Cryptic biodiversity: A portfolio-approach to coral reef fish surveys

Biodiversity conservation and management requires surveillance that captures the full spectrum of taxa. Here, we showcase the potential for a portfolio of visual, extractive, and molecular methods for detecting previously hidden components of tropical fish biodiversity in an economically and culturally valuable marine site that spans a tropical-temperate ecotone—the Ningaloo Coast World Heritage Area. With scale and practicality in mind, we demonstrate how environmental DNA (eDNA) methods deployed in a stratified sampling design can yield a more comprehensive monitoring program for species presence than current alternatives (e.g., extractive sampling via anesthetic). eDNA from filtered water samples detected up to six times as many cryptobenthic fish species per site than samples collected with anesthetic, indicating it is a potentially powerful tool for assessing biodiversity of tropical fishes. However, there were also species that were only found when using anesthetic and the contribution of cryptobenthic species to overall diversity of the fish assemblage was unexpectedly low, suggesting not all cryptobenthic fish species have been detected with eDNA. There were also distinct differences in cryptobenthic assemblages both among sites and sample depths (2–3 m) when using eDNA from filtered water, suggesting this technique may be able to identify fine scale spatial differences in cryptobenthic fish assemblage. eDNA collected from water detects the most cryptobenthic species and is therefore an efficient tool for rapidly assessing biodiversity, but extractive techniques may still be required for biological and monitoring studies, and when combined with eDNA sampling provides the most comprehensive assessment of cryptobenthic fishes.