DOI: 10.5061/dryad.4tmpg4f5x
title: Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications

description: Bait and pond stores comprise potential, yet poorly understood, vectors
 for aquatic invasive species (AIS). We tested for AIS and illegal native
 species in 51 bait and 21 pond stores from the central Great Lakes (Lake
 Erie, Ohio and Lake St. Clair, Michigan) and the adjacent Wabash River
 (Indiana) using environmental DNA (eDNA) metabarcode assays of water
 samples and morphological identifications. Retailers were questioned about
 supply chains, and anglers surveyed about baitfish use and disposal.
 Assays revealed unadvertised species eDNA in 100% of bait stores, with 61%
 containing illegal native non-bait (totaling 13 species) and 88% having
 AIS (11 species). Illegal native non-bait species included juvenile
 walleye, yellow perch, and white sucker eDNA. AIS eDNA included Eurasian
 ruffe in seven stores (all states), silver carp in five (including a Lake
 Erie store in two separate years), and bighead carp in two Lake Erie
 stores that also had silver carp. Among pond stores, two in Lake St. Clair
 had bighead carp eDNA, one also contained silver carp, and a Wabash River
 location showed European ide. Unadvertised invasive snails were discerned
 in 55% of pond stores. Four contained zebra mussel eDNA and two had
 invasive bryozoans. Illegal native species and AIS were widespread, but
 showed little relationship to the retailers’ variable and extensive supply
 chains. Live baitfish releases were reported by 50% of Lake Erie anglers
 and 35% in Lake St. Clair. Consumer behavior and AIS prevalence in the
 bait and pond trades thus pose serious risks for introductions and spread.
description: MetaTrim.py: See README.md SeqTabToFasta.pl:
 script converts SeqTab format files with results from Dada2 (R package) to
 FASTA files for each sample. Expects an input file named SeqTab.txt in the
 CWD. BlastCylce500.pl: script performs BLAST searches
 for every sequence in files ending with ".fasta" in the CWD.
 BLAST searches are performed against custom databases for all
 Actinopterygii on GenBank and only fishes in the Great Lakes. If file
 name begins with "m" (MiFish), sequences are blasted against 12S
 databases, otherwise, against
 Cytochrome <em>b</em> databases.
 BlastCycle500Remote.pl: script performs BLAST searches for every
 sequence in files ending with ".fasta" in the CWD. BLAST is
 performed remotely against the entirety of GenBank.
 SummarizeBlasteDNAEnvironmentSepASVs.pl: script summarizes BLAST
 results (files ending in "Res.txt" from BlastCycle500.pl").
 Species names for hits with &gt;90% query cover and identity are
 concatenated if the e value is the lowest for all hits. Returns a txt file
 with summarized hits per sample. Expects an input file named InReads.txt
 in the CWD. This file is tab delimited. The first value should be the
 sample name identical to that used as input in the above script, followed
 by tab, then the number of reads in that sample. This allows calculation
 of proportion of read represented by the hit.
 BOPPSummarize*.py: script removes species hits that do not occur
 at a portion above the error for a specific marker in a specific sample,
 unless the occur in multiple markers in that same sample. Hits are then
 compared against morphological results from bait and pond stores. Several
 inputs are required and are included in this repository. They include a
 file showing the error rate calculated from positive controls for each
 marker on each sequencing run (ErrorCons.txt; if none is supplied, the
 default value will be 0.001), a shop key file (ShopKeybaitShops.txt), a
 file indicating the legality of species in each state sampled
 (SppStatusBait.txt), morphological results from each store at the time of
 sampling (InMorph.txt), and BLAST results files (summarized by the script
 above, separated by marker).