TY - JOUR
T1 - Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system
AU - Shaw, Jennifer L.A.
AU - Clarke, Laurence J.
AU - Wedderburn, Scotte D.
AU - Barnes, Thomas C.
AU - Weyrich, Laura S.
AU - Cooper, Alan
N1 - Funding Information:
The LRMW fyke net sampling was funded by The Murray–Darling Basin Authority's the Living Murray Initiative, and was managed by Adrienne Rumbelow from the Department of Environment, Water and Natural Resources (DEWNR), South Australia. The fyke net sampling was conducted in accordance with South Australia's Fisheries Management Act 2007 (exemption no. 9902595 and 9902676) and The University of Adelaide's Animal Ethics Policy (approval no. S-2012-167). We would like to thank Douglas Green from DEWNR for providing the fyke net data for the six NPR sites. The eDNA aspect of this project was financially supported by the Australian Research Council (ARC) linkage grant LP0991985 .
Publisher Copyright:
© 2016 Elsevier Ltd.
PY - 2016/5/1
Y1 - 2016/5/1
N2 - Regular biological surveys are essential for informed management of freshwater ecosystems. However, current morphology-based biodiversity surveys can be invasive, time-consuming, and financially expensive. Recently, environmental DNA (eDNA) sequencing has been suggested as an alternative non-invasive, time- and cost-effective biological survey tool. However, eDNA sequencing tools require experimental validation in natural ecosystems before confidence in their use can be assumed. In this study, we compare fish community data obtained via eDNA metabarcoding to that of conventional fyke netting within two complex and drought-prone river systems. We also compare different eDNA sampling strategies and genetic markers for detecting rare and threatened fish species. We were able to detect 100% of the fyke net caught-species from eDNA when appropriate sampling strategies were used, including threatened and invasive species. Specifically, we found that two 1 L water samples per site were insufficient for detecting less abundant taxa; however, five 1 L samples per site enabled a 100% detection rate. Further, sampling eDNA from the water column appeared to be more effective for detecting fish communities than eDNA from sediments. However, on a per site basis, community discrepancies existed between the two methods, highlighting the benefits and limitations of both approaches. We demonstrate that careful interpretation of eDNA data is crucial as bioinformatic identification of sequences, without logical inference or local knowledge, can lead to erroneous conclusions. We discuss these discrepancies and provide recommendations for fish eDNA metabarcoding surveys.
AB - Regular biological surveys are essential for informed management of freshwater ecosystems. However, current morphology-based biodiversity surveys can be invasive, time-consuming, and financially expensive. Recently, environmental DNA (eDNA) sequencing has been suggested as an alternative non-invasive, time- and cost-effective biological survey tool. However, eDNA sequencing tools require experimental validation in natural ecosystems before confidence in their use can be assumed. In this study, we compare fish community data obtained via eDNA metabarcoding to that of conventional fyke netting within two complex and drought-prone river systems. We also compare different eDNA sampling strategies and genetic markers for detecting rare and threatened fish species. We were able to detect 100% of the fyke net caught-species from eDNA when appropriate sampling strategies were used, including threatened and invasive species. Specifically, we found that two 1 L water samples per site were insufficient for detecting less abundant taxa; however, five 1 L samples per site enabled a 100% detection rate. Further, sampling eDNA from the water column appeared to be more effective for detecting fish communities than eDNA from sediments. However, on a per site basis, community discrepancies existed between the two methods, highlighting the benefits and limitations of both approaches. We demonstrate that careful interpretation of eDNA data is crucial as bioinformatic identification of sequences, without logical inference or local knowledge, can lead to erroneous conclusions. We discuss these discrepancies and provide recommendations for fish eDNA metabarcoding surveys.
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U2 - 10.1016/j.biocon.2016.03.010
DO - 10.1016/j.biocon.2016.03.010
M3 - Article
AN - SCOPUS:84960969815
SN - 0006-3207
VL - 197
SP - 131
EP - 138
JO - Biological Conservation
JF - Biological Conservation
ER -