Optimization of environmental DNA-based methods: a case study for detecting brook trout (<i>Salvelinus fontinalis</i>).

ABSTRACT: The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods across the eDNA workflow reduces the sensitivity of eDNA surveys and precludes the reliable comparison of findings across studies, respectively. DNA extraction is a prime target for optimization efforts because the extraction method is highly variable across eDNA studies despite being one of the most influential factors in detection efficiency across the entire post-collection workflow. Sequence analysis is arguably the least standardized step in the workflow, with new bioinformatics pipelines frequently emerging in the literature and being

SUBMITTER: Myler E 

PROVIDER: S-EPMC12906266 | biostudies-literature | 2026

REPOSITORIES: biostudies-literature