Detection of threatened delta smelt in the gut contents of the invasive mississippi silverside in the san francisco estuary using taqman assays

Transactions of the American Fisheries Society

Volumn 141, Issue 6, 2012, Pages 1600-1607

  Baerwald, Melinda R ^a   Schreier, Brian M ^b   Schumer, Gregg ^c   May, Bernie ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CALIFORNIA DEPARTMENT OF WATER RESOURCES   (United States)

^c Cramer Fish Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84883255853     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1080/00028487.2012.717521     Document Type: Article

References (43)

1. Albaina, A., C. J. Fox, N. Taylor, E. Hunter, M. Maillard, and M. I. Taylor. 2010. A TaqMan real-time PCR based assay targeting plaice (Pleuronectesplatessa L.) DNA to detect predation by the brown shrimp (Crangon crangon L.) and the shore crab (Carcinus maenas L.): assay development and validation. Journal of Experimental Marine Biology and Ecology 391:178-189.
2. Baerwald, M. R., G. Schumer, B. M. Schreier, and B. May. 2011. TaqMan assays for the genetic identification of delta smelt (Hypomesus transpacificus) and wakasagi smelt (Hypomesusnipponensis). MolecularEcology Resources 11:784-785.
3. Baeta, A., N. Niquil, J. C. Marques, and J. Patricio. 2011. Modelling the effects of eutrophication, mitigation measures and an extreme flood event on estuarine benthic food webs. Ecological Modelling 222:1209-1221.
4. Bailey, K. M., and E. D. Houde. 1989. Predation on eggs and larvae of marine fishes and the recruitment problem. Advances in Marine Biology 25:1-83.
5. Baxter, R., R. Breuer, L. Brown, L. Conrad, F. Feyrer, S. Fong, K. Gehrts, L. Grimaldo, B. Herbold, P. Hrodey, A. Mueller-Solger, T. Sommer, and K. Souza. 2010. 2010 pelagic organism decline work plan and synthesis of results. Interagency Ecological Program for the San Francisco Estuary, California Department of Water Resources, Sacramento. Available: www.water.ca.gov/iep/docs/FinalPOD2010Workplan12610.pdf. (May 2012).
6. Bennett, W. A. 2005. Critical assessment of the delta smelt population in the San Francisco Estuary, California. San Francisco Estuary and Watershed Sciencee [online serial] 3(2).
7. Bennett, W. A., and P. B. Moyle. 1996. Where have all of the fishes gone? interactive factors producing fish declines in the Sacramento-San Joaquin estuary. Pages519-542 in J. T. Hollibaugh, editor. San Francisco Bay: The ecosystem. American Association for the Advancement of Science, San Francisco.
8. Burns, M., and H. Valdivia. 2008. Modelling the limit of detection in real-time quantitative PCR. European Food Research and Technology 226:1513-1524.
9. Caraguel, C. G. B., H. Stryhn, N. Gagn, I. R. Dohoo, and K. L. Hammell. 2011. Selection of a cutoff value for real-time polymerase chain reaction results to fit a diagnostic purpose: analytical and epidemiologic approaches. Journal of Veterinary Diagnostic Investigation 23:2-15.
10. Carreon-Martinez, L., T. B. Johnson, S. A. Ludsin, and D. D. Heath. 2011. Utilization of stomach content DNA to determine diet diversity in piscivorous fishes. Journal of Fish Biology 78:1170-1182.
11. Cohen, A. N., and J. T. Carlton. 1998. Accelerating invasion rate in a highly invaded estuary. Science 279:555-558.
12. Cushing, D. H. 1990. Plankton production and year-class strength in fish populations: an update of the match/mismatch hypothesis. Advances in Marine Biology 26:249-293.
13. Dunshea, G. 2009. DNA-based diet analysis for any predator. PLoS (Public Library of Science) Onee [online serial] 4(4):e5252.
14. Ehrenfeld, J. G. 2010. Ecosystem consequences of biological invasions. Annual Review of Ecology, Evolution, and Systematics 41:59-80.
15. Feyrer, F., B. Herbold, S. A. Matern, and P. B. Moyle. 2003. Dietary shifts in a stressed fish assemblage: consequences of a bivalve invasion in the San Francisco Estuary. Environmental Biology of Fishes 67:277-288.
16. Fisch, K., T. Rettinghouse, L. Ellison, G. Tigan, J. Lindberg, and B. May. 2009. Delta smelt refugial population development and genetic management: 2009 season summary. Interagency Ecological Program Newsletter 22:3-9.
17. Glibert, P. M. 2010. Long-term changes in nutrient loading and stoichiometry and their relationships with changes in the food web and dominant pelagic fish species in the San Francisco Estuary, California. Reviews in Fisheries Science 18:211-232.
18. Grimaldo, L. F., T. Sommer, N. Van Ark, G. Jones, E. Holland, P. B. Moyle, B. Herbold, and P. Smith. 2009. Factors affecting fish entrainment into massive water diversions in a tidal freshwater estuary: can fish losses be managed? North American Journal of Fisheries Management 29:1253-1270.
19. Harper, G. L., R. A. King, C. S. Dodd, J. D. Harwood, D. M. Glen, M. W. Bruford, and W. O. C. Symondson. 2005. Rapid screening of invertebrate predators for multiple prey DNA targets. Molecular Ecology 14:819-827.
20. Hoegh-Guldberg, O., and J. F. Bruno. 2010. The impact of climate change on the world’s marine ecosystems. Science 328:1523-1528.
21. Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991.Evolutionofthe cytochrome b gene of mammals. Journal of Molecular Evolution 32:128-144.
22. Kimmerer, W. J. 2002. Effects of freshwater flow on abundance of estuarine organisms: physical effects or trophic linkages? Marine Ecology Progress Series 243:39-55.
23. Kimmerer, W. J., E. Gartside, and J. J. Orsi. 1994. Predation by an introduced clam as the likely cause of substantial declines in zooplankton of San Francisco Bay. Marine Ecology Progress Series 113:81-93.
24. King, R. A., D. S. Read, M. Traugott, and W. O. C. Symondson. 2008. Molecular analysis of predation: a review of best practice for DNA-based approaches. Molecular Ecology 17:947-963.
25. Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the USA 86:6196-6200.
26. Keister, F. W., D. Schnack, and C. Molmann. 2003. Scientific knowledge of biological processes that are potentially useful in fish stock predictions. Scientia Marina 67(Supplement 1):101-127.
27. Leggett, W. C., and E. Deblois. 1994. Recruitmentin marine fishes: is itregulated by starvation and predation in the egg and larval stages? Netherlands Journal of Sea Research 32:119-134.
28. Legler, N. D., T. B. Johnson, D. D. Heath, and S. A. Ludsin. 2010. Water temperature and prey size effects on the rate of digestion of larval and early juvenile fish. Transactions of the American Fisheries Society 139:868-875.
29. Mac Nally, R., J. R. Thomson, W. J. Kimmerer, F. Feyrer, K. B. Newman, A. Sih, W. A. Bennett, L. Brown, E. Fleishman, S. D. Culberson, and G. Castillo. 2010. Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR). Ecological Applications 20:1417-1430.
30. Mills, C. E., and F. Sommer. 1995. Invertebrateintroductions in marinehabitats: two species of hydromedusae (Cnidaria) native to the Black Sea, Maeotias inexspectata and Blackfordia virginica, invade San Francisco Bay. Marine Biology 122:279-288.
31. Nichols, F. H., J. E. Cloern, S. N. Luoma, and D. H. Peterson. 1986. The modification of an estuary. Science 231:567-573.
32. Nobriga, M. L., and F. Feyrer. 2008. Diet composition in San Francisco Estuary striped bass: does trophic adaptability have its limits? Environmental Biology ofFishes 83:495-503.
33. Polis, G. A., C. A. Myers, and R. D. Holt. 1989. The ecology and evolution of intraguild predation: potential competitors that eat each other. Annual Review of Ecology and Systematics 20:297-330.
34. Rosel, P. E., and T. D. Kocher. 2002. DNA-based identification of larval cod in stomach contents of predatory fishes. Journal of Experimental Marine Biology and Ecology 267:75-88.
35. Schooley, J. D., A. P. Karam, B. R. Kesner, P. C. Marsh, C. A. Pacey, and D. J. Thornbrugh. 2008. Detection of larval remains after consumption by fishes. Transactions of the American Fisheries Society 137:1044-1049.
36. Sheppard, S. K., and J. D. Harwood. 2005. Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Functional Ecology 19:751-762.
37. Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, M. Nobriga, and K. Souza. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 32:270-277.
38. Swain, D. P., and A. F. Sinclair. 2000. Pelagic fishes and the cod recruitment dilemma in the northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences 57:1321-1325.
39. Symondson, W. O. C. 2002. Molecular identification of prey in predator diets. Molecular Ecology 11:627-641.
40. Thomson, J. R., W. J. Kimmerer, L. R. Brown, K. B. Newman, R. Mac Nally, W. A. Bennett, F. Feyrer, and E. Fleishman. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications 20:1431-1448.
41. USFWS (U.S. Fish and Wildlife Service). 1993. Endangered and threatened wildlife and plants: determination of threatened status for the delta smelt. Federal Register58:42(5 March 1993):12854-12864.
42. Wang, J.C.S. 1986. Fishes of the Sacramento-San JoaquinEstuary and adjacent waters, California: a guide to the early life histories. Interagency Ecological Program, Technical Report 9, California Department of Water Resources, Sacramento.
43. Wurtsbaugh, W., and H. Li. 1985. Diel migrations of a zooplanktivorous fish (Menidia beryllina) in relation to the distribution of its prey in a large eu-trophic lake. Limnology and Oceanography 30:565-576.