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

to maximize biodiversity detection while minimizing cost and effort. In our case study, the sampling effort was limited, and thus there are several ways the proportion of species detected could be improved: (1) increasing sampling effort in the field by sampling more sites, (2) col- lecting more replicate biological samples at each site, and (3) including additional amplicons during laboratory processing. Given the limited extent and breadth of our sampling effort, the conclusions regarding the effect of covariates and the estimates of occupancy, capture, and detection probabilities for individual species should not be extrapolated to other systems. Fur- ther research should investigate the impacts of variation in sequencing depth and amplicons targeted on detection probability in metabarcoding studies, particularly in other ecosystems and across greater spatial scales. Through the inclusion of environmental and experimental covariates, the multi-species occupancy framework can be applied for direct ecological assessment and to improve the methodology for next-generation biodiversity assessment. Metabarcoding results are often presented as taxonomic lists of species presence with alpha and beta-diversity estimates, and Fig 4. Mean detection probability estimated from occupancy model 9 (ψ(.) θ(.) p(amplicon)) for each species plotted by amplicon and phylum for metazoan phyla only. The band in the middle of the box represents the median and the upper and lower edges of the box represent the upper and lower quartiles. The whiskers represent 1.5 times the inter-quartile range.

https://doi.org/10.1371/journal.pone.0224119.g004 PLOS ONE Multi-species occupancy models for metabarcoding PLOS ONE | https://doi.org/10.1371/journal.pone.0224119 March 19, 2020 11 / 17