DOI: 10.5061/dryad.c59zw3rj9
title: Data from: Hydrodynamics and aquatic vegetation drive spatial patterns of environmental DNA in ponds

description: 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.
description: 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. 
description: # Data from: Hydrodynamics and aquatic vegetation drive spatial patterns
 of environmental DNA in ponds
 [https://doi.org/10.5061/dryad.c59zw3rj9](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](https://doi.org/10.5281/zenodo.10067780).