Abstract
Introduction Estimating the genetic diversity of cetaceans at sea, particularly abundant social delphinids, can be difficult with traditional biopsy sampling of individuals. Environmental DNA (eDNA) metabarcoding has been shown to be a powerful tool for the identification of species assemblages and estimation of genetic diversity, especially in aquatic environments. Methods We collected 126 samples of seawater from within the immediate vicinity of schools of dolphins during 15 encounters with the four most common delphinid taxa in the waters around Santa Catalina Island, California, USA: long-beaked common dolphins ( Delphinus delphis bairdii , n = 8), short-beaked common dolphins ( D. d. delphis , n = 3), common bottlenose dolphins ( Tursiops truncatus , n = 2), and Risso's dolphins ( Grampus griseus , n = 2). Next-generation sequencing was used to assign Amplicon Sequence Variants (ASVs) of mitochondrial DNA to species using GenBank and a region-specific reference database. Results A total of 240 ASVs were resolved for the four species. ASV richness and the effective number of ASVs, or true diversity, measured as Hill numbers of order 1, were consistent with known characteristics of the four species. Despite collecting up to 12 samples from a single group, a rarefaction analysis indicated that the population diversity was not fully represented for the more abundant species (genus Delphinus), but were closely approximated for G. griseus . Discussion This study demonstrates the application of eDNA for estimating population genetic diversity of abundant species and makes recommendations for improving future studies to better capture this diversity in wild delphinid populations. This provides a more solid foundation for studies using eDNA to monitor these species, which often include those in close proximity to anthropogenic threats.