TY - JOUR
T1 - Identifying error and accurately interpreting environmental DNA metabarcoding results
T2 - A case study to detect vertebrates at arid zone waterholes
AU - Furlan, Elise M.
AU - Davis, Jenny
AU - Duncan, Richard P.
N1 - Funding Information:
We thank the Joint Management Committees of the Tjorita/West MacDonnell Ranges and Watarrka National Parks for allowing access to field sites for eDNA collection. Thanks to A. Adamack for contributing to the study ideas and S. Votto for assistance in the field. Funding was provided through the Invasive Animals Cooperative Research Centre (Project 1.W.2) and a University of Canberra Early Career Researcher Grant.
Funding Information:
We thank the Joint Management Committees of the Tjorita/West MacDonnell Ranges and Watarrka National Parks for allowing access to field sites for eDNA collection. Thanks to A. Adamack for contributing to the study ideas and S. Votto for assistance in the field. Funding was provided through the Invasive Animals Cooperative Research Centre (Project 1.W.2) and a University of Canberra Early Career Researcher Grant.
Publisher Copyright:
© 2020 John Wiley & Sons Ltd
PY - 2020/9/1
Y1 - 2020/9/1
N2 - Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide-ranging applications from characterizing local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.
AB - Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide-ranging applications from characterizing local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.
KW - arid zone biodiversity
KW - eDNA metabarcoding
KW - false detection
KW - false positive
KW - terrestrial fauna
KW - type I error
UR - http://www.scopus.com/inward/record.url?scp=85087747541&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/57050503-586c-3525-bba8-c40aac67280d/
U2 - 10.1111/1755-0998.13170
DO - 10.1111/1755-0998.13170
M3 - Review article
AN - SCOPUS:85087747541
SN - 1755-098X
VL - 20
SP - 1259
EP - 1276
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 5
ER -