TY - JOUR
T1 - Critical considerations for the application of environmental DNA methods to detect aquatic species
AU - Goldberg, Caren S.
AU - Turner, Cameron R.
AU - Deiner, Kristy
AU - Klymus, Katy E.
AU - Thomsen, Philip Francis
AU - Murphy, Melanie A.
AU - Spear, Stephen F.
AU - McKee, Anna
AU - Oyler-McCance, Sara J.
AU - Cornman, Robert Scott
AU - Laramie, Matthew B.
AU - Mahon, Andrew R.
AU - Lance, Richard F.
AU - Pilliod, David S.
AU - Strickler, Katherine M.
AU - Waits, Lisette P.
AU - Fremier, Alexander K.
AU - Takahara, Teruhiko
AU - Herder, Jelger E.
AU - Taberlet, Pierre
N1 - Funding Information:
This manuscript is a product of collaborations that formed as a result of a symposium on environmental DNA that occurred at the 2013 International Congress for Conservation Biology in Maryland, USA. CSG, KMS, AKF and LPW were supported in part by the Department of Defense Environmental Security Technology Certification Program (RC-201204 and RC-201205). PFT was supported by the Danish National Research Foundation. MAM was supported in part by NSF grant # EPS-1208909 and Wyoming EPSCOR WyCEHG seed grant. CRT was supported in part by NSF IGERT award 0504495. KD was supported in part by US DoD SERDP RC-2240. JEH was supported by the Dutch Network Ecological Monitoring, Rijkswaterstaat, NVWA, STOWA and several Dutch Waterboards. PT is co-inventor of several patents concerning the DNA-based identification of plants, vertebrates, amphibians, fishes and earthworms. These patents only restrict commercial applications and have no impact on the use of the method by academic researchers. PT is member of the scientific committee of the SPYGEN company (http://www.spygen.com). CRT is currently a scientist in a commercial company, ecoSysGen, which specializes in genetic and genomic analysis of environmental mixtures for ecosystem monitoring. CRT did not receive funding from ecoSysGen, while this study was conducted. We thank E. Monroe and two anonymous reviewers for insightful feedback. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. This manuscript does not include data.
Publisher Copyright:
© 2016 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of the British Ecological Society
PY - 2016/11/1
Y1 - 2016/11/1
N2 - Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.
AB - Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.
KW - biodiversity
KW - eDNA
KW - invasive species
KW - non-destructive sampling
KW - quantitative PCR
KW - reporting guidelines
UR - http://www.scopus.com/inward/record.url?scp=84994472166&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.12595
DO - 10.1111/2041-210X.12595
M3 - Review article
AN - SCOPUS:84994472166
VL - 7
SP - 1299
EP - 1307
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
SN - 2041-210X
IS - 11
ER -