Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United States

Abstract

An accurate, comprehensive reference sequence library maximizes information gained from environmental DNA (eDNA) metabarcoding of marine fishes. Here, we used a regional checklist and early results from an ongoing eDNA time series to target mid-Atlantic U.S. coastal fishes lacking reference sequences. We obtained 60 specimens representing 31 species from NOAA trawl surveys and institutional collections, and analyzed 12S and COI barcode regions, the latter to confirm specimen identification. Combined with existing GenBank accessions, the enhanced 12S dataset covered most (74%) of 341 fishes on New Jersey State checklist including 95% of those categorized abundant or common. For eDNA time series, we collected water samples approximately twice monthly for 24 months at an ocean and a bay site in New Jersey. Metabarcoding was performed using separate 12S primer sets targeting bony and cartilaginous fishes. Bioinformatic analysis of Illumina MiSeq fastq files with the augmented library yielded exact matches for 90% of the 104 fish amplicon sequence variants generated from field samples. Newly obtained reference sequences revealed two southern U.S. species as relatively common warm season migrants: Gulf kingfish (Menticirrhus littoralis) and Brazilian cownose ray (Rhinoptera brasiliensis). A beach wrack specimen corroborated the local presence of Brazilian cownose ray. Our results highlight the value of strengthening reference libraries and demonstrate that eDNA can help detect range shifts including those of species overlooked by traditional surveys.

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

“…In many cases, eDNA detected cryptic, nocturnal, rare, or elusive species missed by conventional surveys (Thomsen et al, 2016;Closek et al, 2019;Bessey et al, 2020). Further, more recent studies highlight improved species detection in marine systems with better populated reference libraries (Stoeckle et al, 2020) and multiple markers (Lafferty et al, 2020). Marine systems are especially difficult to sample comprehensively with conventional methods, and eDNA metabarcoding could expand the scale and resolution of monitoring at lower relative cost and effort.…”

Gap analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians

“…Our analysis further elucidate the necessity of filling the gaps in the barcode libraries used. It is evident that the level of taxonomic detection and degree of accuracy by newly developed molecular tools is directly contingent on the reference libraries' completion and reliability of the DNA records [21,24,32,33]. Given our increased reliance on molecular taxonomy as a robust tool [4], strengthening the existing reference libraries is a need for a wide range of scientific and applied purposes, such as monitoring, eDNA, and metabarcoding approaches, all targeting matched identifications and for assessments of biodiversity and abundance [5,[14][15][16][17]33].…”

Gap-analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians

“…Our analysis further elucidate the necessity of lling the gaps in the barcode libraries used. It is evident that the level of taxonomic detection and degree of accuracy by newly developed molecular tools is directly contingent on the reference libraries completion and reliability of the DNA records [26][27][28][29]. Given our increased reliance on molecular taxonomy as a robust tool [4], strengthening the existing reference libraries is a need for a wide range of scienti c and applied purposes, such as monitoring, eDNA and metabarcoding approaches, all targeting matched identi cations and for assessments of biodiversity and abundance [5,14-…”