Data from: Enabling quantitative eDNA monitoring in lotic ecosystems by incorporating hydrological characteristics and allometric scaling

This dataset accompanies the study “Enabling quantitative eDNA monitoring in lotic ecosystems by incorporating hydrological characteristics and allometric scaling” and contains environmental DNA (eDNA) quantification data from controlled mesocosm experiments and field surveys in lotic ecosystems in Flanders, Belgium. Data were collected between January–June 2023 and September 2023 and include droplet digital PCR (ddPCR)–based species-specific eDNA concentrations, metabarcoding-derived estimates, electrofishing observations, and hydrological covariates. The dataset links fish abundance, biomass, and allometrically scaled biomass to eDNA signals while accounting for river discharge and habitat characteristics, enabling quantitative, fishery-independent biodiversity monitoring in flowing waters. Dataset Data_eDNAQuantification_Clean.csv, created on the 31st of July 2025. This is the cleaned, ready-to-use dataset containing both mesocosm and field experimental data, both eDNA detections, as well as electrofishing data. This dataset can be used with the provided script Script_eDNAQuantification_Clean.R. It has the following columns: ID: an identification number for easy sorting of the data. Method: detections arrise from either the mesocosm experiment (Mesocosm) or from observational surveys via either eDNA-based methods, or electrofishing activities (Field). FilterNo: If applicable, the filter code was given for the eDNA samples. VolumeFilteredMl: The volume of water filtered to obtain the eDNA sample, given in ml. MesocosmNo: The number of the tank in which the fish were kept is included. Group: Two size classes were used during the mesocosm experiment, Small vs. Large. Data lines from the field surveys are appointed NA values in this column. Date: collection/sampling date. Location: Relevant only for the field surveys. Data lines from the mesocosm experiment are appointed NA values in this column. The column includes the name of the studied river, and more detailed information relating to the exact placement of the sample within the study location. Species: Latin name of the species studied. AbundanceNo: Number of fish used or counted. BiomassG: Total ammount of biomass, given in grams. AlloBiomass: Allometrically scaled biomass, following Yates et al., 2021. Also given in grams. ddPCR1: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the first technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software. ddPCR2: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the second technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software. ddPCR3: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the third technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software. ddPCR: Averaged concentration of eDNA calculated as the mean of the previously provided technical replicate values. RiverDischargeRate: Relevant only for the field surveys. Data lines from the mesocosm experiment are appointed NA values in this column. Calculated following Van Driessche et al., 2022. ddPCRRiazSample: eDNA concentration of the amplified Riaz fragment. MBRiazTotalReads: Total number of reads generated during amplification of the Riaz fragment. MBSpeciesAbsReads: Number of reads of the studies species resulting from the Riaz metabarcoding analyses. PercentageRiaz: Relative read abundance of the species compared to the total amount of Riaz eDNA amplified, i.e. the species-specific fraction. SpConcViaRiaz: the species-specific eDNA concentration (resembling the ddPCR measurements above), but this time derived from the metabarcoding analyses. Latitude: coordinates for the sampling location, added for mapping purposes. Longitude: coordinates for the sampling location, added for mapping purposes. Ruggedness: Terrain Ruggedness Index, extracted from a Digital Elevation Model using QGIS software, as a proxy for habitat heterogeneity. Script Script_eDNAQuantification_Clean.R, created on the 31st of July 2025. This R script contains the statistical analyses applied to the dataset in support of Van Driessche et al. (2026).本数据集配套于题为《通过纳入水文特征与异速生长尺度化方法实现流水生态系统定量环境DNA（eDNA）监测》的研究，包含来自比利时佛兰德斯地区流水生态系统的受控中宇宙实验与野外调查的环境DNA定量数据。数据采集时段为2023年1月至6月及2023年9月，涵盖基于液滴数字PCR（ddPCR）的物种特异性eDNA浓度数据、宏条形码（metabarcoding）分析估算结果、电捕鱼观测数据与水文协变量。本数据集将鱼类丰度、生物量及经异速生长尺度化处理的生物量与eDNA信号相关联，同时纳入河流流量与栖息地特征作为控制变量，可为流水生境提供无需依赖渔业调查的定量生物多样性监测手段。 ### 数据集 `Data_eDNAQuantification_Clean.csv` 于2025年7月31日生成。该数据集为经过清洗的可用数据集，涵盖中宇宙实验与野外调查的实验数据、eDNA检测结果及电捕鱼数据，可配合提供的`Script_eDNAQuantification_Clean.R`脚本使用。其包含以下字段： 1. **ID**：用于数据快速排序的唯一标识编号。 2. **Method**：检测来源类别，分为中宇宙实验（Mesocosm）或野外观测调查（含eDNA检测方法或电捕鱼活动，Field）。 3. **FilterNo**：若适用，为eDNA样本的滤膜编号。 4. **VolumeFilteredMl**：用于获取eDNA样本的过滤水体体积，单位为毫升。 5. **MesocosmNo**：养殖实验鱼的中宇宙水箱编号。 6. **Group**：中宇宙实验设置了两种体型等级：小型（Small）与大型（Large）；野外调查数据的该字段值为NA。 7. **Date**：样本采集日期。 8. **Location**：仅适用于野外调查，中宇宙实验数据的该字段值为NA。该字段包含研究河流名称，以及样本在研究区域内具体布设位置的详细信息。 9. **Species**：研究物种的拉丁学名。 10. **AbundanceNo**：实验使用或野外计数的鱼类数量。 11. **BiomassG**：总生物量，单位为克。 12. **AlloBiomass**：经异速生长尺度化处理的生物量，遵循Yates等人2021年的研究方法，单位为克。 13. **ddPCR1**：首次技术/实验室重复实验中，通过液滴数字PCR（ddPCR）引物探针体系（针对花鳅*Barbatula barbatula*则采用引物检测）得到的eDNA拷贝数，经过滤水体体积标准化，计算由Quantasoft软件完成。 14. **ddPCR2**：第二次技术/实验室重复实验的eDNA拷贝数，处理规则与ddPCR1一致。 15. **ddPCR3**：第三次技术/实验室重复实验的eDNA拷贝数，处理规则与ddPCR1一致。 16. **ddPCR**：基于上述三次技术重复值的均值计算得到的平均eDNA浓度。 17. **RiverDischargeRate**：仅适用于野外调查，中宇宙实验数据的该字段值为NA，计算方法遵循Van Driessche等人2022年的研究。 18. **ddPCRRiazSample**：Riaz片段扩增得到的eDNA浓度。 19. **MBRiazTotalReads**：Riaz片段扩增过程中生成的总测序读长数。 20. **MBSpeciesAbsReads**：Riaz宏条形码分析中目标物种的读长数。 21. **PercentageRiaz**：目标物种相对于总扩增Riaz eDNA的相对读长丰度，即物种特异性占比。 22. **SpConcViaRiaz**：通过宏条形码分析得到的物种特异性eDNA浓度，与前述ddPCR测量结果对应。 23. **Latitude**：采样地点的纬度坐标，用于可视化制图。 24. **Longitude**：采样地点的经度坐标，用于可视化制图。 25. **Ruggedness**：地形崎岖度指数（Terrain Ruggedness Index），通过QGIS软件从数字高程模型（Digital Elevation Model）中提取，作为栖息地异质性的替代指标。 ### 脚本 `Script_eDNAQuantification_Clean.R` 于2025年7月31日生成，该R脚本包含用于本数据集的统计分析代码，以支撑Van Driessche等人2026年的研究。