An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the Western Atlantic

Abstract

<jats:title>Abstract</jats:title><jats:p>The Critically Endangered Smalltooth Sawfish, <jats:italic>Pristis pectinata</jats:italic>, was once widespread in the tropical and subtropical waters of the Atlantic Ocean, but following substantial declines over the past century, the core population is currently confined to southwest Florida in the U.S. and the Bahamas. Recent research and verified public encounter reports suggests that this core population may be stabilizing and, potentially, expanding into formerly occupied areas of their historic range in the Western Atlantic; however, the status of this species in non-core waters is not well understood. Environmental DNA (eDNA) methods provide a relatively cost effective and rapid assessment tool for monitoring species occurrence in aquatic habitats. Here, we have developed an eDNA tool: a species-specific Droplet Digital™ PCR (ddPCR™) assay targeting a 100-base pair portion of the mitochondrial NADH dehydrogenase subunit 2 gene in <jats:italic>P</jats:italic>. <jats:italic>pectinata</jats:italic>, with the ability to reliably detect as little as 0.25 pg of target DNA. The assay was validated by collecting and analyzing a water sample from known <jats:italic>P</jats:italic>. <jats:italic>pectinata</jats:italic> nursery habitat in Florida, which was found to contain an average of 11.54 copies of target DNA/µL (SE = 0.72) in the reaction. The assay was then further tested by placing a juvenile sawfish in an <jats:italic>ex situ</jats:italic> tank and analyzing water samples collected at time intervals. The implementation of this eDNA tool into field surveys will provide additional, reliable data to assess species recovery and aid in prioritizing localities beyond the core range in which to focus research and education initiatives.</jats:p>

Targeted Next Generation Sequencing of environmental DNA improves detection and quantification of invasive European green crab (Carcinus maenas)

“…The significant positive relationships observed between eDNA concentration and CPUE for qPCR and tNGS assays support the use of eDNA as a metric for species abundance, an important result that has been established in multiple previous studies and confirmed here for green crab (Doi et al, 2017; Knudsen et al, 2019; Lacoursière-Roussel et al, 2016; Lehman et al, 2019; Shelton et al, 2019). The tNGS method shows higher precision relative to qPCR for predicting CPUE, and this difference is most apparent at low abundances where the predicted abundance (CPUE) confidence interval for tNGS is much smaller than qPCR.…”

“…The application of eDNA is generally limited to presence/absence surveys, but eDNA has shown to be positively correlated with species abundance in laboratory and field-based surveys (Doi et al, 2017; Knudsen et al, 2019; Lacoursière-Roussel et al, 2016; Lehman et al, 2019; Shelton et al, 2019). High variation in quantitative results from field surveys and a lack of rigorous validation in controlled laboratory settings have lead to considerable scrutiny of these methods (Mauvisseau, Burian, et al, 2019).…”

“…Quantitative eDNA applications have been successfully compared with traditional survey methods for species at risk (Lehman et al, 2019; Shelton et al, 2019), invasive species (Thomas et al, 2019), and fisheries stock assessments (Doi et al, 2017; Knudsen et al, 2019; Lacoursière-Roussel et al, 2018). In general, eDNA availability of a focal species is positively correlated with the abundance of that species in the vicinity (Doi et al, 2017; Knudsen et al, 2019; Lacoursière-Roussel et al, 2016; Lehman et al, 2019; Shelton et al, 2019). The decay rate of eDNA has been experimentally observed at hours to days and the geographic area which it may represent is highly variable among environments (i.e.…”

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay

“…Given the rarity of shark eDNA targets and the limitations of real-time PCR we suggest that future applications of this and similar assays should use digital droplet PCR (ddPCR) 54 for the high resolution quantification of rare target eDNA. This has recently been trialed for the detection of elasmobranch eDNA 20,23,55 , but has yet to be implemented for the spatio-temporal tracking of abundance.…”

Sawfish, Read in Tooth and Saw: rostral teeth as endogenous chemical records of movement and life-history in a critically endangered species

“…However, community-based approaches and opportunistic catch data is often of low-resolution. Further, designation of important habitat is often done without the opportunity for thorough assessment of local behavior and ecology, as evidenced by habitat designation of the smalltooth sawfish in the United States which is only now being supplemented by direct studies of movement and location using telemetry (Wiley & Simpfendorfer, 2010; Norton et al, 2012; Graham et al, 2020), and presence/absence studies using environmental DNA (eDNA) techniques (Simpfendorfer et al, 2016; Lehman et al, 2020).…”