Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes
- 748 Downloads
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.
KeywordsNon-native catfishes Predation Clupeidae DNA barcoding MtDNA Universal fish primers
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.
- 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. 765–842Google Scholar
- BOL (2015) Barcode of Life. http://www.boldsystems.org/. Accessed March 16, 2015.
- Chandler L (1998) Trophic ecology of native and introduced catfishes in the tidal James river. Virginia Commonwealth University, Virginia. Master’s thesisGoogle Scholar
- Curio E (1976) The ethology of predation. Zoophysiology and Ecology, volume 7. Springer-Verlag, BerlinGoogle Scholar
- 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 733–779Google Scholar
- Goodnight JH, Sall JP, Sarle WS (1982) The GLM procedure. SAS User's Guide, Statistics, pp. 139–199Google Scholar
- Graham K (1999) A review of the biology and management of blue catfish. Am Fish Soc Symp 24:37–49Google Scholar
- 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 77:349–367Google Scholar
- 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 35:607–621Google Scholar
- 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.
- Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc Royal Soc London B Biol Sci 270:313–322Google Scholar
- 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. 23–35Google Scholar
- Jenkins RE, Burkhead NM (1994) The freshwater fishes of Virginia. American Fisheries Society, BethesdaGoogle Scholar
- 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 27:81–96Google Scholar
- Pierce GJ, Boyle PR, Watt J, Grisley M (1993) Recent advances in diet analysis of marine mammals. Symp Zool Soc London 66:214–261Google Scholar
- SAS Instiute (2013) JMP®, Version 11.0. SAS Institute Inc. Cary, NC, U.S.A.Google Scholar
- 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. 369–382Google Scholar
- 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. 343–353Google Scholar
- 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. 109–126Google Scholar
- Zar JH (1999) Biostatistical analysis. Pearson Education, IndiaGoogle Scholar