Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes

For nearly 15 years now, environmental DNA has demonstrated its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration and primer choice have been less explored or need to be optimized according to specific survey objectives and study site characteristics. We evaluated these factors to help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of 520 sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum depth of 1,000 reads per sample), showed..., ,