Advancing eDNA methods for monitoring sharks and rays
File(s)
Author(s)
Dunn, Nicholas
Type
Thesis
Abstract
As a result of overexploitation, many elasmobranch populations are in decline. To best protect remaining populations, efficient and effective monitoring methods are required. Recently, an increasing number of studies are using environmental DNA (eDNA) for biodiversity monitoring.
This thesis explores the use of eDNA methods for monitoring elasmobranch populations. Using species- specific qPCR assays to investigate the presence of two elasmobranch species across a year in a Welsh Bay, I show that the critically endangered angelshark (Squatina squatina) can be detected throughout the year and that the number of detections peak in the summer months and is detected more readily than the thornback ray (Raja clavata). I then examine the diversity of elasmobranchs around a remote atoll in the Chagos Archipelago using eDNA metabarcoding and identify ten elasmobranch species. The grey reef shark (Carcharhinus amblyrhynchos) and the silvertip shark (Carcharhinus albimarginatus) were present throughout the atoll and their presence across the archipelago was further explored using species-specific methods. Detections were significantly lower around atolls in the north of the archipelago where illegal fishing is ongoing, indicating that eDNA is able to pick up signals of population suppression across broad scales. Finally, I present a novel method for assessing the distribution of eDNA using particle tracking. I add degradation into simulations to predict the origins of detected eDNA in the Chagos Archipelago and predict that most particles travel less than two kilometres before being degraded. I also apply the method to produce a probability landscape for the distribution of white shark (Carcharodon carcharias) eDNA in the Sicilian Channel, identifying a hotspot off the western tip of Sicily.
Overall, I conclude that eDNA can be used to advance our understanding of elasmobranchs but suggest that caution is needed when utilising these methods for monitoring populations at low densities. I discuss knowledge gaps that require attention before the methods can be reliably used to monitor elasmobranchs.
This thesis explores the use of eDNA methods for monitoring elasmobranch populations. Using species- specific qPCR assays to investigate the presence of two elasmobranch species across a year in a Welsh Bay, I show that the critically endangered angelshark (Squatina squatina) can be detected throughout the year and that the number of detections peak in the summer months and is detected more readily than the thornback ray (Raja clavata). I then examine the diversity of elasmobranchs around a remote atoll in the Chagos Archipelago using eDNA metabarcoding and identify ten elasmobranch species. The grey reef shark (Carcharhinus amblyrhynchos) and the silvertip shark (Carcharhinus albimarginatus) were present throughout the atoll and their presence across the archipelago was further explored using species-specific methods. Detections were significantly lower around atolls in the north of the archipelago where illegal fishing is ongoing, indicating that eDNA is able to pick up signals of population suppression across broad scales. Finally, I present a novel method for assessing the distribution of eDNA using particle tracking. I add degradation into simulations to predict the origins of detected eDNA in the Chagos Archipelago and predict that most particles travel less than two kilometres before being degraded. I also apply the method to produce a probability landscape for the distribution of white shark (Carcharodon carcharias) eDNA in the Sicilian Channel, identifying a hotspot off the western tip of Sicily.
Overall, I conclude that eDNA can be used to advance our understanding of elasmobranchs but suggest that caution is needed when utilising these methods for monitoring populations at low densities. I discuss knowledge gaps that require attention before the methods can be reliably used to monitor elasmobranchs.
Version
Open Access
Date Issued
2022-07
Date Awarded
2022-12
Copyright Statement
Creative Commons Attribution NonCommercial Licence
License URL
Advisor
Savolainen, Vincent
Carbone, Chris
Curnick, David
Sponsor
Natural Environment Research Council (Great Britain)
Publisher Department
Life Sciences
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)