Predicting habitat suitability for rare plants at local spatial scales using a species distribution model

Ecological Applications

Volumn 21, Issue 1, 2011, Pages 33-47

  Gogol Prokurat, Melanie ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Biogeographic Data Branch   (United States)

Author keywords

Conservation planning; Edaphic endemic; Gabbro; Goodness of fit; Habitat suitability; Maxent species distribution model; Rare plants

Indexed keywords

ABUNDANCE; ACCURACY ASSESSMENT; CONSERVATION PLANNING; DATA SET; DISCRIMINANT ANALYSIS; ENDEMIC SPECIES; FINE GRAINED SEDIMENT; GRAIN SIZE; HABITAT CONSERVATION; HABITAT TYPE; NUMERICAL MODEL; POPULATION DISTRIBUTION; POPULATION MODELING; PRIORITIZATION; RARE SPECIES; SOIL TYPE; SPATIAL ANALYSIS; SPECIES OCCURRENCE; THRESHOLD; TRADE-OFF;

ARTICLE; ECOSYSTEM; ENVIRONMENTAL PROTECTION; PLANT; THEORETICAL MODEL;

CONSERVATION OF NATURAL RESOURCES; ECOSYSTEM; MODELS, THEORETICAL; PLANTS;

CALIFORNIA; EL DORADO COUNTY; UNITED STATES;

EID: 79955532021     PISSN: 10510761     EISSN: None     Source Type: Journal    
DOI: 10.1890/09-1190.1     Document Type: Article

References (73)

1. Alexander, E. B. 1991. Gabbro and its soils. Fremontia 21:8-10.
2. Araú jo, M. B., and A. Guisan. 2006. Five (or so) challenges for species distribution modelling. Journal of Biogeography 33: 1677-1688. (Pubitemid 44370084)
3. Arundel, S. T. 2005. Using spatial models to establish climatic limiters of plant species' distributions. Ecological Modelling 182:159-181. (Pubitemid 40078200)
4. Austin, M. P. 2002. Spatial prediction of species distribution: an interface between ecological theory and statistical modeling. Ecological Modeling 157:101-118. (Pubitemid 35255409)
5. Barry, S., and J. Elith. 2006. Error and uncertainty in habitat models. Journal of Applied Ecology 43:413-423. (Pubitemid 43725546)
6. Boyd, R. 1987. The effects of controlled burning on three rare plants. Pages 513-517 in T. S. Elias, editor. Conservation and management of rare and endangered plants. California Native Plant Society, Sacramento, California, USA.
7. Chefaoui, R. M., and J. M. Lobo. 2008. Assessing the effects of pseudo-absences on predictive distribution model performance. Ecological Modelling 210:478-486. (Pubitemid 350299678)
8. CNDDB. 2008. California Natural Diversity Database. Biogeographic Data Branch, California Department of Fish and Game, Sacramento, California, USA.
9. CNPS. 2001. Inventory of rare and endangered plants of California. Sixth edition. California Native Plant Society, Sacramento, California, USA.
10. Crist, E. P., and R. Cicone. 1984. A physically-based transformation of Thematic Mapper data-the TM Tasseled Cap. IEEE Transactions on Geosciences and Remote Sensing GE-22:256-263. (Pubitemid 14608494)
11. Crossman, N. D., and D. A. Bass. 2008. Application of common predictive habitat techniques for post-border weed risk management. Diversity and Distributions 14:213-224. (Pubitemid 351208164)
12. Elith, J., and M. Burgman. 2002. Predictions and their validataion: rare plants in the central highlands, Victoria, Australia. Pages 303-314 in J. M. Scott, et al., editors. Predicting species occurrences: issues of accuracy and scale. Island Press, Washington, D.C., USA.
13. Elith, J., et al. 2006. Novel methods improve prediction of species' distributions from occurrence data. Ecography 29: 129-151.
14. Engler, R., A. Guisan, and L. Rechsteiner. 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)
15. ESRI. 2007. ArcGIS 9.2. ESRI, Redlands, California, USA.
16. Fielding, A. H., and J. F. Bell. 1997. A review of methods for the assessment of prediction errors in conservation presence/ absence models. Environmental Conservation 24:38-49. (Pubitemid 27376840)
17. Fisher, R. A. 1922. On the interpretation of v2 from contingency tables, and the calculation of P. Journal of the Royal Statistical Society 85:87-94.
18. Gogol-Prokurat, M. 2009. Ecology and demography of four rare endemic plants on gabbro soils: implications for habitat suitability modeling and conservation. Dissertation. University of California, Davis, California, USA.
19. 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. (Pubitemid 38069867)
20. Guisan, A., O. Broennimann, R. Engler, M. Vust, N. Yoccoz, A. Lahmann, and N. Zimmerman. 2006. Using niche-based models to improve the sampling of rare species. Conservation Biology 20:501-511.
21. Guisan, A., and J. P. Theurillat. 2000. Equilibrium modeling of alpine plant distribution: How far can we go? Phytocoenologia 30:353-384. (Pubitemid 32043186)
22. Guisan, A., and W. Thuiller. 2005. Predicting species distribution: offering more than simple habitat models. Ecology Letters 8:993-1009. (Pubitemid 41247275)
23. Guisan, A., N. Zimmerman, J. Elith, C. Graham, S. Phillips, and A. Peterson. 2007. What matters for predicting the occurrences of trees: techniques, data, or species characteristics? Ecological Monographs 77:615-630. (Pubitemid 351342484)
24. Harrison, S. 1997. How natural habitat patchiness affects the distribution of diversity in California serpentine chaparral. Ecology 78:1898-1906.
25. Harrison, S., H. D. Safford, J. B. Grace, J. H. Viers, and K. F. Davies. 2006. Regional and local species Ricahness in an insular environment: serpentine plants in California. Ecological Monographs 76:41-56.
26. Hernandez, P. A., C. H. Graham, L. L. Master, and D. L. Albert. 2006. The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography 29:773-785. (Pubitemid 44630203)
27. Hickman, J. C. 1993. The Jepson manual: higher plants of California. University of California Press, Berkeley, California, USA.
28. Hirzel, A., and A. Guisan. 2002. Which is the optimal sampling strategy for habitat suitability modelling? Ecological Modelling 157:331-341. (Pubitemid 35255421)
29. Hirzel, A. H., and G. Le Lay. 2008. Habitat suitability modelling and niche theory. Journal of Applied Ecology 45:1372-1381.
30. Hosmer, D. W., T. Hosmer, S. Le Cessie, and S. Lemeshow. 1997. A comparison of goodness-of-fit tests for the logistic regression model. Statistics in Medicine 16:965-980. (Pubitemid 27198985)
31. Hosmer, D. W., and S. Lemeshow. 2000. Logistic regression. Second edition. Wiley-Interscience, New York, New York, USA.
32. Jiménez-Valverde, A., J. M. Lobo, and J. Hortal. 2008. Not as good as they seem: the importance of concepts in species distribution modelling. Diversity and Distributions 14:885-890.
33. Johnson, C. J., and M. P. Gillingham. 2005. An evaluation of mapped species distribution models used for conservation planning. Environmental Conservation 32:117-128. (Pubitemid 41391666)
34. Kruckeberg, A. R. 1984. California serpentines: flora, vegetation, geology, soils and management problems. University of California Press, Berkeley, California, USA.
35. Loarie, S. R., B. E. Carter, K. Hayhoe, S. McMahon, R. Moe, C. A. Knight, and D. Ackerly. 2008. Climate change and the future of California's endemic flora. PLoS ONE 3:e2502.
36. Lobo, J. M., A. Jimenez-Valverde, and R. Real. 2008. AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography 17: 145-151. (Pubitemid 351228538)
37. Loiselle, B. A., C. A. Howell, C. H. Graham, J. M. Goerck, T. Brooks, K. G. Smith, and P. H. Williams. 2003. Avoiding pitfalls of using species distribution models in conservation planning. Conservation Biology 17:1591-1600. (Pubitemid 37538199)
38. Maimon, O. Z., and L. Rokach. 2005. Introduction to supervised methods. Pages 149-164 in Data mining and knowledge discovery handbook. Springer Science and Business, New York, New York, USA.
39. Marage, D., L. Garraud, and J.-C. Rameau. 2008. The influence of management history on spatial prediction of Eryngium spinalba, an endangered endemic species. Applied Vegetation Science 11:139-148. (Pubitemid 351895720)
40. Marmion, M., M. Parviainen, M. Luoto, R. K. Heikkinen, and W. Thuiller. 2009. Evaluation of consensus methods in predictive species distribution modelling. Diversity and Distributions 15:59-69.
41. Meentemeyer, R. K., A. Moody, and J. Franklin. 2001. Landscape-scale patterns of shrub-species abundance in California chaparral: the role of topographically mediated resource gradients. Plant Ecology 156:19-41. (Pubitemid 34004085)
42. Mittermeier, R. A., P. R. Gil, M. Hoffman, J. Pilgrim, T. Brooks, C. G. Mittermeier, J. Lamoreux, and G. A. B. Da Fonseca. 2005. Hotspots revisited: earth's biologically Ricahest and most endangered terrestrial ecoregions. University of Chicago Press, Chicago, Illinois, USA.
43. Nosal, T. 1997. A demographic study of Stebbin's morningglory (Calystegia stebbinsii, Brummit, Convolvulaceae), a California state-listed and federal listed endangered plant species. Thesis. California State University, Sacramento, California, USA.
44. Pearson, R. G., T. P. Dawson, and C. Liu. 2004. Modelling species distributions in Britain: a hierarchical integration of climate and land-cover data. Ecography 27:285-298. (Pubitemid 38826104)
45. Peterson, A. T. 2006. Uses and requirements of ecological niche models and related distributional models. Biodiversity Informatics 3:59-72.
46. Phillips, S., R. Anderson, and R. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231-259. (Pubitemid 41680650)
47. Phillips, S. J., M. Dudk, J. Elith, C. H. Graham, A. Lehmann, J. Leathwick, and S. Ferrier. 2009. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecological Applications 19:181-197.
48. Prendergast, J. R., R. M. Quinn, and J. H. Lawton. 1999. The gaps between theory and practice in selecting nature reserves. Conservation Biology 13:484-492. (Pubitemid 29267057)
49. Pulliam, H. R. 2000. On the relationship between niche and distribution. Ecology Letters 3:349-361. (Pubitemid 30597802)
50. Rodriguez, J. P., L. Brotons, J. Bustamante, and J. Seoane. 2007. The application of predictive modelling of species distribution to biodiversity conservation. Diversity and Distributions 13:243-251. (Pubitemid 46633449)
51. Sattler, T., F. Bontadina, A. H. Hirzel, and R. Arlettaz. 2007. Ecological niche modelling of two cryptic bat species calls for a reassessment of their conservation status. Journal of Applied Ecology 44:1188-1199. (Pubitemid 350029238)
52. Sawyer, J. O., and T. Keeler-Wolf. 1995. A manual of California vegetation. California Native Plant Society, Sacramento, California, USA.
53. Schwartz, M. W., L. R. Iverson, A. M. Prasad, S. N. Matthews, and R. J. O'Connor. 2006. Predicting extinctions as a result of climate change. Ecology 87:1611-1615. (Pubitemid 44141540)
54. Scott, J. M., P. Heglund, and M. Morrison, editors. 2002. Predicting species occurrences: issues of accuracy and scale. Island Press, Washington, D.C.
55. Sing, T., O. Sander, N. Beerenwinkel, and T. Lengauer. 2005. ROCR: visualizing classifier performance in R. Bioinformatics 21:3940-3941. (Pubitemid 41535515)
56. Soberón, J. 2007. Grinnellian and Eltonian niches and geographic distributions of species. Ecology Letters 10: 1115-1123.
57. Soil Survey Staff. 2006. U.S. General Soil Map (STATSGO2) for El Dorado County, California. Natural Resources Conservation Service, United States Department of Agricaulture. Available online at (http://soildatamart.nrcs.usda. gov)
58. Springer, R. K. 1980. Geology of the Pine Hill intrusive complex, a layered gabbroic body in the western Sierra Nevada foothills, California. Geological Society of America Bulletin 91:1536-1626.
59. Stockwell, D. R. B., and A. T. Peterson. 2002. Effects of sample size on accuracy of species distribution models. Ecological Modelling 148:1-13. (Pubitemid 34124426)
60. Thomaes, A., T. Kervyn, and D. Maes. 2008. Applying species distribution modelling for the conservation of the threatened saproxylic Stag Beetle (Lucanus cervus). Biological Conservation 141:1400-1410.
61. Thorn, J. S., V. Nijman, D. Smith, and K. A. I. Nekaris. 2009. Ecological niche modeling as a technique for assessing threats and setting conservation priorities for Asian slow lorises (Primates: Nycticebus). Diversity and Distributions 15:289-298.
62. Thuiller, W., M. B. Araujo, and S. Lavorel. 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)
63. Thuiller, W., M. B. Araujo, and S. Lavorel. 2004a. Do we need land-cover data to model species distributions in Europe? Journal of Biogeography 31:353-361. (Pubitemid 38319044)
64. Thuiller, W., L. Brotons, M. B. Araujo, and S. Lavorel. 2004b. Effects of restRicating environmental range of data to project current and future species distributions. Ecography 27:165-172. (Pubitemid 38497933)
65. Trani, M. K. 2002. The influence of spatial scale on landscape pattern description and wildlife habitat assessment. Pages 141-156 in M. J. Scott, P. Heglund, and M. Morrison, editors. Predicting species occurrences: issues of accuracy and scale. Island Press, Washington, D.C., USA.
66. Underwood, E. C., R. Klinger, and P. E. Moore. 2004. Predicting patterns of non-native plant invasions in Yosemite National Park, California, USA. Diversity and Distributions 10:447-459. (Pubitemid 39260381)
67. USDA. 1997. Ecological subregions of California. USDA Forest Service, Pacific Southwest Region, San Francisco, California, USA.
68. USFWS. 2002. Recovery plan for gabbro soils plants of the central Sierra Nevada foothills. U.S. Fish and Wildlife Service, Portland, Oregon, USA.
69. USGS. 2005. Preliminary integrated databases for the United States-Western states: California. U.S. Geological Survey, Reston, Virginia, USA.
70. Vaughan, I., and S. Ormerod. 2005. The continuing challenges of testing species distribution models. Journal of Applied Ecology 42:720-730. (Pubitemid 41710795)
71. Williams, J. N., C. Seo, J. Thorne, J. Nelson, S. Erwin, J. O'Brien, and M. W. Schwartz. 2009. Using species distribution models to predict new occurrences for rare plants. Diversity and Distributions 15:565-576.
72. Wisz, M. S., R. J. Hijmans, J. Li, A. T. Peterson, C. H. Graham, A. Guisan, and NCEAS. Predicting Species Distributions Working Group. 2008. Effects of sample size on the performance of species distribution models. Diversity and Distributions 14:763-773.
73. Woodward, F. I., and B. G. Williams. 1987. Climate and plant distribution at global and local scales. Vegetatio 69:189-197.