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

RESEARCH ARTICLE Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA Beverly McClenaghanID1, Zacchaeus G. CompsonID1, Mehrdad Hajibabaei1,2,3* 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 * hajibabaei@gmail.com Abstract Environmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid bio- diversity assessment. As with any ecological survey, false negatives can arise during sam- pling 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 experi- mental 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 practition- ers with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms. Introduction

Environmental DNA (eDNA) as a signal for diversity detection is rapidly advancing. In fresh- water systems, in particular, eDNA is now used as a bioassessment tool in both single-species qPCR-based studies and in sequencing-based metabarcoding community assessments [1–3]. Approaches based on eDNA are also gaining traction in the marine environment [4,5]. Oceans are complex, highly diverse, and difficult to sample; therefore, identifying organisms from all trophic levels and taxonomic groups from a single survey method will greatly facilitate rapid, consistent biodiversity surveys [6]. eDNA metabarcoding provides a streamlined method of biodiversity assessment, generating high-resolution biodiversity data with time and effort sav- ings during sample collection and analysis [7,8]. However, there are several levels of uncertainty associated with eDNA sampling for com- munity assessments. The potential for false negatives during sampling, where a species present in the environment is not detected in surveys, can bias results [9]. False negatives can occur PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.0224119 March 19, 2020 1 / 17 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: McClenaghan B, Compson ZG, Hajibabaei M (2020) Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA. PLoS ONE 15(3): e0224119. https:// doi.org/10.1371/journal.pone.0224119 Editor: Hideyuki Doi, University of Hyogo, JAPAN Received: October 4, 2019 Accepted: February 16, 2020

Published: March 19, 2020 Copyright: © 2020 McClenaghan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All sequencing data have been deposited into NCBI’s Sequence Read Archive under accession number PRJNA574050. 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