A Non-Invasive Technique for Tracking a Marine Predator (Phoca vitulina) Through Molecular Scat Analysis

As ecosystems are subjected to increased urbanization, habitat loss, and resource depletion, management practices will benefit from higher resolution models of local trophic dynamics. Harbor seals (Phoca vitulina), the most abundant marine mammal in the Salish Sea of British Columbia and Washington State, are of great regional interest due to their consumption of species of conservation concern such as Chinook salmon (Oncorhynchus tshawytscha) and Pacific herring (Clupea pallasii). This ecologically influential diet can vary with season, region, and local sex ratios, creating localized pressures on prey species. Variation in diet has been observed at the individual level, an important consideration for examining the total influence of predators that have previously been treated as species-wide averages. This project aimed to develop a method that allows researchers to track individual specialization rates in a protected marine predator by testing if 1) harbor seal scat represents a suitable source of DNA for individual identification through single nucleotide polymorphism (SNP) genotypes produced by direct sequencing, and 2) prey reads could be detected within the sequence data for simultaneous diet analysis without the need for PCR-based methods. SNP loci identified in this study successfully distinguished individual seals with confidence, however read alignments to prey references indicated potentially erroneous classifications. This indicates prey analyses through direct read counts will benefit from more research such as direct feeding trials and digestion correction factors, or from employing more robust techniques (or a combination of methods). Nonetheless, this direct sequencing pipeline of scat DNA for marker identification, individual identification, and simultaneous prey analysis from one sample type provides important considerations for highly scalable/cost-effective non-invasive investigations of regional trophic dynamics in complex and/or understudied systems