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

Abstract

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 the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost-effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding still suffers from gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining is still the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions. The manuscript relies on 8 separate data sets and an R file to analyze them.  Each data file has an accompanying metadata file and information file. The subset of data used is provided in the data archive (Schmelzle&Kinziger_occupancy.csv) so that analyses can be reproduced but should be cited as Schmelzle, Molly C.; Kinziger, Andrew P. (2015). Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species [Dataset]. Dryad. https://doi.org/10.5061/dryad.6rs23