[https://doi.org/10.5061/dryad.n8pk0p342]

General information

Author Information

Corresponding author:
Jennie J. Wiggins
Fish Biologist, Lodi Fish and Wildlife Office
US Fish and Wildlife Service
jennie_wiggins@fws.gov

Co-Authors:
Vanessa D. Tobias
Mathematical Statistician, Lodi Fish and Wildlife Office
US Fish and Wildlife Service
vanessa_tobias@fws.gov

Erika F. Holcombe
Supervisory Fish Biologist, Lodi Fish and Wildlife Office
US Fish and Wildlife Service
erika_holcombe@fws.gov

Katie Karpenko
Research Associate, Genidaqs Laboratory
Cramer Fish Sciences
katie.karpenko@fishsciences.net

Eric R. Huber
Supervisory Fish Biologist, Lodi Fish and Wildlife Office
US Fish and Wildlife Service
eric_huber@fws.gov

Andrew C. Goodman
Fish Biologist, Lodi Fish and Wildlife Office
US Fish and Wildlife Service
andrew_goodman@fws.gov

Date of data collection: Pilot Study- March 2022; Main Study (including calibration experiment)- February 2023 – June 2023

Geographic location of data collection: All data were collected at San Luis National Wildlife Refuge (Merced County, California, USA)

Data and file overview

This dataset contains 8 CSV files:
• All_Variable_descriptions.csv
• catch_loach_data.csv
• loach_length_data.csv
• eDNA_detections_site_data.csv
• Resampled_eDNA_detections_site_data.csv
• PilotStudy_qPCR_RAW.csv
• CalibrationExperiment_qPCR_RAW.csv
• MainStudy_qPCR_RAW.csv

File descriptions:

All_Variable_descriptions.csv contains 4 columns and 151 rows of descriptions for all the variables used within the 7 other CSV files associated with this dataset.

catch_loach_data.csv contains 21 variables and 897 (898 with column headers) rows of data related to loach capture per minnow trap collected during trapping efforts for the Pilot Study and the Main Study. This file only contains data related to trapped sites. Columns are study, round, site_name, trap_name, habitat_type, trap_num, latitude, longitude, date_set, time_set, date_pulled, time_pulled, total_time_fished, loach_captured, dissolved_oxygen, conductivity, temperature, turbidity, depth, velocity, notes. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file. Environmental data has not been scrubbed for outliers.

loach_length_data.csv contains 16 variables and 676 (677 with column headers) rows of length data for each loach collected during trapping efforts for the Pilot Study and the Main Study. Columns are study, round, site_name, trap_name, habitat_type, trap_num, latitude, longitude, date_set, time_set, date_pulled, time_pulled, species_name, species_code, total_length, notes. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file.

eDNA_detections_site_data.csv contains 16 variables and 377 (378 with column headers) rows of categorical and environmental data related to all sites sampled for eDNA and/or trapped during the Pilot Study or Main Study. Columns are study, round, site_name, habitat_type, latitude, longitude, date, sampled_eDNA, detection, trapped, dissolved_oxygen, conductivity, temperature, turbidity, depth, velocity. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file. Environmental data has not been scrubbed for outliers.

Resampled_eDNA_detections_site_data.csv contains 15 variables and 38 (39 with column headers) rows of categorical and environmental data related to sites that were re-sampled for eDNA if loach were captured there during trapping efforts for the Main Study. Columns are study, round, site_name, habitat_type, latitude, longitude, date, detection, dissolved_oxygen, conductivity, temperature, turbidity, depth, velocity, notes. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file. Environmental data has not been scrubbed for outliers.

PilotStudy_qPCR_RAW.csv contains 20 variables and 540 (541 with column headers) rows of qPCR results for all filters collected during the Pilot Study. Columns are projectID, project_type, extraction_order, date, site_name, filter_replicate, FilterID, vol_filtered_ml, location, location_broad, extraction_date, control, month, year, field_notes, technical_replicate, Cq, target, relative_conc_ng/uL, relative_conc_weighted_by_vol. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file.

CalibrationExperiment_qPCR_RAW.csv contains 33 variables and 630 (631 with column headers) rows of qPCR results for all filters collected during the eDNA calibration experiment of the Main Study. Columns are projectID, project_type, extraction_order, date, name, filter_replicate, FilterID, vol_filtered_ml, location, location_broad, extraction_date, lat, lon, control, month, year, field_notes,dist_lc_m, lc_deploy_time, lc_remove_time, lc_spp_1, lc_spp_2, spp_1_wt_g, spp_2_wt_g , vel_m_s, vel_ft_sec, turb_ntu, depth_m, technical_replicate, Cq, relative_conc_ng/uL, target. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file.

MainStudy_qPCR_RAW.csv contains 22 variables and 2674 (2675 with column headers) rows of qPCR results for all filters collected during the Main Study. Columns are projectID, project_type, extraction_order, date, site_name, filter_replicate, FilterID, vol_filtered_ml, location, location_broad, extraction_date, lat, lon, control, month, year, field_notes, technical_replicate, Cq, target, relative_conc_ng/uL, relative_conc_weighted_by_vol. A complete description of all the variables used in this file can be found in the All_Variable_descriptions.csv file.

Methodological information

Please refer to the associated paper for a more detailed overview of data collection, processing, and analyses for this dataset.

eDNA sample collection: Environmental DNA samples were collected by simultaneously filtering water through three Millipore® Sterivex™-HV 0.45 μm sterile PVDF membrane filter units (Millipore Sigma, Burlington, MA, USA) using three Masterflex® L/S Easy-Load II peristaltic pumps. Environmental DNA field controls were collected at the start of each sampling day to confirm that field equipment was free of contamination.

Pilot Study: We selected 127 random sampling sites made up of an approximately equal number of habitat types termed ponds (n=62) and canals (n=65). One baited minnow trap was set at each of the selected locations for approximately 24 h. A random subset of sites was also sampled for eDNA, including 20 canal sites and eight pond sites. We measured the total length (TL) of all trapped loaches to the nearest mm. Species identification was genetically confirmed for each specimen captured resulting in 17 Paramisgurnus dabryanus (Large-Scale Loach) and one Misgurnus mizolepis (Fine-Scale Loach).

Calibration of eDNA: To better understand eDNA transport and persistence within the sampling area, we conducted a fixed-point eDNA study in a small shallow canal and a large deep canal. We created a fixed source of eDNA using known quantities of commercially available frozen Engraulis mordax (Northern Anchovy; 16 g) and Hemiramphus brasiliensis (Ballyhoo; 100 g). Velocity and turbidity were measured prior to sampling using a Global Water FP111 Flow Probe (YSI Inc., Yellow Springs, OH, USA) and a Hach 2100Q Turbidity Meter (Hach Co., Loveland, CO, USA), respectively. After the calculated dispersal time had passed, we collected eDNA samples simultaneously in triplicate at six set distances from the tethered fish. Once complete, eDNA sources were removed from each canal. The eDNA collection process was repeated at the same locations the following day to determine if eDNA from the proxy species remained in the system after 24 h.

Main Study: We sampled 250 of 300 randomly generated canal sites for loach eDNA. Pond habitats were not sampled in the main study.  Environmental DNA sampling (week 1, 3, 5) and loach trapping (week 2, 4, 6) alternated weekly to permit strategic deployment of traps based on the previous week’s eDNA results. Each set of an eDNA sampling week and its associated trapping week was referred to as one “round.” Areas containing the highest concentrations of loach eDNA received priority for trapping. Two additional weeks (week 7-8; extra_1, extra_2) of trapping only were conducted after the eDNA filter budget was exhausted. At sites where loach eDNA was detected, we deployed 10 minnow traps over a total of 260 m moving upstream. Traps soaked for approximately 24 h before they were removed. Sites where loach were captured, were resampled for eDNA the following week (designated by an ‘RX’ in the site name). We measured the TL of all trapped loaches to the nearest mm. Species identification for the loaches collected during this study have not been genetically confirmed and thus have been assigned a generic species name and code at the time of this publication. Environmental data were collected at each site one time before eDNA sampling and one time before trapping. 

Code/Software

The statistical code for reproducing the analyses in the associated manuscript can be found at https://github.com/USFWS/LFWO-Loach-eDNA.git. The scripts were created using R version 4.3.1 "Beagle Scouts".