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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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Baumann JR, Kwak T (2011) Trophic relations of introduced Flathead Catfish in an Atlantic River. Trans Am Fish Soc 140:1120–1134
Beauchamp DA, Wahl DH, Johnson BM (2007) Predator-prey interactions. In Guy CS, Brown ML (eds). Analysis and interpretation of freshwater fisheries data. American Fisheries Society, Bethesda, pp. 765–842
BOL (2015) Barcode of Life. http://www.boldsystems.org/. Accessed March 16, 2015.
Brown JJ, Perillo J, Kwak TJ, Horwitz RJ (2005) Implications of Pylodictis olivaris (flathead catfish) introduction into the Delaware and Susquehanna drainages. Northeast Nat 12:473–484
Cambray JA (2003) Impact on indigenous species biodiversity caused by the globalization of alien recreational freshwater fisheries. Hydrobiologia 500:217–230
Carreon-Martinez L, Johnson TB, Ludsin SA, Heath DD (2011) Utilization of stomach content DNA to determine diet diversity in piscivorous fishes. J Fish Biol 78:1170–1182
Chandler L (1998) Trophic ecology of native and introduced catfishes in the tidal James river. Virginia Commonwealth University, Virginia. Master’s thesis
Cote IM, Green SJ, Morris Jr JA, Akins JL, Steinke D (2013) Diet richness of indo-pacific lionfish revealed by DNA barcoding. Mar Ecol 472:249–256
Curio E (1976) The ethology of predation. Zoophysiology and Ecology, volume 7. Springer-Verlag, Berlin
Deagle BE, Jarmin SN, Pemberton D, Gales NJ (2005) Genetic screening in the gut contents from a giant squid, Archituthus sp. J Hered 96:417–423
Garvey JE, Chipps SR (2012) Diets and energy flow. In Zale AV, Parrish DL, Sutton TM (eds). Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland, pp 733–779
Goodnight JH, Sall JP, Sarle WS (1982) The GLM procedure. SAS User's Guide, Statistics, pp. 139–199
Graham K (1999) A review of the biology and management of blue catfish. Am Fish Soc Symp 24:37–49
Greenlee RS, Lim C (2011) Searching for equilibrium: population parameters and variable recruitment in introduced blue catfish populations in four Virginia tidal river systems. Trans Am Fish Soc 77:349–367
Guier CR, Nichols LE, Ravhels RT (1984) Biological investigations of flathead catfish in the Cape Fear River. Proc Ann Conf Southeast Assoc Fish Wild Agen 35:607–621
Hall, T (2013) BioEdit: Biological sequence alignment editor for Win 95/98/NT/2 K/XP/7, version 7.1.9. www.mbio.ncsu.edu/bioedit.bioedit.
Hardy CM, Krull ES, Hartley DM, Oliver RL (2010) Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Mol Ecol 19:197–212
Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc Royal Soc London B Biol Sci 270:313–322
Hyslop EJ (1980) Stomach contents analysis - a review of methods and their application. J Fish Biol 17:411–429
Ivanova NV, Zemlak TS, Hanner RH, Herbert PDN (2007) Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes 7:544–548
Jackson DC (1999) Flathead Catfish: biology, fisheries and management. In Irwin ER, Hubert WA, Rabeni CF, Schramm HL Jr, Coon T (eds). Catfish 2000: Proceedings of the International Ictalurid Symposium. American Fisheries Society Symposium 24, American Fisheries Society, Bethesda, MD, pp. 23–35
Jenkins RE, Burkhead NM (1994) The freshwater fishes of Virginia. American Fisheries Society, Bethesda
Jo H, Gim JA, Jeong KS, Kim HS, Joo GJ (2013) Application of DNA barcoding for identification of freshwater carnivorous fish diets: is number of prey items dependent on size class for Micropterus salmoides? Ecol Evol 4:219–229
Kress WJ, Erickson DL (2012) DNA barcodes: methods and protocols. Meth Mol Biol 858:3–8
Legler ND, Johnson TB, Heath DD, Ludsin S (2010) Water temperature and prey size effects on the rate of digestion of larval and early juvenile fish. Trans Am Fish Soc 139:868–875
NCBI (2007) Basic Local Alignment Search Tool. National Center for Biotechnology Information. http://blast.ncbi.nlm.nih.gov/blast.cgi. Accessed 3 March 2015
Oguto-Ohwayo R (1990) The decline of the native fishes of lakes Victoria and Kyoga (East Africa) and the impact of introduced species, especially the Nile perch, Lates niloticus, and the Nile tilapia, Oreochromis niloticus. Env Biol Fishes 27:81–96
Pierce GJ, Boyle PR, Watt J, Grisley M (1993) Recent advances in diet analysis of marine mammals. Symp Zool Soc London 66:214–261
Pine WE, Kwak TJ, Waters DS, Rice JA (2005) Diet selectivity of introduced flathead catfish in coastal rivers. Trans Am Fish Soc 134:901–909
Pombo L, Elliot M, Rebelo JE (2005) Environmental influences on fish assemblage distribution of an estuarine coastal lagoon, ria de Aveiro (Portugal). Sci Mar 69:143–159
Prime JH, Hammond PS (1990) The diet of grey seals from the south-western north sea assessed from analyses of hard parts in faeces. J Appl Ecol 27:435–447
Recchia CA, Read AJ (1989) Stomach contents of harbour porpoises, Phocoena phocoena (L.), from the Bay of Fundy. Canad J Zool 67:2140–2146
SAS Instiute (2013) JMP®, Version 11.0. SAS Institute Inc. Cary, NC, U.S.A.
Schloesser RW, Fabrizio MC, Latour RJ, Garman GC, Greenlee B, Groves M, Gartland J (2011) Ecological role of Blue Catfish in Chesapeake Bay communities and implications for management. In Michaletz PH, Travnichek VH (eds). Conservation, Ecology, and Management of Catfish: The Second International Symposium. Amer Fish Soc Symp 77, Bethesda, Maryland, pp. 369–382
Schooley JD, Karam AP, Kresner BR, Marsh PC, Pacey CA, Thornbrugh DJ (2008) Detection of larval remains after consumption by fishes. Trans Am Fish Soc 137:1044–1049
Simberloff D (2005) Non-native species do threaten the natural environment! J Agric Environ Ethics 18:595–607
Smith PJ, McVeagh SM, Allain V, Sanchez C (2005) DNA identification of gut contents of large pelagic fish. J Fish Biol 67:1178–1183
Stein RA (1979) Behavioral response of prey to fish predators. In: Stroud RH, Clepper H (eds) Black bass biology and management. Sport Fishing Institute, Washington, DC, pp. 343–353
Ward RD, Zemlack TS, Innes BH, Last PR, Herbert PDN (2005) DNA barcoding Australia’s fish species. Phil Trans Roy Soc London B Biol Sci 360:1847–1857
Waters DS, Kwak TJ, Arnett JB (2004) Evaluation of stomach tubes and gastric lavage for sampling diets from blue catfish and flathead catfish. Am J Fish Manag 24:258–261
Weigt LA, Driskell AC, Baldwin CC, Ormos A (2012) DNA barcoding fishes. In Lopez LDA, Erickson DL (eds). Methods in molecular biology. Springer, New York, pp. 109–126
Zar JH (1999) Biostatistical analysis. Pearson Education, India
Zaret TM, Paine RT (1973) Species introduction in a tropical lake. Science 182:449–455
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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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
- Non-native catfishes
- DNA barcoding
- Universal fish primers