(2) Read numbers were significantly correlated to the total surface area of the fish population, and numerical abundance to a lesser degree however, dominant taxa largely drove those correlations, and simulations showed that biases in the most abundant taxa will have disproportionate effects on the strength of the correlation.
Our results demonstrate that (1) ultra‐high‐throughput sequencing on the newer NovaSeq patterned flow cell provided reliable detection of very rare taxa-with detections of a single individual.
The fish species and abundances in the system were recorded during piscicide treatment and subsequent native species restocking. Mitochondrial 12S eDNA amplicon sequencing via Illumina NovaSeq was analyzed using the DADA2 model‐based exact sequence inference. In this study, we examine methodological approaches to improve eDNA metabarcoding assessments of community structure using fish community diversity in a pond in south Florida using MiFish primers modified to improve cichlid detection. Further, hyper‐abundant species may disproportionately affect community composition assessments and impair the detection of rare species (i.e., “species masking”). However, limitations of metabarcoding include taxon‐specific biases in amplification and sequencing that distort assessments of community composition. Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non‐invasive sampling of biological communities than conventional methods.
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