Abstract
Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among the most threatened and rare elasmobranch species and are difficult to detect in turbid, coastal habitats. Reliable cost-effective tools to detect these species are urgently needed to increase their conservation potential. Characterization of environmental DNA (eDNA) extracted from water samples has garnered significant appeal for detection of rare and threatened species. To assist conservation and monitoring efforts for sawfishes using eDNA, species-specific TaqMan quantitative polymerase chain reaction assays were developed and validated to detect 1.25–5 copies of a 12S rRNA gene fragment. Filter samples were collected in Northern Territory, Australia to assess the utility of the developed eDNA assays and compare the efficacy of preservation and extraction workflows for detecting rare species. Dwarf sawfish (Pristis clavata) were detected in three of 20 sites, and there was a significant effect of preservation and extraction workflow on total eDNA yield and subsequent detection success. Longmire's preserved samples extracted using glycogen-aided precipitation yielded a significantly higher concentration of total eDNA (n = 60; β = 1.27, t(95) = 8.172, P < 0.0001) and yielded positive P. clavata eDNA detections compared to ethanol preserved samples extracted using QIAGEN DNeasy kit, which did not yield any positive detections. The optimized eDNA assays were developed to support monitoring efforts for endangered sawfishes. Importantly, this study demonstrates that choice of preservation and extraction workflow requires careful consideration, especially when detection of rare or threatened species can have important management and conservation outcomes.
| Original language | English |
|---|---|
| Pages (from-to) | 2131-2148 |
| Number of pages | 18 |
| Journal | Aquatic Conservation: Marine and Freshwater Ecosystems |
| Volume | 31 |
| Issue number | 8 |
| Early online date | Apr 2021 |
| DOIs | |
| Publication status | Published - Aug 2021 |
Bibliographical note
Funding Information:This work was supported by a Save Our Seas Foundation Keystone Grant awarded to C.A.S. and D.R.J. M.K.C. was supported by a Research Training Programme Scholarship at James Cook University (JCU), JCU Prestige Scholarship, and Australian Government's National Environmental Science Programme (NESP) Top‐up Scholarship. P.M.K. was supported by the NESP Marine Biodiversity Hub Project A1. R.E. was supported by the NESP Northern Australia Environmental Resources Hub Project 4.3. Field work was conducted on the traditional country of the Larrakia, Bininj, and Mungguy people. We gratefully acknowledge the traditional custodians for allowing access to and to conduct this research on their sea country. We also acknowledge the Bindal and Wulgurukaba people who are the traditional custodians of the country where all other components of this research were conducted. We are grateful to Heather Robson and Wayne Morris (Grover® Scientific) for the opportunity to field test Grover® eDNA pumps and filter cartridges, Jenny Bigman who supported field sampling, and Melissa Joyce who provided administrative support. We thank Madeline Green (Otlet; otlet.io); William White (Commonwealth Scientific and Industrial Research Organisation; CSIRO); and Blanche D'Anastasi, Andrew Chin, and Ana Barbosa Martins (JCU) for providing shark and ray tissue samples; and Pierre Feutry (CSIRO) for providing sequence data. We also thank Technical Application Specialists from Life Science Solutions, ThermoFisher Scientific, Victoria, Australia for technical support with assay development.
Publisher Copyright:
© 2021 John Wiley & Sons, Ltd.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
