Contrasting the contributions of <scp>12S eDNA</scp> metabarcoding, visual surveys and anaesthetic collections to the historical regional diversity of cryptobenthic and conspicuous fish

Taxonomic gaps in community biodiversity assessments are now commonly addressed by combining traditional monitoring methods and environmental DNA (eDNA) metabarcoding, widely recognized for having the ability to uncover rare and cryptic diversity. However, only a few studies have assessed the efficacy of this novel technique for detecting cryptobenthic fishes and tested the limitations of incomplete genetic reference availability for a historically neglected component of fish communities. Our goals were (i) to compare cryptobenthic and conspicuous fish detections by 12S eDNA metabarcoding, visual surveys and anaesthetic fish collections, and (ii) to compare emerging regional diversity patterns against a long-term historical record for the Gulf of California. Despite adding new local references for 36 cryptobenthic fishes, 12S eDNA metabarcoding detected only seven taxa. Visual surveys provided similar results, highlighting fish collections as the primary source, with 57 cryptobenthic fishes recovered. Conspicuous fishes had an equal and highly complementary contribution by 12S eDNA and visual surveys. When combining contemporary detections from all methods, we recovered 43% of cryptobenthic and 16% of conspicuous fishes, relative to the historical records. The spatial community structure for detected cryptobenthic fishes differed from historical expectations and conspicuous fishes, showing no differences in community richness nor composition between Northern and Central Gulf communities. Our study highlights the limitations of eDNA for monitoring cryptobenthic fishes, and that their patterns of community structuring are driven by distinct factors compared to conspicuous fishes.