Which DNA Marker Best Identifies Marine Fish? A Landmark Benchmark Puts

A new benchmarking study in Metabarcoding and Metagenomics tackles a key practical problem for eDNA metabarcoding: which genetic marker—and which fragment—most reliably identifies marine fish at species level. Led by researchers using public NCBI GenBank sequences, the study compared 12S rRNA, 16S rRNA and COI, alongside two widely used amplicons for each marker. Using two complementary datasets—one based on mitochondrial genomes that extract multiple target regions from the same individuals, and another using independently deposited sequences reflecting real reference libraries—the team assessed discriminatory power by testing which species sequences formed monophyletic clades. In mitochondrial-genome results, COI regions (Folmer and Leray-Lobo) led with 89.2% and 87.0% monophyly, while a short 12S Teleo fragment averaged under 70 base pairs scored 71.6%, the lowest.