The development and validation of eDNA protocols for detecting the presence and movement of mako sharks in Victoria

Sharks play an important role in marine ecosystems by being apex predators that feed on animals lower down the food web. This helps to regulate and maintain an ecosystem by balancing the food web, as they directly limit populations of prey below them. When an apex predator is removed from the community, the entire ecosystem is at risk of collapse. Due to centuries of overfishing, sharks are now deemed as critically endangered. In many parts of the world there has been little action by fisheries regulators in managing targeted and accidental shark captures, and remote fishing communities that have high levels of poverty make it difficult to track capture rates due to poorly recorded data. In Australia, the shortfin mako shark, Isurus oxyrinchyus, is increasingly being targeted as a recreational fisheries species. However, there is currently a lack of information on patterns of movement and near shore visitation rates for this species, which are urgently needed to inform effective management. In south-eastern Australia, I. oxyrinchyus are currently being monitored and tracked for fisheries via baiting, hooking, and tagging, however this is costly and can only be done for a limited number of individuals. Environmental DNA (eDNA) is an emerging technology that provides a rapid, targeted, and cost-effective tool for detecting the presence of a species and can provide crucial information on the movement and near shore visitation rates of sharks to better inform management. In this study, I test and validate a qPCR assay designed to be specific to I. oxyrinchyus. The qPCR assay was shown to be highly species specific and did not cross amplify with 14 other Australian shark species tested. Analyses on the limits of detection (LOD) showed that the assay was highly sensitive and could reliably detect DNA concentrations as low as 1.31 pg/μl. A controlled laboratory eDNA decay trial showed that after approximately 48-hours, the concentration of eDNA reaches the LOD and becomes increasing difficult to reliably detect. This indicates that sharks may be detectable within an area up to two days after a visitation. Finally, the assay was shown to reliably amplify field 4 water samples collected from around a shortfin mako shark capture. The results from this study demonstrate that this qPCR assay is highly species specific and sensitive for detecting I. oxyrinchyus in the field and provides a new tool to help current tracking of this species and understanding movement and near shore visitation rates.