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

occupancy models that include sequencing depth as a covariate will allow the variation in sequencing effort, which cannot always be controlled, to be accounted for when making eco- logical conclusions about biodiversity and occupancy. The mean probability of capture estimate of 0.98 suggests a high probability of collecting a species’ DNA in a given sample. However, the mean detection probability was relatively low at 0.15, likely because many species were not detected consistently by multiple amplicons, and a Fig 2. (A) Community mean occupancy by water depth (m) and (C) community mean probability of detection by sequencing depth predicted using a multi- species, multi-scale community occupancy model. The dashed lines represent the 95% confidence interval. Parameter estimate for each species for (B) the effect of water depth on occupancy and (D) the effect of sequencing depth on detection in a multi-species, multi-scale community occupancy model. Solid red line indicates the community mean and dashed red lines indicate the upper and lower limits of the 95% confidence intervals of the community mean parameter estimate. Blue lines indicate 95% confidence intervals of individual species parameter estimates that do not overlap with 0. Grey lines indicate 95% confidence intervals of individual species parameter estimates that do overlap with 0. https://doi.org/10.1371/journal.pone.0224119.g002 PLOS ONE Multi-species occupancy models for metabarcoding PLOS ONE | https://doi.org/10.1371/journal.pone.0224119 March 19, 2020 9 / 17