Identification of seagrasses in the gut of a marine herbivorous fish using DNA barcoding and visual inspection techniques

Journal of Fish Biology

Volumn 79, Issue 1, 2011, Pages 112-121

  Chelsky Budarf, A ^a,b   Burfeind, D D ^a,b   Loh, W K W ^a,c   Tibbetts, I R ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b GRIFFITH UNIVERSITY   (Australia)

^c BOND UNIVERSITY   (Australia)

Author keywords

Intergenic spacer; Siganus fuscescens; Single strand conformational polymorphism (SSCP); trnH psbA

Indexed keywords

PLANT DNA; RIBOSOMAL SPACER DNA;

ANIMAL; ARTICLE; DIET; DNA BARCODING; FISH; GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SINGLE STRAND CONFORMATION POLYMORPHISM; SPECIES DIFFERENCE; STOMACH JUICE; ZOSTERACEAE;

ANIMALS; DIET; DNA BARCODING, TAXONOMIC; DNA, PLANT; DNA, RIBOSOMAL SPACER; FISHES; GASTROINTESTINAL CONTENTS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; SPECIES SPECIFICITY; ZOSTERACEAE;

ALGAE; MAGNOLIOPHYTA; SIGANUS FUSCESCENS;

EID: 79959883541     PISSN: 00221112     EISSN: 10958649     Source Type: Journal    
DOI: 10.1111/j.1095-8649.2011.02999.x     Document Type: Article

References (31)

1. Alberto, F., Massa, S., Manent, P., Diaz-Almela, E., Arnaud-Haond, S., Duarte, C. M. & Serrão, E. A. (2008). Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean-Atlantic transition region. Journal of Biogeography 35, 1279-1294. DOI: 10.1111/j.1365-2699.2007.01876.x
2. Barbour, A. B., Montgomery, M. L., Adamson, A. A., Díaz-Ferguson, E. & Silliman, B. R. (2010). Mangrove use by the invasive lionfish Pterois volitans. Marine Ecology Progress Series 401, 291-294.
3. Blankenship, L. E. & Yayanos, A. A. (2005). Universal primers and PCR of gut contents to study marine invertebrate diets. Molecular Ecology 14, 891-899. DOI: 10.1111/j.1365-294X.2005.02448.x
4. Carr, A., Tibbetts, I. R., Kemp, A., Truss, R. & Drennan, J. (2006). Inferring parrotfish (Teleostei: Scaridae) pharyngeal mill function from dental morphology, wear, and microstructure. Journal of Morphology 267, 1147-1156. DOI: 10.1002/jmor.10457
5. Cocheret de la Morinière, E., Pollux, B. J. A., Nagelkerken, I., Hemminga, M. A., Huiskes, A. H. L. & van der Velde, G. (2003). Ontogenetic dietary changes of coral reef fishes in the mangrove-seagrass-reef continuum: stable isotopes and gut-content analysis. Marine Ecology Progress Series 246, 279-289.
6. Dunn, M. R., Szabo, A., McVeagh, M. S. & Smith, P. J. (2010). The diet of deepwater sharks and the benefits of using DNA identification of prey. Deep-Sea Research I 57, 923-930.
7. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B 270, 313-321.
8. Hosseini, R., Schmidt, O. & Keller, M. A. (2008). Factors affecting detectability of prey DNA in the gut contents of invertebrate predators: a polymerase chain reaction-based method. Entomologia Experimentalis et Applicata 126, 194-202. DOI: 10.1111/j.1570-7458.2007.00657.x
9. Jarman, S. N. & Wilson, S. G. (2004). DNA-based species identification of krill consumed by whale sharks. Journal of Fish Biology 65, 586-591. DOI: 10.1111/j.1095-8649.2004.00466.x
10. Kress, W. J. & Erickson, D. L. (2007). A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2, e508.
11. Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A. & Janzen, D. H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences 102, 8369-8374.
12. Les, D. H., Cleland, M. A. & Waycott, M. (1997). Phylogenetic studies in Alismatidae, II: evolution of marine angiosperms (seagrasses) and hydrophily. Systematic Botany 22, 443-463.
13. Les, D. H., Moody, M. L., Jacobs, S. W. L. & Bayer, R. J. (2002). Systematics of seagrasses (Zosteraceae) in Australia and New Zealand. Systematic Botany 27, 468-484.
14. Lugendo, B. R., Nagelkerken, I., van der Velde, G. & Mgaya, Y. D. (2006). The importance of mangroves, mud and sand flats, and seagrass beds as feeding areas for juvenile fishes in Chwaka Bay, Zanzibar: gut content and stable isotope analyses. Journal of Fish Biology 69, 1639-1661. DOI: 10.1111/j.1095-8649.2006.01231.x
15. Matheson, C. D., Muller, G. C., Junnila, A., Vernon, K., Hausmann, A., Miller, M. A., Greenblatt, C. & Schlein, Y. (2008). A PCR method for detection of plant meals from the guts of insects. Organisms Diversity & Evolution 7, 294-303.
16. McIntyre, C. P., Wressnig, A. M. & McRae, C. R. (2007). Fish gut content analysis by thermochemolysis with tetramethylammonium hydroxide (TMAH) and gas chromatography-mass spectrometry (GC-MS). Journal of Analytical and Applied Pyrolysis 80, 6-15.
17. Nejstgaard, J. C., Frischer, M. E., Simonelli, P., Troedsson, C., Brakel, M., Adiyaman, F., Sazhin, A. F. & Artigas, L. F. (2008). Quantitative PCR to estimate copepod feeding. Marine Biology 153, 565-577.
18. Page, R. D. M. (1996). TreeView: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12, 357-358.
19. Pillans, R. D., Franklin, C. E. & Tibbetts, I. R. (2004). Food choice in Siganus fuscescens: influence of macrophyte nutrient content and availability. Journal of Fish Biology 64, 297-309. DOI: 10.1046/j.1095-8649.2003.00261.x
20. Posada, D. & Crandall, K. A. (1998). ModelTest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
21. Ragupathy, S., Newmaster, S. G., Murugesan, M. & Balasubramaniam, V. (2009). DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Molecular Ecology Resources 9, 164-171. DOI: 10.1111/j.1755-0998.2009.02641.x
22. Reusch, T. B. H. (2006). Does disturbance enhance genotypic diversity in clonal organisms? A field test in the marine angiosperm Zostera marina. Molecular Ecology 15, 277-286. DOI: 10.1111/j.1365-294X.2005.02779.x
23. Sang, T., Crawford, D. J. & Stuessy, T. F. (1997). Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84, 1120-1136.
24. Smith, P. J., McVeagh, S. M., Allain, V. & Sanchez, C. (2005). DNA identification of gut contents of large pelagic fishes. Journal of Fish Biology 67, 1178-1183. DOI: 10.1111/j.0022-1112.2005.00804.x
25. Soininen, E. M., Valentini, A., Coissac, E., Miquel, C., Gielly, L., Brochmann, C., Brysting, A. K., Sønstebø, J. H., Ims, R. A., Yoccoz, N. G. & Taberlet, P. (2009). Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology 6, No. 16.
26. Swofford, D. L. (2002). PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). Sunderland, MA: Sinauer Associates, Inc.
27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876-4882.
28. Tibbetts, I. R. & Carseldine, L. (2003). Anatomy of a hemiramphid pharyngeal mill with reference to Arrhamphus sclerolepis krefftii (Steindachner) (Teleostei: Hemiramphidae). Journal of Morphology 255, 228-243. DOI: 10.1002/jmor.10057
29. Waycott, M., McMahon, K., Mellors, J., Calladine, A. & Kleine, D. (2004). A Guide to Tropical Seagrasses of the Indo-West Pacific. Townsville: James Cook University.
30. Waycott, M., Procaccini, G., Les, D. H. & Reusch, T. B. H. (2006). Seagrass evolution, ecology and conservation: a genetic perspective. In Seagrasses: Biology, Ecology and Conservation (Larkum, A. W. D., Orth, R. J. & Duarte, C. M., eds), pp. 25-50. Dordrecht: Springer.
31. Woodland, D. J. (1990). Revision of the fish family Siganidae with descriptions of two new species and comments on distribution and biology. Indo-Pacific Fishes 19, 1-136.