eDNA metabarcoding detection of nearshore juvenile white sharks (Carcharodon carcharias) and prey fish communities

Abstract

Traditional methods for assessing fish communities often face biased catchabilities, resulting in inconsistent detection of certain species. Pelagic elasmobranchs, such as white sharks (Carcharodon carcharias) are challenging to detect and quantify due to their low density, large size, and high mobility. Metabarcoding, an emerging approach, identifies species through genetic sequencing of environmental DNA (eDNA) samples, but requires further calibration due to its novelty. We assessed the efficacy of eDNA approaches to detect white sharks and associated fish prey communities. Juvenile white sharks (JWS) in the Southern California Bight form dense aggregations, offering a unique setting to compare methods. We collected eDNA from 491 seawater samples at three current and two former aggregation sites. Metabarcoding and white shark-specific qPCR were compared to aerial drone surveys and passive acoustic telemetry for JWS, and to beach seines and baited remote underwater videos for the broader fish community. Overall, metabarcoding captured the greatest species richness of the community methods. We found that metabarcoding detection probability of fish caught by beach seine was predicted by abundance, but not biomass; notably high-biomass catches were primarily elasmobranchs. Quantitative PCR was twice as effective as metabarcoding in detecting JWS presence, and raw acoustic detections best predicted metabarcoding results. Potential differences in eDNA shedding rate between teleosts and elasmobranchs may explain why JWS were less effectively detected by eDNA approaches, and why only seine count influenced detection probability. Species-specific primers may better capture low-density elasmobranchs. Despite limitations, metabarcoding represents an effective complementary tool to biomonitoring due to the additional diversity captured.