dataset is licensed under a (CC0 1.0) Creative Commons Attribution Non Commercial 1.0 Generic. This data was used generated in the Research Article (manuscript): Van Driessche, C., Everts, T., Neyrinck, S., Halfmaerten, D., Verschelde, P., Breine, J., Bonte, D., & Brys, R. (2024) eDNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary. Science of the Total Environment.# 数据集相关研究：环境DNA metabarcoding（environmental DNA metabarcoding, eDNA）反映斯海尔德河河口（Scheldt Estuary）鱼类群落的时空变化模式 ## 一、基本信息 **数据集标题**："环境DNA metabarcoding反映斯海尔德河河口鱼类群落的时空变化模式" **项目负责人**：Charlotte Van Driessche（[[e-mail]](mailto:[e-mail])） **共同研究者**：Teun Everts、Sabrina Neyrinck、David Halfmaerten、Pieter Verschelde、Jan Breine、Dries Bonte、Rein Brys **数据采集时段**：2021年4月、7月、9月 **数据采集地理范围**：比利时佛兰德斯（北部地区） **关键词**：生物多样性监测、集成采样、检测灵敏度、参考数据库、盐度、季节性洄游 **主要资助方**：佛兰德斯研究基金会战略基础研究项目资助（FWO-SB，CVD的项目编号：1S23822N；TE的项目编号：1S01822N）以及自然与森林研究所 本研究产出了一套更新后的metabarcoding参考数据库，可通过以下链接获取：[https://doi.org/10.5281/zenodo.10422227](https://doi.org/10.5281/zenodo.10422227) ## 二、数据概览与方法学信息 ### 数据文件1：VanDriessche et al. 2024_ObiTools Count Table_Riaz.xlsx **文件创建日期**：2023年10月26日 本数据集包含8个工作表： 1. `info_tab`：信息汇总表，重复本数据集的相关说明以方便Excel文件的使用，并逐一阐释各工作表的用途 2. `raw_table_sorted`：经ObiTools导出的排序后原始计数表 3. `table_allreps_id100_all`：以`raw_table_sorted`为基础，移除了与参考数据库匹配度低于100%的序列，以及所有样本中reads数少于500的序列 4. `table_allreps_id100_all_frac`：与工作表3内容一致，但以相对频率而非绝对计数呈现结果 5. `table_allreps_id100_agglomerate`：以工作表3为基础，将具有相同分类学归属的序列计数进行求和整合 6. `table_allreps_id100_aggl_frac`：与工作表5内容一致，但以相对频率而非绝对计数呈现结果 7. `table_allreps_id100_agglomerated_fish`：以工作表5为基础，仅保留鱼类物种，并移除鱼类占比低于5%的样本 8. `table_allreps_id100_agglomerated_fish_f`：与工作表7内容一致，但以相对频率而非绝对计数呈现结果 文件中单元格标注的"NA"代表"无可用数据（Not Available）"，例如当遗传序列仅鉴定至属级而非种级时。 所有工作表采用统一的布局格式，各列含义说明如下： - ASV：扩增子序列变异（amplicon sequence variant, ASV）编号 - family_name：拉丁科名 - genus_name：拉丁属名 - species_name：拉丁种名 - familie：科名的荷兰语译法 - categorie：高级分类群的荷兰语译法（例如鱼类） - full_name：结合B、C、D列信息的完整物种名称 - sequence：用于与参考数据库比对匹配的实际序列 - ASV：与A列内容一致 其余列均为样本识别码，其构成规则为：过滤编码+采样季节与年份+采样点名称+低潮（E）或高潮（V）+与拖网采样对应的重复1或2+采样深度（o=深层，m=中层，b=表层）+所用引物检测体系（Riaz或Teleo）+技术重复编号（1、2或3），示例：E2020KRW004_L21_Doel_E1O_Riaz_1 ### 数据文件2：VanDriessche et al. 2024_ObiTools Count Table_Teleo.xlsx **文件创建日期**：2023年9月19日 本数据集包含8个工作表，各工作表含义与上述数据文件1完全一致，样本识别码示例为：E2020KRW004_L21_Doel_E1O_Teleo_1 ### 数据文件3：VanDriessche et al. 2024_Raw Stow.xlsx **文件创建日期**：2021年11月20日 本数据集仅包含1个工作表： 1. `stow_net_raw`：拖网采样原始数据表，以物种个体数计，为拖网的总捕获量，相关数据也发布于vis.inbo数据门户 各列含义说明如下： - Study_site：采样点（包括Doel、安特卫普、Steendorp或Branst） - Date：采样日期 - Tide：低潮或高潮 - Season：采样季节（春季、夏季或秋季） 其余列为经形态学鉴定的鱼类拉丁种名。 ## 三、共享与访问信息 本数据集采用CC0 1.0知识共享署名非商业性通用许可协议（Creative Commons Attribution Non Commercial 1.0 Generic, CC0 1.0）进行授权。 本数据曾用于发表于《整体环境科学》（Science of the Total Environment）的研究论文： Van Driessche, C., Everts, T., Neyrinck, S., Halfmaerten, D., Verschelde, P., Breine, J., Bonte, D., & Brys, R. (2024) 环境DNA metabarcoding反映斯海尔德河河口鱼类群落的时空变化模式.