Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

Beverly McClenaghan; Zacchaeus G Compson; Mehrdad Hajibabaei

doi:10.1371/journal.pone.0224119

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

PLoS One. 2020 Mar 19;15(3):e0224119. doi: 10.1371/journal.pone.0224119. eCollection 2020.

Authors

Beverly McClenaghan¹, Zacchaeus G Compson¹, Mehrdad Hajibabaei^{1

2

3}

Affiliations

¹ Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.
² Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
³ Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada.

Abstract

Environmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aquatic Organisms / genetics*
Biodiversity*
DNA Barcoding, Taxonomic*
DNA, Environmental / genetics*

Substances

DNA, Environmental

Grants and funding

This work was partly funded through a Petroleum R&D Grant from InnovateNL (contract number 5405.2121.101), an award from the Atlantic Canada Opportunities Agency’s Atlantic Innovation Fund (project number 781-37749-207993), and a grant from Petroleum Research Newfoundland and Labrador. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of Petroleum Research or its members. B.M. and Z.G.C. are employees of eDNAtec Inc. and M.H. is the founder and Chief Scientific Officer of eDNAtec Inc. The compensations for authors B.M., Z.G.C. and M.H. were supported by the funder, but the funder did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.