2b-RAD STRUCTURE alignment of Ophionotus victoriae (STACKS)

1,739 bi-allelic SNP loci using using the STACKS software package

Quantifying Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms

The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications

Ophionotus_cleaned_fasta

Compressed fasta files that have been screened for quality, size and presence of the AlfI restriction site. This data is ready for further processing through STACKS software, Eli Meyer's (Oregon State University) scripts (https://github.com/Eli-Meyer) or through custom software

astrotoma_94_955

This is the main data matrix file, ready for downstream analyses

Astrotoma_cleaned_fasta

This file contains all sample files. All files have be checked for quality, size, and the presence of the restriction enzyme AlfI. Samples are ready for further processing through custom pipelines or through programs such as STACKS

README_Astrotoma

README file describing the details of all uploaded dat

Concentrations of genomic DNA from target and non-target organisms present in heterogeneous samples.

<p>For each target organism, 100 µL of sample was prepared that included the equivalent amount of DNA from a single target organism larvae (see text), background DNA (<i>Daphnia magna</i>) and the other two non-target species at high concentrations. Additionally, for each target organism, blank samples that included DNA from non-target organisms and background DNA were also prepared and tested as the background for each heterogeneous sample.</p

Nyquist plots (Realized impedance change (Z_re) vs. imaginary impedance change [<b>13</b>] (|Z_im|) for heterogeneous sample tests for <i>Limnoperna fortunei</i>, <i>Dreissena bugensis</i>, and <i>Erocheir sinensis.</i>

<p>Each column represents the tests of each heterogeneous sample for the identified target species (n = 3). Black squares indicate test samples and red triangles indicate background signal. Symbols on each individual chart indicate the result of the detection experiment for the target species. The accuracy of our detection in the double-blind tests was 100%.</p

HCO-2198 used as reverse primer in ssPCR amplification [20]; <i>D. bugensis</i> forward primer from C. Nowak, pers. com. <i>Limnoperna</i> markers from Pie et al. [16].

<p>HCO-2198 used as reverse primer in ssPCR amplification <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017280#pone.0017280-Folmer1" target="_blank">[20]</a>; <i>D. bugensis</i> forward primer from C. Nowak, pers. com. <i>Limnoperna</i> markers from Pie et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017280#pone.0017280-Pie1" target="_blank">[16]</a>.</p

Schematic diagram of carbon nanotube chip design and its functionality.

<p>Chip design, fabrication, and processing are described elsewhere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017280#pone.0017280-Basuray1" target="_blank">[13]</a>.</p