Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

Abstract

Environmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a noninvasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multi-stage workflow. Imperfect detection in the multi-stage workflow of eDNA metabarcoding also raises an issue of study design: namely, how available resources should be allocated among the different stages to optimize survey efficiency. Here, we propose a variant of the multispecies site occupancy model for eDNA metabarcoding studies where samples are collected at multiple sites within a region of interest. This model describes the variation in sequence reads, the unique output of the high-throughput sequencers, in terms of the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity, allowing the decomposition of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the efficiency of species detection with a limited budget. An application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and lower dominance of the sequences. The expected abundance of sequence reads was predicted to vary by up to 23.5 times between species. An analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred in order to achieve better species detection efficiency, provided that a throughput of tens of thousands of sequence reads was secured. The proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently.

Net overboard: Comparing marine eDNA sampling methodologies at sea to unravel marine biodiversity

“…Detectability of particular taxa (e.g., species of environmental concern, such as pests or pathogens) may depend on multiple factors, including physiological peculiarities or spatiotemporal distribution patterns (Mathieu et al, 2020; Moushomi et al, 2019). Therefore, when assessing the performance of sampling workflows, it is useful to evaluate multispecies detection probabilities by applying probabilistic modelling, such as the occupancy modelling approach used in the present and other studies (Fukaya et al, 2021; MacKenzie et al, 2002, 2005; Sutter & Kinziger, 2019). Here, the observed workflow‐related detection probabilities were consistent between 18S rRNA and COI genes, which is a promising result as it suggests that our findings can be generalized for different metabarcoding markers.…”

freqpcr: Estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples

“…As long as qPCR is used to estimate population allele frequency, the use of statistical inferences on the bulk samples, as presented in this study, will continue to be a realistic option for regional/temporal allele monitoring. Likewise, our model approach to the individual DNA yields can also be extended to the NGS‐based estimation procedures since the gamma distribution has been used to quantify environmental and forensic DNA (Cowell et al, 2007 ; Fukaya et al, 2021 ).…”

“…This error structure was originally developed by Sudo et al ( 2021 ) to model allele frequencies measured via quantitative sequencing, in which the gamma distributions were used to approximate the yield variations due to body weight plus post‐mortem DNA degradation on a trap. Of note, the gamma distribution has recently been used to approximate the DNA release of aquatic animals and DNA abundance in water (Fukaya et al, 2021 ).…”

Multispecies site occupancy modelling and study design for spatially replicated environmental DNA metabarcoding

“…DRR274455–DRR274604). The dataset and codes are archived in the Dryad Digital Repository https://doi.org/10.5061/dryad.3bk3j9kkm (Fukaya et al, 2021).…”