Getting the most from eDNA sampling: Problems and solutions for quantitative estimates and rare species detection. Aquatic vertebrate metagenome

Metabarcoding of environmental DNA (eDNA) can provide more comprehensive, efficient, and non-invasive sampling of biological communities than conventional methods, but current methods have important limitations. One limitation is that taxon-specific biases in DNA amplification and sequencing can distort assessments of community composition. Another is that and hyper-abundant species may disproportionately affect community assessments and impair the detection of rare species (species masking). In this study, we examine methodological approaches to improve eDNA metabarcoding assessments of community structure during whole fish community removal, census, and reintroduction experiment. Fish diversity in a pond in south Florida was characterized by 12s mitochondrial eDNA amplicon sequencing via Illumina Novaseq 6000. The fish present in the system were quantified, followed by native species restocking.