Development and application of DNA techniques for validating and improving pinniped diet estimates

Abstract

Abstract. Polymerase chain reaction techniques were developed and applied to identify DNA from .40 species of prey contained in fecal (scat) soft-part matrix collected at terrestrial sites used by Steller sea lions (Eumetopias jubatus) in British Columbia and the eastern Aleutian Islands, Alaska. Sixty percent more fish and cephalopod prey were identified by morphological analyses of hard parts compared with DNA analysis of soft parts (hard parts identified higher relative proportions of Ammodytes sp., Cottidae, and certain Gadidae). DNA identified 213 prey occurrences, of which 75 (35%) were undetected by hard parts (mainly Salmonidae, Pleuronectidae, Elasmobranchii, and Cephalopoda), and thereby increased species occurrences by 22% overall and species richness in 44% of cases (when comparing 110 scats that amplified prey DNA). Prey composition was identical within only 20% of scats. Overall, diet composition derived from both identification techniques combined did not differ significantly from hard-part identification alone, suggesting that past scat-based diet studies have not missed major dietary components. However, significant differences in relative diet contributions across scats (as identified using the two techniques separately) reflect passage rate differences between hard and soft digesta material and highlight certain hypothesized limitations in conventional morphological-based methods (e.g., differences in resistance to digestion, hard part regurgitation, partial and secondary prey consumption), as well as potential technical issues (e.g., resolution of primer efficiency and sensitivity and scat subsampling protocols). DNA analysis of salmon occurrence (from scat soft-part matrix and 238 archived salmon hard parts) provided species-level taxonomic resolution that could not be obtained by morphological identification and showed that Steller sea lions were primarily consuming pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Notably, DNA from Atlantic salmon (Salmo salar) that likely originated from a distant fish farm was also detected in two scats from one site in the eastern Aleutian Islands. Overall, molecular techniques are valuable for identifying prey in the fecal remains of marine predators. Combining DNA and hard-part identification will effectively alleviate certain predicted biases and will ultimately enhance measures of diet richness, fisheries interactions (especially salmonrelated ones), and the ecological role of pinnipeds and other marine predators, to the benefit of marine wildlife conservationists and fisheries managers.

Combining hard-part and DNA analyses of scats with biologging and stable isotopes can reveal different diet compositions and feeding strategies within a fur seal population

“…In addition, use of the DNA-based method increased the number of prey occurrences detected by ~25% compared to hard-part method alone, which helped to refine the richness (6 more species of fish detected) and composition of northern fur seals diet. This is in agreement with results on Steller sea lions (~22% more prey species identified using DNAbased methods; Tollit et al 2009), but the degree of refinement achieved using DNA-based methods was much less than in studies on captive fur seals (Casper et al 2007a). One of the possible reasons for this is that in our study scats were randomly collected on the rookery with no particular care given to their freshness.…”

“…This consistency between the 2 methods was also shown for harbour seals and Steller sea lions at the population level (only species of minor importance differed between methods; Tollit et al 2009), which indicates that major errors or omissions are unlikely in diet estimates. Compared to the more traditional method of hard-part identification, DNA-based methods have several advantages.…”

“…Compared to the more traditional method of hard-part identification, DNA-based methods have several advantages. They can detect prey to a finer taxonomic level than hard-parts analyses, and they perform particularly well for prey species that are morphologically identified by structures other than otoliths (Tollit et al 2009). For example, our DNA analyses assigned occurrences of salmonids and cephalopods to the species level, while hardparts could only identify them at the family level (Fig.…”

“…It is non-invasive, has the advantages of being quick and relatively inexpensive, and is more sensitive than hard-part remains methods (Deagle et al 2009). For example, DNA analyses detected prey to a finer taxonomic level than hard-parts analyses in Steller sea lions Eumetopia jubatus and harbour seals Phoca vitulina (Tollit et al 2009, Thomas et al 2017. The quantitative capabilities of DNA metabarcoding (i.e.…”

California and Steller sea lion use of a major winter haulout in the Salish Sea over 45 years

“…Lowry et al 1991) or more complex and arguably higher-resolution methods such as the use of PCR techniques to identify prey DNA (e.g. Tollit et al 2009). …”