Experimental and environmental factors affect spurious detection of ecological thresholds

Ecology

Volumn 93, Issue 1, 2012, Pages 17-23

  Daily, Jonathan P ^a   Hitt, Nathaniel P ^a   Smith, David R ^a   Snyder, Craig D ^a  

^a U S GEOLOGICAL SURVEY   (United States)

Author keywords

Ecological thresholds; Nonparametric change point analysis; Piecewise quantile regression; SiZer; Stream benthic macroinvertebrates; Type I error

Indexed keywords

BENTHOS; BOOTSTRAPPING; DETECTION METHOD; ENVIRONMENTAL FACTOR; ENVIRONMENTAL GRADIENT; EXPERIMENTAL STUDY; MACROINVERTEBRATE; STREAMWATER; THRESHOLD;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; ECOSYSTEM; INVERTEBRATE; METHODOLOGY; PHYSIOLOGY; POPULATION DYNAMICS; RESEARCH; RIVER; STATISTICS;

ANIMALS; ECOSYSTEM; INVERTEBRATES; MODELS, BIOLOGICAL; POPULATION DYNAMICS; RESEARCH; RIVERS; STOCHASTIC PROCESSES;

EID: 84863371111     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/11-0516.1     Document Type: Article

References (47)

1. Anderson, M. J. 2008. Animal-sediment relationships revisited: characterising species' distributions along an environmental gradient using canonical analysis and quantile regression splines. Journal of Experimental Marine Biology and Ecology 366:16-27.
2. Andersen, T., J. Carstensen, E. Hernández-García, and C. M. Duarte. 2009. Ecological thresholds and regime shifts: approaches to identification. Trends in Ecology and Evolution 24:49-57.
3. Austin, M. 2007. Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modelling 2007:1-19. (Pubitemid 44828248)
4. Badgley, C., and D. L. Fox. 2000. Ecological biogeography of North American mammals: species density and ecological structure in relation to environmental gradients. Journal of Biogeography 27:1437-1467. (Pubitemid 32375734)
5. Baker, M. E., and R. S. King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1:25-37.
6. Breiman, L. 2001. Statistical modeling: the two cultures (with comments and a rejoinder by the author). Statistical Science 16:199-231.
7. Breiman, L., J. H. Friedman, R. A. Olshen, and C. J. Stone. 1984. Classification and regression trees. Wadsworth International Group, Belmont, California, USA.
8. Brenden, T. O., L. Wang, and Z. Su. 2008. Quantitative identification of disturbance thresholds in support of aquatic resource management. Environmental Management 42:821-432.
9. Bryce, S. A., G. A. Lomnicky, and P. R. Kaufmann. 2010. Protecting sediment-sensitive aquatic species in mountain streams through the application of biologically based streambed sediment criteria. Journal of the North American Benthological Society 29:657-672.
10. Buhlmann, P., and B. Yu. 2002. Analyzing bagging. Annals of Statistics 30:927-961. (Pubitemid 37095335)
11. Buhl-Mortensen, L. 1996. Type-II statistical errors in environmental science and the precautionary principle. Marine Pollution Bulletin 32:528-531. (Pubitemid 26325307)
12. Cade, B. S., and B. R. Noon. 2003. A gentle introduction to quantile regression for ecologists. Frontiers in Ecology and the Environment 1:412-420.
13. Cao, Y., and C. P. Hawkins. 2005. Simulating biological impairment to evaluate the accuracy of ecological indicators. Journal of Applied Ecology 42:954-965. (Pubitemid 41727036)
14. Chaudhuri, P., and W. Loh. 2002. Nonparametric estimation of conditional quantiles using quantile regression trees. Bernoulli 8:561-576. (Pubitemid 44242663)
15. Chaudhuri, P., and J. S. Marron. 1999. SiZer for exploration of structures in curves. Journal of the American Statistical Association 94:807-823.
16. Clements, W. H., N. K. M. Vieira, and D. L. Sondregger. 2010. Use of ecological thresholds to assess recovery in lotic ecosystems. Journal of the North American Benthological Society 29:1017-1023.
17. Dodds, W. K., W. H. Clements, K. Gido, R. H. Hilderbrand, and R. S. King. 2010. Thresholds, breakpoints, and nonlinearity in freshwaters as related to management. Journal of the North American Benthological Society 29:988-997.
18. Duggins, J. W. 2010. Parametric resampling methods for retrospective changepoint analysis. Dissertation. Virginia Tech, Blacksburg, Virginia, USA.
19. Evans-White, M. A., W. K. Dodds, D. G. Huggins, and D. S. Baker. 2009. Thresholds in macroinvertebrate biodiversity and stoichiometry across water-quality gradients in Central Plains (USA) streams. Journal of the North American Benthological Society 28:855-868.
20. Freund, J. G., and J. T. Petty. 2007. Response of fish and macroinvertebrate bioassessment indices to water chemistry in a mined Appalachian watershed. Environmental Management 39:707-720. (Pubitemid 46632387)
21. Gentry, A. H. 1988. Changes in plant community diversity and floristic composition on environmental and geographical gradients. Annals of the Missouri Botanical Garden 75:1-34.
22. Groffman, P. M., et al. 2006. Ecological thresholds: the key to successful environmental management or an important concept with no practical application? Ecosystems 9:1-13.
23. Hall, D. G., C. C. Childers, J. E. Eger, and J. C. Allen. 1997. Citrus rust mite (Acari: Eriophyidae) counts on fruit and the negative binomial distribution. Florida Entomologist 80:1-10. (Pubitemid 27169449)
24. Harding, J. S., E. F. Benfield, P. V. Bolstad, G. S. Helfman, and E. B. D. Jones III. 1998. Stream biodiversity: the ghost of land use past. Proceedings of the National Academy of Sciences USA 95:14843-14847. (Pubitemid 29003718)
25. Hare, S. R., and N. J. Mantua. 2000. Empirical evidence for North Pacific regime shifts in 1977 and 1989. Progress in Oceanography 47:103-145.
26. Herlihy, A. T., D. P. Larsen, S. G. Paulsen, N. S. Urquhart, and B. J. Rosenbaum. 2000. Designing a spatially balanced, randomized site selection process for regional stream surveys: the EMAP mid-Atlantic pilot study. Environmental Monitoring and Assessment 63:95-113. (Pubitemid 30399295)
27. King, R. S., and C. J. Richardson. 2003. Integrating bioassessment and ecological risk assessment: an approach to developing numerical water-quality criteria. Environmental Management 31:795-809. (Pubitemid 37075827)
28. Koenker, R. 2010. quantreg: quantile regression. R package version 4.53. http://CRAN. R-project.org/package=quantreg
29. Kunin, W. E., S. Hartley, and J. J. Lennon. 2000. Scaling down: on the challenge of estimating abundance from occurrence patterns. American Naturalist 156:560-566.
30. Liaw, A., and M. Wiener. 2002. Classification and regression by random Forest. R News 2 3:18-22.
31. May, R. M. 1977. Thresholds and breakpoints in ecosystems with a multiplicity of stable states. Nature 269:471-477.
32. Melles, S., S. Glenn, and K. Martin. 2003. Urban bird diversity and landscape complexity: species-environment associations along a multiscale habitat gradient. Conservation Ecology 7(1):5.
33. Paine, R. T. 1966. Food web complexity and species diversity. American Naturalist 100:65-75.
34. Qian, S. S., R. S. King, and C. J. Richardson. 2003. Two statistical methods for the detection of environmental thresholds. Ecological Modelling 166:87-97. (Pubitemid 37537751)
35. R Development Core Team. 2010. R: a language and environment for statistical computing. R Project for Statistical Computing, Vienna, Austria.
36. Royle, J. A., and J. D. Nichols. 2003. Estimating abundance from repeated presence-absence data or point counts. Ecology 84:777-790. (Pubitemid 36893064)
37. Scheffer, M. 1990. Multiplicity of stable states in freshwater systems. Hydrobiologia 200/201:475-486.
38. Schwarz, G. 1978. Estimating the dimension of a model. Annals of Statistics 6:461-464.
39. Sonderegger, D. 2010. SiZer: significant zero crossings. R package version 0.1-3. http://CRAN. R-project.org/package=SiZer
40. Sonderegger, D. L., H. Wang, W. H. Clements, and B. R. Noon. 2009. Using SiZer to detect thresholds in ecological data. Frontiers in Ecology and the Environment 7:190-195.
41. Therneau, T. M., and B. Atkinson. (2010). rpart: recursive partitioning. R package version 3. 1-47. http://CRAN. R-project.org/package=rpart
42. Toms, J. D., and M. L. Lesperance. 2003. Piecewise regression: a tool for identifying ecological thresholds. Ecology 84:2034-2041. (Pubitemid 37435678)
43. Tong, H. 1983. Threshold models in non-linear time series analysis. Springer-Verlag, New York, New York, USA.
44. Utz, R. M., R. H. Hilderbrand, and D. M. Boward. 2009. Identifying regional differences in threshold responses of aquatic invertebrates to land cover gradients. Biological Indicators 9:556-567.
45. van de Koppel, J., M. Rietkerk, and F. J. Weissing. 1997. Catastrophic vegetation shifts and soil degradation in terrestrial grazing systems. Trends in Ecology and Evolution 12:352-356.
46. Wang, L., D. Robertson, and P. Garrison. 2007. Linkages between nutrients and assemblages of macroinvertebrates and fish in wadeable streams: implication to nutrient criteria development. Environmental Management 39:194-212. (Pubitemid 44974351)
47. Yuan, L. L., and S. B. Norton. 2003. Comparing responses of macroinvertebrate metrics to increasing stress. Journal of the North American Benthological Society 22:308-322. (Pubitemid 36720300)