Tidewater goby and estuarine fish records from seining, qPCR and metabarcoding data for Southern California estuaries in 2023

Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost-effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining required twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with..., Water samples were taken for eDNA at four sites known to contain tidewater gobies in the past: 16 samples Calleguas Creek (34 06' 42\", 119 04' 54\", Ventura County), 21 samples at Ormond Lagoon (34 8' 23\", 119 11' 20\", just west of NVBC), and 17 samples at Santa Clara River Mouth (34 4' 8\", 119 15' 53\", Ventura County). In addition, two samples were taken at Mugu Lagoon (34 5' 30\", 119 7' 21\", Ventura County) and 20 samples were taken at Devereux Slough (34 25' 4\", 119 52' 27\", Santa Barbara County). I used commercial aquatic eDNA kits from Jonah Ventures ® for US $90 each (this cost includes supplies, sequencing and bioinformatics). At all sites, nearshore water samples were taken for environmental DNA wearing latex gloves to reduce contamination with human DNA. Samples were then filtered through a 1-micron disk filter by pushing water through the filter with a 60cc luer-lock syringe until clogging (mean sample volume: 174 cc +/- 0.141 S.D.). Filter capsules were purged of water before ..., , # Tidewater goby and estuarine fish records from seining, qPCR and metabarcoding data for Southern California Estuaries in 2023

This data archive includes R code and data for reproducing the analyses and figures in Lafferty, **Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes.**
 
To view the supplementary tables, open the Fig&TableSuppl.docx file. This file also includes the manuscript figures and tables and some explanatory text about how to generate them.

To reproduce the figures, open the Fig&TableCode.Rmd in R studio and be sure the needed csv files included in the Dryad repository are in the working directory. The data files include more information than used in the analyses and can be used for other purposes. The code is not software, nor is it intended as an R package, but the code is annotated so others can understand and manipulate it.

For each CSV file there is an associated metadata file...