Abstract
The integration of eDNA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. This study aimed to compare eDNA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4–6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus ‘positive’ filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.
Highlights
Many shark populations have been heavily impacted by overexploitation and environmental disturbances[1,2,3,4,5,6]
limit of detection (LOD) and limit of quantification (LOQ) were determined at a concentration of 13.1 × 10−6 ng/μL of genomic DNA (gDNA)
LOD and LOQ were determined at a gDNA concentration of 13.1 × 10−6 ng/μL; the average Cq was 42.09
Summary
Many shark populations have been heavily impacted by overexploitation and environmental disturbances[1,2,3,4,5,6]. EDNA approaches are based on the isolation, amplification and sequencing of DNA traces from skin cells, egestion, and metabolic waste left behind in the e nvironment[14,15]. They offer a promising avenue for non-invasive, cost-effective, and scalable monitoring studies of aquatic organisms that can achieve very high replication independent of fisheries[16,17]. Promising as a method for shark detection, more research in well-studied ecosystems is necessary to understand whether eDNA monitoring can be used to track population dynamics over time. We predicted that C. limbatus eDNA detection, measured in this study by the proportion of positive filters (i.e. C. limbatus detected) and the relative DNA concentrations measured on these filters, would be significantly higher in spring and early summer than in late summer and fall
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