Metabarcoding analysis of the Pacific harbor seal diet in Mexico

Massive sequencing has improved the predator diet analysis, making it possible to identify taxa with low or no detectability via traditional scatological methods. In Mexico, the Pacific harbor seal ( Phoca vitulina richardii ) diet has been understudied, with the importance of invertebrates or cartilaginous fish as prey currently unknown. This study aims to characterize the harbor seal diet through metabarcoding and to compare results with those obtained via the analysis of the hard remains taken from the same samples. Samples were collected at four breeding colonies during the molting season. Libraries were constructed following an Illumina dual-indexed strategy using specific eukaryote (18S rRNA), chordate and cephalopod (16S mtDNA) primers to amplify the prey’s DNA, and blocking primers to avoid predator DNA amplification. Libraries were sequenced on the MiSeq ® platform (Illumina), generating 848,411 reads. The quality control and taxonomic assignment for the sequences were performed in silico using bioinformatic tools. The present study, identified 49 prey (mostly bony fish), including 14 species of invertebrates, hagfish, and elasmobranchs, thus widening knowledge of the Pacific harbor seal’s diet. While 19 prey species were identified using both the hard remains and metabarcoding analysis, methods (with only four identified to genus level), lower prey richness was found in the hard remains. The main prey items around all islands were longfin sanddab ( Citharichthys xanthostigma ) and California lizardfish ( Synodus lucioceps ). Metabarcoding analysis is a new approach for studying the diet of key species in a highly productive and changing ecosystem, such as the California Current System.