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

• Published in: Ecological Applications
• Main Authors: Tollit, Dominic J., Schulze, Angela D., Trites, Andrew W., Olesiuk, Peter F., Crockford, Susan J., Gelatt, Thomas S., Ream, Rolf R., Miller, Kristina M.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2009
• Subjects: Keta; Atlantic salmon; Oncorhynchus gorbuscha; Salmo salar; Alaska; Aleutian Islands
• Online Access: http://dx.doi.org/10.1890/07-1701.1; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1890%2F07-1701.1; https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/07-1701.1

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 ...