A Hierarchical Community Occurrence Model for North Carolina Stream Fish

REFERENCES

• Allan, D., D. Erickson, and J. Fay. 1997. The influence of catchment land use on stream integrity across multiple spatial scales. Freshwater Biology 37:149–161.
   Web of Science ®Google Scholar
• Allan, J. D. 2004. Landscapes and riverscapes: the influence of land use on stream ecosystems. Annual Review of Ecology, Evolution, and Systematics 35:257–284.
   Web of Science ®Google Scholar
• Azeria, E. T., D. Fortin, C. Hébert, P. Peres-Neto, D. Pothier, and J.-C. Ruel. 2009. Using null model analysis of species co-occurrences to deconstruct biodiversity patterns and select indicator species. Diversity and Distributions 15:958–971.
   Web of Science ®Google Scholar
• Blevins, Z., E. Effert, D. Wahl, and C. Suski. 2013. Land use drives the physiological properties of a stream fish. Ecological Indicators 24:224–235.
   Web of Science ®Google Scholar
• Brooks, D. R., R. L. Mayden, and D. A. McLennan. 1992. Phylogeny and biodiversity: conserving our evolutionary legacy. Trends in Ecology and Evolution 7:55–59.
   PubMed Web of Science ®Google Scholar
• Caro, T. M., and G. O’Doherty. 1999. On the use of surrogate species in conservation biology. Conservation Biology 13:805–814.
   Web of Science ®Google Scholar
• Carpenter, S. R., E. H. Stanley, and M. J. Vander Zanden. 2011. State of the world's freshwater ecosystems: physical, chemical, and biological changes. Annual Review of Environment and Resources 36:75–99.
   Web of Science ®Google Scholar
• Chittick, B., M. Stoskopf, N. Heil, J. Levine, and M. Law. 2001. Evaluation of Sandbar Shiner as a surrogate for assessing health risks to the endangered Cape Fear Shiner. Journal of Aquatic Animal Health 13:86–95.
   Web of Science ®Google Scholar
• Dudgeon, D., A. H. Arthington, M. O. Gessner, Z.-I. Kawabata, D. J. Knowler, C. Lévêque, R. J. Naiman, A.-H. Prieur-Richard, D. Soto, and M. L. Stiassny. 2006. Freshwater biodiversity: importance, threats, status and conservation challenges. Biological Reviews 81:163–182.
   PubMed Web of Science ®Google Scholar
• Elith, J., and J. R. Leathwick. 2009. Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution, and Systematics 40:677–697.
   Web of Science ®Google Scholar
• Foley, J. A., R. DeFries, G. P. Asner, C. Barford, G. Bonan, S. R. Carpenter, F. S. Chapin, M. T. Coe, G. C. Daily, and H. K. Gibbs. 2005. Global consequences of land use. Science 309:570–574.
   PubMed Web of Science ®Google Scholar
• Gevrey, M., F. Sans-Piche, G. Grenouillet, L. Tudesque, and S. Lek. 2009. Modeling the impact of landscape types on the distribution of stream fish species. Canadian Journal of Fisheries and Aquatic Sciences 66:484–495.
   Web of Science ®Google Scholar
• Grez, A. A., T. A. Rand, T. Zaviezo, and F. Castillo-Serey. 2013. Land use intensification differentially benefits alien over native predators in agricultural landscape mosaics. Diversity and Distributions 19:749–759.
   Web of Science ®Google Scholar
• Gu, W., and R. K. Swihart. 2004. Absent or undetected? Effects of non-detection of species occurrence on wildlife–habitat models. Biological Conservation 116:195–203.
   Web of Science ®Google Scholar
• Homer, C., J. Dewitz, J. Fry, M. Coan, N. Hossain, C. Larson, N. Herold, A. McKerrow, J. N. VanDriel, and J. Wickham. 2007. Completion of the 2001 National Land Cover Database for the conterminous United States. Photogrammetric Engineering and Remote Sensing 73:337–341.
   Web of Science ®Google Scholar
• Jelks, H. L., S. J. Walsh, N. M. Burkhead, S. Contreras-Balderas, E. Diaz-Pardo, D. A. Hendrickson, J. Lyons, N. E. Mandrak, F. McCormick, J. S. Nelson, S. P. Plantania, B. A. Porter, C. B. Renaud, J. J. Schmitter-Soto, E. B. Taylor, and M. L. Warren Jr. 2008. Conservation status of imperiled North American freshwater and diadromous fishes. Fisheries 33:372–407.
   Web of Science ®Google Scholar
• Karr, J. R. 1981. Assessment of biotic integrity using fish communities. Fisheries 6(6):21–27.
   Web of Science ®Google Scholar
• Kéry, M., B. Gardner, and C. Monnerat. 2010. Predicting species distributions from checklist data using site-occupancy models. Journal of Biogeography 37:1851–1862.
   Web of Science ®Google Scholar
• Kéry, M., and M. Schaub. 2012. Bayesian population analysis using WinBUGS: a hierarchical perspective. Academic Press, San Diego, California.
   Google Scholar
• Kuhn, M., and K. Johnson. 2013. Applied predictive modeling. Springer, New York.
   Google Scholar
• Lammert, M., and J. D. Allan. 1999. Assessing biotic integrity of streams: effects of scale in measuring the influence of land use/cover and habitat structure on fish and macroinvertebrates. Environmental Management 23:257–270.
   PubMed Web of Science ®Google Scholar
• Lapointe, N. W., and T. Light. 2012. Landscape-scale determinants of non-native fish communities. Diversity and Distributions 18:282–293.
   Web of Science ®Google Scholar
• Leung, B., and R. J. Steele. 2013. The value of a datum–how little data do we need for quantitative risk analysis? Diversity and Distributions 19:617–628.
   Web of Science ®Google Scholar
• Lu, Y., J. E. Bauer, E. A. Canuel, Y. Yamashita, R. Chambers, and R. Jaffé. 2013. Photochemical and microbial alteration of dissolved organic matter in temperate headwater streams associated with different land use. Journal of Geophysical Research: Biogeosciences 118:566–580.
   Web of Science ®Google Scholar
• Malmqvist, B., and S. Rundle. 2002. Threats to the running water ecosystems of the world. Environmental Conservation 29:134–153.
   Web of Science ®Google Scholar
• Meador, M. R., and D. M. Carlisle. 2009. Predictive models for fish assemblages in eastern U.S. streams: implications for assessing biodiversity. Transactions of the American Fisheries Society 138:725–740.
   Web of Science ®Google Scholar
• NCDENR (North Carolina Department of Environment and Natural Resources). 2006. Standard operating procedure for stream fish communities. NCDENR, Raleigh.
   Google Scholar
• NOAA (National Oceanic and Atmospheric Administration). 2010. Development sprawl impacts on the terrestrial carbon dynamics of the United States: data download. NOAA , Silver Spring, Maryland. Available: www.ngdc.noaa.gov/dmsp/download_sprawl.html. (June 2014).
   Google Scholar
• Olden, J. D., L. N. Poff, M. R. Douglas, M. E. Douglas, and K. D. Fausch. 2004. Ecological and evolutionary consequences of biotic homogenization. Trends in Ecology and Evolution 19:18–24.
   PubMed Web of Science ®Google Scholar
• Ovaskainen, O., and J. Soininen. 2011. Making more out of sparse data: hierarchical modeling of species communities. Ecology 92:289–295.
   PubMed Web of Science ®Google Scholar
• Paller, M. H. 1995. Relationships among number of fish species sampled, reach length surveyed, and sampling effort in South Carolina coastal plain streams. North American Journal of Fisheries Management 15:110–120.
   Google Scholar
• Paul, M. J., and J. L. Meyer. 2001. Streams in the urban landscape. Annual Review of Ecology and Systematics 32:333–365.
   Google Scholar
• Ricketts, T. H., E. Dinerstein, D. M. Olson, and C. Loucks. 1999. Who's where in North America? Bioscience 49:369–381.
   Web of Science ®Google Scholar
• Royle, J. A., and R. M. Dorazio. 2008. Hierarchical modeling and inference in ecology: the analysis of data from populations, metapopulations and communities. Academic Press, New York.
   Google Scholar
• Spiegelhalter, D., A. Thomas, N. Best, and D. Lunn. 2004. WinBUGS user manual. Medical Research Council, Biostatistics Unit, Cambridge, UK.
   Google Scholar
• Sutherland, A. B., J. L. Meyer, and E. P. Gardiner. 2002. Effects of land cover on sediment regime and fish assemblage structure in four southern Appalachian streams. Freshwater Biology 47:1791–1805.
   Web of Science ®Google Scholar
• Tyre, A. J., B. Tenhumberg, S. A. Field, D. Niejalke, K. Parris, and H. P. Possingham. 2003. Improving precision and reducing bias in biological surveys: estimating false-negative error rates. Ecological Applications 13:1790–1801.
   Web of Science ®Google Scholar
• Wagner, T., J. T. Deweber, J. Detar, D. Kristine, and J. A. Sweka. 2014. Spatial and temporal dynamics in Brook Trout density: implications for population monitoring. North American Journal of Fisheries Management 34:258–269.
   Web of Science ®Google Scholar
• Wagner, T., D. B. Hayes, and M. T. Bremigan. 2006. Accounting for multilevel data structures in fisheries data using mixed models. Fisheries 31:180–187.
   Web of Science ®Google Scholar
• Walsh, C. J., A. H. Roy, J. W. Feminella, P. D. Cottingham, P. M. Groffman, and R. P. Morgan II. 2005. The urban stream syndrome: current knowledge and the search for a cure. Journal of the North American Benthological Society 24:706–723.
   Web of Science ®Google Scholar
• Warren, M. L., B. M. Burr, S. J. Walsh, H. L. Bart Jr., R. C. Cashner, D. A. Etnier, B. J. Freeman, B. R. Kuhajda, R. L. Mayden, H. W. Robinson, S. T. Ross, and W. C. Starnes. 2000. Diversity, distribution, and conservation status of the native freshwater fishes of the southern United States. Fisheries 25(10):7–31.
   Web of Science ®Google Scholar
• Zipkin, E. F., J. A. Royle, D. K. Dawson, and S. Bates. 2010. Multi-species occurrence models to evaluate the effects of conservation and management actions. Biological Conservation 143:479–484.
   Web of Science ®Google Scholar