Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes

Abstract

Introduced predators pose ecological impacts upon prey species and receiving ecosystems. Understanding such ecological interactions creates technical challenges including species-specific identification of partially digested prey items in the stomachs of piscivorous predators. We present the first evaluation of DNA barcoding to identify piscine prey in the stomachs of North American catfishes (Family Ictaluridae). Fish prey items of non-native Blue Catfish Ictalurus furcatus and Flathead Catfish Pylodictis olivaris were obtained by gastric lavage and ranked as lightly, moderately, or heavily digested. We used an established cocktail of universal fish primers (FishF2_t1, FishR2_t1, VF2_t1, and FR1d_t1) to amplify the cytochrome oxidase I (COI-3) region of mitochondrial DNA from these samples. Amplification products were subjected to Sanger sequencing, and edited sequences were compared to entries in GenBank. Eighty-six percent of the sequences generated for lightly or moderately digested samples and 66 % of those for heavily digested samples could be assigned to the species level based on similarity with archived COI-3 sequences. While traditional morphological identification led to species-level identification of 65 % of fish prey items, addition of DNA barcoding resulted in identification to species of 88 % of fish prey items overall. Diet items identified by DNA markers included anadromous Striped Bass Morone saxatilis and herrings and shads Alosa spp. that are the focus of fishery restoration programs in these rivers. We found DNA barcoding to be an efficient and cost-effective addition to diet studies of non-native predators.

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Acknowledgments

This study was completed with funds provided by the Virginia Department of Game and Inland Fisheries through a Sport Fish Restoration Grant from the U.S. Fish and Wildlife Service. Funding for the participation of EMH and DJO was provided in part by the Virginia Agricultural Experiment Station and the Hatch Program of the National Institute of Food and Agriculture, U.S. Department of Agriculture. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. Special thanks to Jason Emmel and Tim Lane for their assistance with field collections and laboratory analysis. This report was strengthened by attention to the comments of two anonymous peer reviewers.

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Correspondence to E.M. Hallerman.

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Moran, Z., Orth, D.J., Schmitt, J.D. et al. Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes. Environ Biol Fish 99, 161–167 (2016). https://doi.org/10.1007/s10641-015-0448-7

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Keywords

  • Non-native catfishes
  • Predation
  • Clupeidae
  • DNA barcoding
  • MtDNA
  • Universal fish primers