Abstract
Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.
Highlights
Accurate information on the abundance and spatial distribution of aquatic species is essential for understanding their ecology and for their management in increasingly human-impacted environments
Tests of the molecular beacon assay with fin-clip extracted DNA from river herring and a number of non-target fishes showed that the assay was highly specific to river herring (Fig 2)
No amplification was ever observed for hickory or American shad, which are the two most closely related alosids to river herring and often co-occur with river herring within river systems in Chesapeake Bay [77]
Summary
Available mitochondrial DNA sequences from river herring and a number of phylogenetically similar fish species (e.g. other shad, alosids and clupeids) were collected from NCBI Genbank and aligned in AliView v.1.18 [65] to examine the suitability of different loci for designing a qPCR assay. Significant numbers of sequences were available for cytochrome oxidase 1 (hereafter CO1), cytochrome B, NADH2, and 18SrRNA among others, but only CO1 contained regions with sufficient numbers of diagnostic nucleotide differences between river herring and other closely related alosids for probe design. Hickory shad Alosa mediocris is even more closely related to river herring, but fewer mitochondrial sequences were publicly available, and none for CO1 at the time of assay design. A ~50 bp region of CO1 exhibiting ~8–10 sequence differences between river herring and American or hickory shad
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