Predator-prey interactions within food chains are used to both characterize and understand ecosystems. Traditional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool with diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here, I use multi-locus (16S and COl) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. I use NGS of puffin feces and herring stomach contents to compare traditional and molecular-derived chick diet, to test the similarity between puffin adult and chick diet, and to document herring diet at a taxonomic resolution greater than previous diet-studying methods. I identified more unique prey with our 16S compared to COl barcoding markers (51 and 39 taxa) with only 12 taxa identified by both genes. I found no significant difference between the 16S-identified diets of puffin adults (n=l 7) and chicks (n=41 ). My molecular method is more taxonomically resolved and quantitatively sensitive than traditional methods. Many likely planktonic herring prey were detected in feces from puffin chicks and adults, highlighting the impact secondary consumption may have in the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to food web analysis.
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