Using species distribution models to predict new occurrences for rare plants

Diversity and Distributions

Volumn 15, Issue 4, 2009, Pages 565-576

  Williams, John N ^a   Seo, Changwan ^b   Thorne, James ^a   Nelson, Julie K ^c   Erwin, Susan ^c   O'Brien, Joshua M ^d   Schwartz, Mark W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Seoul   (South Korea)

^c USDA FOREST SERVICE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Edaphic specialist; Endemism; Maxent; Random forests; Rarity; Serpentine

Indexed keywords

FIELD SURVEY; NUMERICAL MODEL; PLANT; POPULATION DISTRIBUTION; RARITY; SERPENTINE; SPECIES OCCURRENCE;

NORTH AMERICA; UNITED STATES;

EID: 67149128316     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/j.1472-4642.2009.00567.x     Document Type: Article

References (75)

1. Alexander, E. (2002). Trinity serpentine soil survey: a detail survey of serpentine soils in the southern exposure of the Rattlesnake Creek Terrane, Klamath Mountains. United States Forest Service, Redding, CA.
2. Austin, M.P. (2002) Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecological Modelling, 157, 101 118. (Pubitemid 35255409)
3. Austin, M. (2007) Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modelling, 200, 1 19. (Pubitemid 44828248)
4. Austin, M.P., Belbin, L., Meyers, J.A., Doherty, M.D. Luoto, M. (2006) Evaluation of statistical models used for predicting plant species distributions: role of artificial data and theory. Ecological Modelling, 199, 197 216. (Pubitemid 44572638)
5. Ballesteros-Barrera, C., Martinez-Meyer, E. Gadsden, H. (2007) Effects of land-cover transformation and climate change on the distribution of two microendemic lizards, genus Uma, of northern Mexico. Journal of Herpetology, 41, 733 740. (Pubitemid 350309075)
6. Beers, T.W., Dress, P.E. Wensel, L.C. (1966) Aspect transformation in site productivity research. Journal of Forestry, 64, 691.
7. Benito Garzon, M., Sanchez De Dios, R. Sainz Ollero, H. (2008) Effects of climate change on the distribution of Iberian tree species. Applied Vegetation Science, 11, 169 178. (Pubitemid 351668897)
8. Bourg, N.A., Mcshea, W.J. Gill, D.E. (2005) Putting a cart before the search: successful habitat prediction for a rare forest herb. Ecology, 86, 2793 2804. (Pubitemid 41408074)
9. Breiman, L. (2001) Random forests. Machine Learning, 45, 5 32. (Pubitemid 32933532)
10. Brose, U., Martinez, N.D. Williams, R.J. (2003) Estimating species richness: sensitivity to sample coverage and insensitivity to spatial patterns. Ecology, 84, 2364 2377. (Pubitemid 37435655)
11. Brotons, L., Thuiller, W., Araujo, M.B. Hirzel, A.H. (2004) Presence-absence versus presence-only modelling methods for predicting bird habitat suitability. Ecography, 27, 437 448. (Pubitemid 38826095)
12. Cabeza, M., Araujo, M.B., Wilson, R.J., Thomas, C.D., Cowley, M.J.R. Moilanen, A. (2004) Combining probabilities of occurrence with spatial reserve design. Journal of Applied Ecology, 41, 252 262. (Pubitemid 38492494)
13. CNPS (2006) Inventory of rare and endangered plants. California Native Plant Society, Sacramento, CA. URL: http://www.cnps.org/inventory
14. Cutler, D.R., Edwards, T.C., Beard, K.H., Cutler, A. Hess, K.T. (2007) Random forests for classification in ecology. Ecology, 88, 2783 2792. (Pubitemid 351345081)
15. Edwards, T.C., Cutler, D.R., Geiser, L., Alegria, J. Mckenzie, D. (2004) Assessing rarity of species with low detectability: lichens in Pacific Northwest forests. Ecological Applications, 14, 414 424. (Pubitemid 38370903)
16. Elith, J., Burgman, M.A. Regan, H.M. (2002) Mapping epistemic uncertainties and vague concepts in predictions of species distribution. Ecological Modelling, 157, 313 329. (Pubitemid 35258968)
17. Elith, J., Graham, C.H., Anderson, R.P., Dudik, M., Ferrier, S., Guisan, A., Hijmans, R.J., Huettmann, F., Leathwick, J.R., Lehmann, A., Li, J., Lohmann, L.G., Loiselle, B.A., Manion, G., Moritz, C., Nakamura, M., Nakazawa, Y., Overton, J.M., Peterson, A.T., Phillips, S.J., Richardson, K., Scachetti-Pereira, R., Schapire, R.E., Soberon, J., Williams, S., Wisz, M.S. Zimmermann, N.E. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography, 29, 129 151.
18. Engler, R., Guisan, A. Rechsteiner, L. (2004) An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data. Journal of Applied Ecology, 41, 263 274. (Pubitemid 38492495)
19. Fielding, A.H. Bell, J.F. (1997) A review of methods for the assessment of prediction errors in conservation presence-absence models. Environmental Conservation, 24, 38 49. (Pubitemid 27376840)
20. Franklin, J. (1995) Predictive vegetation mapping: geographic modelling of biospatial patterns in relation to environmental gradients. Progress in Physical Geography, 19, 474 499. (Pubitemid 26442382)
21. Gardner, R.H. Urban, D.L. (2007) Neutral models for testing landscape hypotheses. Landscape Ecology, 22, 15 29. (Pubitemid 46141379)
22. Gaston, K.J. (2003). The structure and dynamics of geographic ranges. Oxford Series in Ecology and Evolution, Oxford.
23. Gibson, L., Barrett, B. Burbidge, A. (2007) Dealing with uncertain absences in habitat modelling: a case study of a rare ground-dwelling parrot. Diversity and Distributions, 13, 704 713. (Pubitemid 47622016)
24. Gomez-Mendoza, L. Arriaga, L. (2007) Modeling the effect of climate change on the distribution of oak and pine species of Mexico. Conservation Biology, 21, 1545 1555. (Pubitemid 350290864)
25. Guisan, A. Thuiller, W. (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8, 993 1009. (Pubitemid 41247275)
26. Guisan, A., Broennimann, O., Engler, R., Vust, M., Yoccoz, N.G., Lehmann, A. Zimmermann, N.E. (2006) Using niche-based models to improve the sampling of rare species. Conservation Biology, 20, 501 511.
27. Guisan, A., Graham, C.H., Elith, J. Huettmann, F. (2007) Sensitivity of predictive species distribution models to change in grain size. Diversity and Distributions, 13, 332 340. (Pubitemid 46633446)
28. Hanley, J.A. McNeil, B.J. (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 143, 29 36.
29. Hare, K.M., Hoare, J.M. Hitchmough, R.A. (2007) Investigating natural population dynamics of Naultinus manukanus to inform conservation management of New Zealand's cryptic diurnal geckos. Journal of Herpetology, 41, 81 93. (Pubitemid 46761207)
30. Hernandez, P.A., Graham, C.H., Master, L.L. Albert, D.L. (2006) The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography, 29, 773 785. (Pubitemid 44630203)
31. Hernandez, P.A., Franke, I., Herzog, S.K., Pacheco, V., Paniagua, L., Quintana, H.L., Soto, A., Swenson, J.J., Tovar, C., Valqui, T.H., Vargas, J. Young, B.E. (2008) Predicting species distributions in poorly-studied landscapes. Biodiversity and Conservation, 17, 1353 1366.
32. Hickman, J.C. (1993). The Jepson manual: higher plants of California. University of California Press, Berkeley, CA.
33. Hijmans, R.J. Graham, C.H. (2006) The ability of climate envelope models to predict the effect of climate change on species distributions. Global Change Biology, 12, 2272 2281. (Pubitemid 44857703)
34. Hirzel, A.H., Le Lay, G., Helfer, V., Randin, C. Guisan, A. (2006) Evaluating the ability of habitat suitability models to predict species presences. Ecological Modelling, 199, 142 152. (Pubitemid 44572635)
35. Iverson, L.R., Schwartz, M.W. Prasad, A.M. (2004) Potential colonization of newly available tree-species habitat under climate change: an analysis for five eastern US species. Landscape Ecology, 19, 787 799.
36. Jenness, J. (2003) Random point generator 1.27, p. Shareware written in Avenue for ArcGIS 3.2 Available at http://www.jennessent.com/arcview/random- points.htm.
37. Kadmon, R., Farber, O. et al. (2004) Effect of roadside bias on the accuracy of predictive maps produced by bioclimatic models. Ecological Applications, 14, 401 413. (Pubitemid 38370902)
38. Kruckeberg, A.R. (1984) California serpentines: flora, vegetation, geology, soils and management problems. University of California Press, Berkeley, CA.
39. Kvamme, K.L. (1985) Determining empirical relationships between the natural environment and prehistoric site location: a hunter-gatherer example. For concordance in archaeological analysis: bridging data structure, quantitative technique, and theory (ed. by C. Carr pp. 208 238. Westport Publishers, Kansas City, KS.
40. Lek, S., Delacoste, M., Baran, P., Dimopoulos, I., Lauga, J. Aulagnier, S. (1996) Application of neural networks to modelling nonlinear relationships in ecology. Ecological Modelling, 90, 39 52.
41. Linkie, M., Chapron, G., Martyr, D.J., Holden, J. Leader-Williams, N. (2006) Assessing the viability of tiger subpopulations in a fragmented landscape. Journal of Applied Ecology, 43, 576 586. (Pubitemid 43725561)
42. Malanson, G.P., Westman, W.E. Yan, Y.L. (1992) Realized versus fundamental niche functions in a model of chaparral response to climatic change. Ecological Modelling, 64, 261 277. (Pubitemid 23406158)
43. McCune, B. Keon, D. (2002) Equations for potential annual direct incident radiation and heat load. Journal of Vegetation Science, 13, 603 606. (Pubitemid 35259016)
44. McLachlan, J.S., Hellmann, J.J. Schwartz, M.W. (2007) A framework for debate of assisted migration in an era of climate change. Conservation Biology, 21, 297 302. (Pubitemid 46474754)
45. McPherson, J.M. Jetz, W. (2007) Effects of species' ecology on the accuracy of distribution models. Ecography, 30, 135 151. (Pubitemid 46310625)
46. Meynard, C.N. Quinn, J.F. (2007) Predicting species distributions: a critical comparison of the most common statistical models using artificial species. Journal of Biogeography, 34, 1455 1469. (Pubitemid 47094208)
47. Nakamura, G. Nelson, J.K. (2001). Illustrated field guide to selected rare plants of Northern California. University of California Agriculture and Natural Resources, Los Angeles, CA.
48. Naves, J., Wiegand, T., Revilla, E. Delibes, M. (2003) Endangered species constrained by natural and human factors: the case of brown bears in northern Spain. Conservation Biology, 17, 1276 1289. (Pubitemid 37250068)
49. Olden, J.D., Lawler, J.J. Poff, N.L. (2008) Machine learning methods without tears: a primer for ecologists. Quarterly Review of Biology, 83, 171 193.
50. Olivier, F. Wotherspoon, S.J. (2006) Modelling habitat selection using presence-only data: case study of a colonial hollow nesting bird, the snow petrel. Ecological Modelling, 195, 187 204.
51. Papes, M. Gaubert, P. (2007) Modelling ecological niches from low numbers of occurrences: assessment of the conservation status of poorly known viverrids (Mammalia, Carnivora) across two continents. Diversity and Distributions, 13, 890 902. (Pubitemid 47622026)
52. Pearce, J., Ferrier, S. Scotts, D. (2001) An evaluation of the predictive performance of distributional models for flora and fauna in north-east New South Wales. Journal of Environmental Management, 62, 171 184. (Pubitemid 32586750)
53. Pearson, R.G., Raxworthy, C.J., Nakamura, M. Peterson, A.T. (2007) Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. Journal of Biogeography, 34, 102 117. (Pubitemid 44952533)
54. Phillips, S.J., Anderson, R.P. Schapire, R.E. (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231 259. (Pubitemid 41680650)
55. Prasad, A.M., Iverson, L.R. Liaw, A. (2006) Newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems, 9, 181 199.
56. Rabinowitz, D., Cairns, S. Dillon, T. (1986) Seven forms of rarity and their frequency in the flora of the British Isles. Conservation Biology: The Science of Scarcity and Diversity. Xiii+584p ed. by M. E. Soule pp. 182 204. Sinauer Associates, Inc., Sunderland, Mass., USA. Illus. Paper. Maps.
57. Raxworthy, C.J., Martinez-Meyer, E., Horning, N., Nussbaum, R.A., Schneider, G.E., Ortega-Huerta, M.A. Peterson, A.T. (2003) Predicting distributions of known and unknown reptile species in Madagascar. Nature, 426, 837 841. (Pubitemid 38056868)
58. Riley, S.J., Degloria, S.D. Elliot, R. (1999) A terrain ruggedness index that quantifies topographic heterogeneity. Intermountain Journal of Sciences, 5, 1 4.
59. Rushton, S.P., Ormerod, S.J. Kerby, G. (2004) New paradigms for modelling species distributions? Journal of Applied Ecology, 41, 193 200. (Pubitemid 38492490)
60. Sanders, S. McGraw, J.B. (2005) Hydrastis canadensis L. (Ranunculaceae) distribution does not reflect response to microclimate gradients across a mesophytic forest cove. Plant Ecology, 181, 279 288. (Pubitemid 41712731)
61. SAS (2006) JMP. SAS Institute, Cary, NC.
62. Schwartz, M.W., Iverson, L.R., Prasad, A.M., Matthews, S.N. O'connor, R.J. (2006) Predicting extinctions as a result of climate change. Ecology, 87, 1611 1615. (Pubitemid 44141540)
63. Scott, J.M., Heglund, P.J., Morrison, M.L., Haufler, J.B., Raphael, M.G., Wall, W.A. Samson, F.B. (2002) Predicting species occurrences: issues of accuracy and scale. Island Press, Washington, DC.
64. Seoane, J., Carrascal, L.M., Alonso, C.L. Palomino, D. (2005) Species-specific traits associated to prediction errors in bird habitat suitability modelling. Ecological Modelling, 185, 299 308. (Pubitemid 40564506)
65. Stockwell, D.R. Peterson, A.T. (2002a) Controlling bias in biodiversity. Predicting species occurrences: issues of accuracy and scale. (ed. by) J.M. Scott, P.J. Heglund, M.L. Morrison, J.B. Haufler, M.G. Raphael, W.A. wall F.B. Samson, pp. 537 546. Island Press, Washington, DC.
66. Stockwell, D.R.B. Peterson, A.T. (2002b) Effects of sample size on accuracy of species distribution models. Ecological Modelling, 148, 1 13. (Pubitemid 34124426)
67. Stohlgren, T.J., Quinn, J.F., Ruggiero, M. Waggoner, G.S. (1995) Status of biotic inventories in US national parks. Biological Conservation, 71, 97 106.
68. Termansen, M., Mcclean, C.J. Preston, C.D. (2006) The use of genetic algorithms and Bayesian classification to model species distributions. Ecological Modelling, 192, 410 424. (Pubitemid 43188855)
69. Thuiller, W., Araujo, M.B. Lavorel, S. (2003) Generalized models vs. classification tree analysis: predicting spatial distributions of plant species at different scales. Journal of Vegetation Science, 14, 669 680. (Pubitemid 37358376)
70. Wiser, S.K., Peet, R.K. White, P.S. (1998) Prediction of rare-plant occurrence: a southern appalachian example. Ecological Applications, 8, 909 920. (Pubitemid 28553860)
71. Wisz, M.S., Hijmans, R.J., Li, J., Peterson, A.T., Graham, C.H. Guisan, A. (2008) Effects of sample size on the performance of species distribution models. Diversity and Distributions, 14, 763 773.
72. Wright, J.E. Wyld, S.J. (1994) The Rattlesnake Creek Terrane, Klamath Mountains, California - an early Mesozoic volcanic arc and its basement of tectonically disrupted oceanic crust. Geological Society of America Bulletin, 106, 1033 1056.
73. Yee, T.W. Mitchell, N.D. (1991) Generalized additive models in plant ecology. Journal of Vegetation Science, 2, 587 602.
74. Zacharias, M.A. Gregr, E.J. (2005) Sensitivity and vulnerability in marine environments: an approach to identifying vulnerable marine areas. Conservation Biology, 19, 86 97. (Pubitemid 40274143)
75. Zaniewski, A.E., Lehmann, A. Overton, J.M.C. (2002) Predicting species spatial distributions using presence-only data: a case study of native New Zealand ferns. Ecological Modelling, 157, 261 280. (Pubitemid 35255419)