Estimating abundance of fish associated with structured habitats by combining acoustics and optics

The diversity and abundance of fish inhabiting complex reef habitats poses some challenges to surveys based on optical techniques, especially for schooling fish which are difficult to enumerate with such methods. Acoustic surveys are often used effectively to estimate the abundance and distribution of schooling fish but suffer from boundary effects and limited species discrimination. To reconcile these drawbacks, we present an integrated acoustic–optical survey method, to estimate the abundance of fishes in a subtropical reef habitat in Shark Bay, Western Australia, exploiting the unique benefits of each method. Acoustic backscatter attributed to multi‐species groups was partitioned to species with the help of concurrent unbaited remote underwater video. This allowed estimation of the abundance of the important fishery sparid, Chrysophrys auratus, as well as 17 other members of the diverse fish community. The study addresses some of the challenges of assessing abundance of fish species that may be aggregated, but sparsely distributed, associated with a structured habitat, and mixed within a diverse assemblage of other aggregating or solitary fishes in an area where direct capture fisheries survey gears cannot be used. Synthesis and applications. The acoustic–optical survey method provides data that are vital for the assessment of fish species in ecosystems which are difficult, or impossible for certain species, to survey with existing methods. These assessments are, in turn, essential for either ecosystem‐based fishery management or multiple single‐species quota management, which allow for the sustainable management of the associated fisheries. The acoustic–optical survey method provides data that are vital for the assessment of fish species in ecosystems which are difficult, or impossible for certain species, to survey with existing methods. These assessments are, in turn, essential for either ecosystem‐based fishery management or multiple single‐species quota management, which allow for the sustainable management of the associated fisheries.