Estimating the Effects of Environmental Variables and Gear Type on the Detection and Occupancy of Large-River Fishes in a Standardized Sampling Program Using Multiseason Bayesian Mixture Models

References

• Anderson, D. R. 2001. The need to get the basics right in wildlife field studies. Wildlife Society Bulletin 29:1294–1297.
   Web of Science ®Google Scholar
• Bailey, L. L., T. R. Simons, and K. H. Pollock. 2004. Estimating site occupancy and species detection probability parameters for terrestrial salamanders. Ecological Applications 14:692–702.
   Web of Science ®Google Scholar
• Bayley, P. B., and D. J. Austen. 2002. Capture efficiency of a boat electrofisher. Transactions of the American Fisheries Society 131:435–451.
   Web of Science ®Google Scholar
• Bayley, P. B., and J. T. Peterson. 2001. An approach to estimate probability of presence and richness of fish species. Transactions of the American Fisheries Society 130:620–633.
   Web of Science ®Google Scholar
• Bhowmik, N. G., M. Demissie, J. Mick, and B. White. 2001. Watershed based management of the Kankakee River. Watershed Management and Operations Management 2000:1–10.
   Google Scholar
• Bonar, S. A., and W. A. Hubert. 2002. Standard sampling of inland fish: benefits, challenges, and a call to action. Fisheries 27(3):10–16.
   Web of Science ®Google Scholar
• Demissie, M., N. G. Bhowmik, and J. R. Adams. 1983. Hydrology, hydraulics, and sediment transport, Kankakee and Iroquois rivers. Illinois State Water Survey Report of Investigation 103.
   Google Scholar
• Eby, L. A., O. Helmy, L. M. Holsinger, and M. K. Young. 2014. Evidence of climate-induced range contractions in Bull Trout Salvelinus confluentus in a Rocky Mountain watershed. PLoS ONE (Public Library of Science) [online serial] 9:e98812.
   PubMed Web of Science ®Google Scholar
• Elliot, J. M. 1990. The need for long-term investigations in ecology and the contribution of the Freshwater Biological Association. Freshwater Biology 23:1–5.
   Web of Science ®Google Scholar
• Gelman, A., and D. B. Rubin. 1992. Inference from iterative simulation using multiple sequences. Statistical Science 7:457–472.
   Google Scholar
• Guy, C. S., P. J. Braaten, D. P. Herzog, J. Pitlo, and R. S. Rogers. 2009. Warmwater fish in rivers. Pages 59–84 in S. A. Bonar, W. A. Hubert, and D. W. Willis, editors. Standard methods for sampling North American freshwater fishes. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Keith, D., H. R. Akçakaya, S. H. M. Butchart, B. Collen, N. K. Dulvy, E. E. Holmes, J. A. Hutchings, D. Keinath, M. K. Schwartz, A. O. Shelton, and R. S. Waples. 2015. Temporal correlations in population trends: conservation implications from time-series analysis of diverse animal taxa. Biological Conservation 192:247–257.
   Web of Science ®Google Scholar
• Kirsch, J. E., and J. T. Peterson. 2014. A multi-species approach to evaluating the fish assemblage structure within Appalachian streams. Transactions of the American Fisheries Society 143:1358–1371.
   Web of Science ®Google Scholar
• Lyon, J. P., T. Bird, S. Nicol, J. Kearns, J. O’Mahony, C. R. Todd, I. G. Cowx, and C. J. A. Bradshaw. 2014. Efficiency of electrofishing in turbid lowland rivers: implications for measuring temporal change in fish populations. Canadian Journal of Fisheries and Aquatic Sciences 71:878–886.
   Web of Science ®Google Scholar
• McClelland, M. A., K. S. Irons, G. G. Sass, T. M. O’Hara, and T. R. Cook. 2013. A comparison of two electrofishing programmes used to monitor fish on the Illinois River, Illinois, USA. River Research and Applications 29:125–133.
   Web of Science ®Google Scholar
• McClelland, M. A., G. G. Sass, T. R. Cook, K. S. Irons, N. N. Michaels, T. M. O’Hara, and C. S. Smith. 2012. The long-term Illinois River fish population monitoring program. Fisheries 37:340–350.
   Web of Science ®Google Scholar
• Nichols, J. D., T. Boulinier, J. E. Hines, K. H. Pollock, and J. R. Sauer. 1988. Estimating rates of species extinction, colonization and turnover in animal communities. Ecological Applications 8:1213–1225.
   Google Scholar
• Peterson, J. T. 1989. Kankakee River fishes of the Braidwood Station aquatic monitoring area, August 1988. Illinois Natural History Survey, Aquatic Biology Technical Report 89/1, Champaign.
   Google Scholar
• Peterson, J. T., N. P. Banish, and R. F. Thurow. 2005. Are block nets necessary? Movement of stream-dwelling salmonids in response to three common survey methods. North American Journal of Fisheries Management 25:732–743.
   Web of Science ®Google Scholar
• Peterson, J. T., R. F. Thurow, and J. W. Guzevich. 2004. An evaluation of multipass electrofishing for estimating the abundance of stream-dwelling salmonids. Transactions of the American Fisheries Society 133:462–475.
   Web of Science ®Google Scholar
• Pregler, K. C., J. C. Vokoun, T. Jensen, and N. Hagstrom. 2015. Using multimethod occupancy estimation models to quantify gear differences in detection probabilities: is backpack electrofishing missing occurrences for a species of concern? Transactions of the American Fisheries Society 144:89–95.
   Web of Science ®Google Scholar
• Rabeni, C. F., J. Lyons, N. Mercado-Silva, and J. T. Peterson. 2009. Warmwater fish in wadeable streams. Pages 43–58 in S. A. Bonar, W. A. Hubert, and D. W. Willis, editors. Standard methods for sampling North American freshwater fishes. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Reynolds, J. B., and A. L. Kolz. 2012. Electrofishing. Pages 305–361 in A. V. Zale, D. L. Parrish, and T. M. Sutton, editors. Fisheries techniques, 3rd edition. American Fisheries Society, Bethesda, Maryland.
   Google Scholar
• Ridenour, C. J., A. B. Starostka, W. J. Doyle, and T. D. Hill. 2009. Habitat use by Macrhybopsis chubs associated with channel modifying structures in a large regulated river: implications for river modification. River Research and Applications 25:472–485.
   Web of Science ®Google Scholar
• Royle, J. A., and R. M. Dorazio. 2008. Hierarchical modeling and inference in ecology. Academic Press, Amsterdam.
   Google Scholar
• Royle, J. A., and M. Kéry. 2007. A Bayesian state-space formulation of dynamic occupancy models. Ecology 88:1813–1823.
   PubMed Web of Science ®Google Scholar
• Saunders, W. C., K. D. Fausch, and G. C. White. 2011. Accurate estimation of salmonid abundance in small streams using nighttime removal electrofishing: an evaluation using marked fish. North American Journal of Fisheries Management 31:403–415.
   Web of Science ®Google Scholar
• Schloesser, J. T., C. P. Paukert, W. J. Doyle, T. D. Hill, K. D. Steffensen, and V. H. Travnichek. 2012. Heterogeneous detection probabilities for imperiled Missouri River fishes: implications for large-river monitoring programs. Endangered Species Research 16:211–224.
   Google Scholar
• Spiegelhalter, D. J., A. Thomas, N. G. Best, and D. Lunn. 2003. WINBUGS user manual version 1.4. MRC Biostatistics Unit, University of Cambridge, Cambridge, UK.
   Google Scholar
• Stewart, D. R., and J. M. Long. 2016. Using hierarchical Bayesian multispecies mixture models to estimate tandem hoop-net-based habitat associations and detection probabilities of fishes in reservoirs. Transactions of the American Fisheries Society 145:450–461.
   Web of Science ®Google Scholar
• Trautman, M. B. 1981. The fishes of Ohio. Ohio State University Press, Columbus.
   Google Scholar
• Yoccoz, N. G., J. D. Nichols, and T. Boulinier. 2001. Monitoring biological diversity in space and time. Trends in Ecology and Evolution 16:446–453.
   Web of Science ®Google Scholar