A Virtual Museum on the State's Fish Biodiversity

Published Predictive SDM Packages

Published SDM Packages

Method(s) Model/software name Species data type Key Reference/URL
Gower Metric DOMAIN presence-only Carpenter et al. 1993; http://www.cifor.cgiar.org/ http://diva-gis.org
Ecological Niche Factor Analysis (ENFA) BIOMAPPER presence and background Hirzel et al. 2002 http://www2.unil.ch/biomapper/
Maximum Entropy MAXENT presence and background Phillips et al. 2006 www.cs.princeton.edu/~schapire/maxent
Genetic algorithm (GA) GARP pseudo-absence Stockwell and Peters 1999 http://www.lifemapper.org/desktopgarp/
Artificial Neural Network (ANN) SPECIES presence and absence (or pseudo-absence) Pearson et al. 2002
Regression: generalized linear model (GLM), generalized additive model (GAM), boosted regression trees (BRT), multivariate adaptive regression splines (MARS) Implemented in R presence and absence (or pseudo-absence) Lehman et al. 2002; Elith et al. 2006; Leathwick et al. 2006; Elith et al. 2007
Multiple methods BIOMOD presence and absence (or pseudo-absence) Thuiller 2003
Multiple methods OpenModeller depends on method implemented openmodeller.sourceforge.net/


Algorithm & Explanation

Elith, J. et al., 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distributions.

Phillips, S.J. & Dudík, M., 2008.Modeling of species distributions with Maxent: new extensions and acomprehensive evaluation. Ecography, 31(2), pp.161–175.

Phillips, S.J., Anderson, R.P. & Schapire, R.E., 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190(3-4), pp.231–259.

Application (examples of published studies post 2006)

Carnaval, A.C. & Moritz, C. (2008) Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest. Journal of Biogeography, 35, 1187–1201.

Cordellier, M. & Pfenninger, M. (2009) Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora). Molecular Ecology, 18, 534–544.

Elith, J., Graham, C.H., Anderson, R.P. et al. (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography, 29, 129–151.

Graham, C.H. & Hijmans, R.J. (2006) A comparison of methods for mapping species ranges and species richness. Global Ecology & Biogeography, 15, 578.

Kharouba, H.M., Algar, A.C. & Kerr, J.T. (2009) Historically calibrated predictions of butterfly species’ range shift using global change as a pseudo-experiment. Ecology, 90, 2213–2222.

Monterroso, P., Brito, J.C., Ferreras, P. & Alves, P.C. (2009) Spatial ecology of the European wildcat in a Mediterranean ecosystem: dealing with small radio-tracking datasets in species conservation. Journal of Zoology, 279, 27–35.

Murray-Smith, C., Brummitt, N.A., Oliveira-Filho, A.T., Bachman, S., Moat, J., Lughadha, E.M.N. & Lucas, E.J. (2009) Plant diversity hotspots in the Atlantic coastal forests of Brazil. Conservation Biology, 23, 151–163.

Lamb, J.M., Ralph, T.M.C., Goodman, S.M., Bogdanowicz, W., Fahr, J., Gajewska, M., Bates, P.J.J., Eger, J., Benda, P. & Taylor, P.J. (2008) Phylogeography and predicted distribution of African-Arabian and Malagasy populations of giant mastiff bats, Otomops spp. (Chiroptera : Molossidae). Acta Chiropterologica, 10, 21–40.

Peterson, A.T., Papeş, M. & Eaton, M., 2007. Transferability and model evaluation in ecological niche modeling: a comparison of GARP and Maxent. Ecography, 30(4), pp.550–560.

Tinoco, B.A., Astudillo, P.X., Latta, S.C. & Graham, C.H. (2009) Distribution, ecology and conservation of an endangered Andean hummingbird: the Violet-throated Metaltail (Metallura baroni). Bird Conservation International, 19, 63–76.

Tittensor, D.P., Baco, A.R., Brewin, P.E., Clark, M.R., Consalvey, M., Hall-Spencer, J., Rowden, A.A., Schlacher, T., Stocks, K.I. & Rogers, A.D. (2009) Predicting global habitat suitability for stony corals on seamounts. Journal of Biogeography, 36, 1111–1128.

Tognelli, M.F., Roig-Junent, S.A., Marvaldi, A.E., Flores, G.E. & Lobo, J.M. (2009) An evaluation of methods for modelling distribution of Patagonian insects. Revista Chilena De Historia Natural, 82, 347–360. Verbruggen, H., Tyberghein, L., Pauly, K., Vlaeminck, C., Van Nieuwenhuyze, K., Kooistra, W., Leliaert, F. & De Clerck, O. (2009) Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda. Global Ecology and Biogeography, 18, 393–405.

Wang, Y., Xie, B., Wan, F., Xiao, Q. & Dai, L. (2007) The potential geographic distribution of Radopholus similis in China. Agricultural Sciences in China, 6, 1444–1449.

Warren, D. & Seifert, S., 2010. Environmental niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecological Applications.

Ward, D. (2007a) Modelling the potential geographic distribution of invasive ant species in New Zealand. Biological Invasions, 9, 723–735.

Williams, J.N., Seo, C.W., Thorne, J., Nelson, J.K., Erwin, S., O’Brien, J.M. & Schwartz, M.W. (2009) Using species distribution models to predict new occurrences for rare plants. Diversity and Distributions, 15, 565–576. Wollan, A.K., Bakkestuen, V., Kauserud, H., Gulden, G. & Halvorsen, R. (2008) Modelling and predicting fungal distribution patterns using herbarium data. Journal of Biogeography, 35, 2298–2310.

Yates, C., McNeill, A., Elith, J. & Midgley, G. (2010) Assessing the impacts of climate change and land transformation on Banksia in the South West Australian Floristic Region. Diversity and Distributions, 16, 187–201.
Yesson, C. & Culham, A. (2006) A phyloclimatic study of Cyclamen. BMC Evolutionary Biology, 6, 72–95.
Young, B.F., Franke, I., Hernandez, P.A., Herzog, S.K., Paniagua, L., Tovar, C. & Valqui, T. (2009) Using spatial models to predict areas of endemism and gaps in the protection of Andean slope birds. Auk, 126, 554–565.


Algorithm & Explanation

Stockwell, D. R. B. 1999. Genetic algorithms II. Pages 123-144 in A. H. Fielding, editor. Machine learning methods for ecological applications. Kluwer Academic Publishers, Boston.

Stockwell, D. R. B., and D. P. Peters. 1999. The GARP modelling system: Problems and solutions to automated spatial prediction. International Journal of Geographic Information Systems 13:143-158.

Stockwell, D. R. B., and I. R. Noble. 1992. Induction of sets of rules from animal distribution data: A robust and informative method of analysis. Mathematics and Computers in Simulation 33:385-390.

Application (examples of published studies post 1999)

Anderson, R. P., M. Laverde, and A. T. Peterson. 2002a. Geographical distributions of spiny pocket mice in South America: Insights from predictive models. Global Ecology and Biogeography 11:131-141.

Anderson, R. P., M. Laverde, and A. T. Peterson. 2002b. Using niche-based GIS modeling to test geographic predictions of competitive exclusion and competitive release in South American pocket mice. Oikos 93:3-16.

Anderson, R. P., D. Lew, and A. T. Peterson. 2003. Evaluating predictive models of species' distributions: Criteria for selecting optimal models. Ecological Modelling, v. 162, p. 211 232

Chen, G., and A. T. Peterson. 2000. A new technique for predicting distributions of terrestrial vertebrates using inferential modeling. Zoological Research 21:231-237.

Chen, G., and A. T. Peterson. 2002. Prioritization of areas in China for biodiversity conservation based on the distribution of endangered bird species. Bird Conservation International. 12:197-209

Feria, T. P., and A. T. Peterson. 2002. Using point occurrence data and inferential algorithms to predict local communities of birds. Diversity and Distributions 8:49-56.

Godown, M. E., and A. T. Peterson. 2000. Preliminary distributional analysis of U.S. endangered bird species. Biodiversity and Conservation 9:1313-1322.

Peterson, A. T. 2001. Predicting species' geographic distributions based on ecological niche modeling. Condor 103:599-605.

Peterson, A. T., L. G. Ball, and K. C. Cohoon. 2002a. Predicting distributions of tropical birds. Ibis 144:e27-e32.

Peterson, A. T., M. A. Ortega-Huerta, J. Bartley, V. Sanchez-Cordero, J. Soberon, R. H. Buddemeier, and D. R. B. Stockwell. 2002b. Future projections for Mexican faunas under global climate change scenarios. NATURE 416:626-629.

Peterson, A. T., V. Sanchez-Cordero, C. B. Beard, and J. M. Ramsey. 2002c. Ecologic niche modeling and potential reservoirs for Chagas disease, Mexico. Emerging Infectious Diseases 8:662-667.

Peterson, A. T., V. Sanchez-Cordero, J. Soberon, J. Bartley, R. H. Buddemeier, and A. G. Navarro-Siguenza. 2001. Effects of global climate change on geographic distributions of Mexican Cracidae. Ecological Modelling 144:21-30.

Peterson, A. T., D. R. B. Stockwell, and D. A. Kluza. 2002d. Distributional prediction based on ecological niche modeling of primary occurrence data. Pages 617-623 in J. M. Scott, P. J. Heglund, and M. L. Morrison, editors. Predicting Species Occurrences: Issues of Scale and Accuracy. Island Press, Washington, D.C.

Peterson, A. T., and D. A. Vieglais. 2001. Predicting species invasions using ecological niche modeling. BioScience 51:363-371.

Stockwell, D. R. B., and A. T. Peterson. 2002a. Controlling bias in biodiversity data. Pages 537-546 in J. M. Scott, P. J. Heglund, and M. L. Morrison, editors. Predicting Species Occurrences: Issues of Scale and Accuracy. Island Press, Washington, D.C.

Stockwell, D. R. B., and A. T. Peterson. 2002b. Effects of sample size on accuracy of species distribution models. Ecological Modelling 148:1-13.


Algorithm & Explanation

Hirzel, A.H., Hausser, J., Chessel, D. & Perrin, N. (2002) Ecological niche factor analysis: how to compute habitat suitability maps without absence data? Ecology, 83, 2027–2036.

Braunisch V., Bollmann K., Graf R. F., Hirzel A.H. (2008). Living on the edge -- Modelling habitat suitability for species at the edge of their fundamental niche. Ecological Modelling 214, 153-167

Hirzel, A. H. & Le Lay G. (2008). Habitat suitability modelling and niche theory. Journal of Applied Ecology, 45, 1372-1381.

Hirzel, A. H. (2008). Using relative capacity to measure habitat suitability. Israel Journal of Ecology and Evolution, 54, 421-434

Calenge, C., Darmon, G., Basille, M., Loison, A. & Jullien, J.M. (2008) The factorial decomposition of the Mahalanobisdistances in habitat selection studies. Ecology, 89(2), 555-66

Application (examples of published studies obtained from Biomapper)

Jiménez-Valverde, A., Gómez, J.F., Lobo, J.M., Baselga, A. & Hortal, J. (2008) Challenging species distribution models: the case of Maculinea nausithous in the Iberian Peninsula. Annales Zoologici Fennici, 45, 200-10.

Rivera, J.H.V., Huerta, M.A.O. & Guerrer, R. (2008) Analysis of the distribution of Orange-breasted Bunting (Passerina leclanchetii): An endemic species of Mexico's Pacific slope. Ornitologia Neotropical, 19(2), 265-74.

Mertzanis G, Kallimanis AS, Kanellopoulos N, et al. (2008) Brown bear (Ursus arctos L.) habitat use patterns in two regions of northern Pindos, Greece - management implications. Journal of Natural History 42, 301-315.

Strubbe, D. & Matthysen, E. (2008) Predicting the potential distribution of invasive ring-necked parakeets Psittacula krameri in northern Belgium using an ecological niche modelling approach. Biol Invasions, on-line.

Allouche, O., Steinitz, O., Rotem, D., Rosenfeld, A. & Kadmon, R. (2008) Incorporating distance constraints into species distribution models. Journal of Applied Ecology, 45(2), 599-609.

Long, P.R., Zefania, S., Ffrench-Constant, R.H. & Szekely, T. (2008) Estimating the population size of an endangered shorebird, the Madagascar plover, using a habitat suitability model. Animal Conservation, 11(2), 118-27.

Praca, E. & Gannier, A. (2008) Ecological niches of three teuthophageous odontocetes in the northwestern Mediterranean Sea. Ocean Science, 4(1), 49-59.

Skov, H., Humphreys, E., Garthe, S., Geitner, K., Gremillet, D., Hamer, K.C., Hennicke, J., Parner, H. & Wanless, S. (2008) Application of habitat suitability modelling to tracking data of marine animals as a means of analyzing their feeding habitats. Ecological Modelling, 212(3-4), 504-12.

Chefaoui, R.M., Lobo, J.M. 2007. Assessing the conservation status of an iberian moth using pseudo-absences. Journal of Wildlife Management 71:2507-2516.

Estrada-Peña, A., Venzal, J.M. 2007. Climate niches of tick species in the mediterranean region: Modeling of occurrence data, distributional constraints, and impact of climate change. Journal of Medical Entomology 44:1130-1138.

Sattler, T., Bontadina, F., Hirzel, A.H. & Arlettaz, R. (2007) Ecological niche modelling of two cryptic bat species calls for a reassessment of their conservation status. Journal of Applied Ecology, 44(6), 1188-99.

Jimenez-Valverde A, Ortuno VM, Lobo JM (2007) Exploring the distribution of Sterocorax Ortuno, 1990 (Coleoptera, Carabidae) species in the Iberian peninsula. Journal of Biogeography 34, 1426-1438.

Braunisch, V. and Suchant, R. 2007. A model for evaluating the 'habitat potential' of a landscape for capercaillie Tetrao urogallus: a tool for conservation planning. - Wildlife Biology 13: 21-33.


Algorithm & Explanation

Carpenter, G., Gillison, A.N. & Winter, J. (1993) DOMAIN: a flexible modeling procedure for mapping potential distributions of plants and animals. Biodiversity and Conservation, 2, 667–680.