Data from: Hydrodynamics and aquatic vegetation drive spatial patterns of environmental DNA in ponds
Data files
Dec 15, 2025 version files 75.53 KB
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Mayne_et_al._Experiment_2_Data.csv
71.91 KB
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README.md
3.63 KB
Abstract
Environmental DNA (eDNA) sampling is a powerful method for detecting aquatic species at low densities. However, eDNA may remain close to the source in lentic systems, decreasing the effectiveness of eDNA surveys. We conducted cage experiments with salamanders and simultaneous detailed hydrologic and wind measurements to investigate the influence of the physical environment on detection patterns of eDNA in ponds. We found much higher detection rates in the surface layer than at depth, and that aquatic vegetation reduced detection of eDNA produced in open water by 80%–94%. Within the surface mixed layer, detection rates were highest close to the source in the direction of water flow in the bottom half of the layer, and detections farthest from the source occurred when velocities in this sublayer were high. Detections were near zero even close to the source when this sublayer was flowing fast and away from the sampling point. The direction of water flow in this lower half of the surface mixed layer was negatively correlated with wind direction for most of the study. These spatial and temporal dynamics indicate that eDNA transport processes in ponds are highly complex. Sampling away from aquatic vegetation, in the surface mixed layer, and upwind of potential sources, in addition to sampling at many locations within a pond and considering temporal patterns, may improve detection of rare pond species. This work contributes to a growing body of literature characterizing the variability of eDNA detection in lentic systems.
https://doi.org/10.5061/dryad.c59zw3rj9
Description of the data and file structure
Data from a cage experiment to investigate the relationship between water movement and environmental DNA transport in a pond.
Files and variables
File: Mayne_et_al._Experiment_2_Data.csv
Description: Data from Experiment 2 in: Hydrodynamics and Aquatic Vegetation Drive Spatial Patterns of Environmental DNA in Ponds, Environmental DNA
Variables
- Round – Order of pond sampling events in Experiment 2 labeled R1-R8.
- date – Date that the sampling occurred (2021-08-09 to 2021-08-29).
- time – The time the sample was collected in PDT (24 hr).
- sample_id - The location in the pond where the sample was collected. Sample labels follow the naming convention in the figure below.
- pos_wells - Number of replicates that tested positive for tiger salamander eDNA (0-3).
- neg_wells - Number of replicates that did not amplify tiger salamander eDNA (0-3). neg_wells = 3-pos_wells.
- veg - Presence of aquatic vegetation at the sampling location. 0 = No aquatic vegetation (open water) and 1 = Sample collected within aquatic vegetation. Presence recorded at the time of sample collection.
- sqrt.dist_enc - Square root of the distance from the sample collection location to the center of the enclosure in meters.
- dir_enc - Direction from the enclosure to the sampling location (°).
- sqrt.temp - Square root of the mixed layer temperature (°C). The temperature is 120-minute average taken from the center of the pond.
- ml_avedepth.cm - Average depth of the mixed layer over 120-minute interval prior to sampling (cm).
- bt.spd.mm - Combined water speed variable from the top and bottom of the mixed layer (mm/s).
- t.spd.mm - Water speed in the upper half of the mixed layer (mm/s). Average speed over 120-minute interval prior to sample collection.
- b.spd.mm - Water speed in the lower half of the mixed layer (mm/s). Average speed over 120-minute interval prior to sample collection.
- tflow.10 - Difference between the direction of the water in the upper half of the mixed layer over 120-minute interval prior to sampling and the direction of the sampling location. Divided by 10 for scaling.
- bflow.10 - Difference between the direction of the water in the lower half of the mixed layer over 120-minute interval prior to sampling and the direction of the sampling location. Divided by 10 for scaling.
- btflow.10 - Minimum of tflow.10 and bflow.10.
- nw120.dir.diff.10 - Difference between the direction of the wind over 120-minute interval prior to sampling and the direction of the sampling location.
- X87_recipTs - Estimated Mixing Time (1/Ts). The inverse timescale for mixing by shear dispersion (1/Ts). See methods section in publication for calculations.
- scx87_recipTs - X87_recipTs centered and scaled using the “scale” function in R (version 4.2.1), which subtracts the mean and divides by the standard deviation.
Locations of sample_id: image can be found in file Locations_of_sample_id.jpg (found on Zenodo in 'Supplemental Information' under Related Works)
Code/software
.csv file
Access information
Other publicly accessible locations of the data:
- Raw data from Experiment 2 temperature loggers and ADCPs are available at Zenodo, https://doi.org/10.5281/zenodo.10067780.
Water samples were collected using a line and pulley system and temperature loggers, acoustic Doppler current profilers, and a wind meter were used to collect data on thermal stratification, water movement, and wind direction and speed. Environmental DNA samples were collected using 5 micron PES filter membranes and hand vacuum pumps in the field and analyzed in triplicate using a quantitative PCR assay.