An evaluation of methods for modelling species distributions
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Abstract
Aim Various statistical techniques have been used to model species probabilities of occurrence in response to environmental conditions. This paper provides a comprehensive assessment of methods and investigates whether errors in model predictions are associated to specific kinds of geographical and environmental distributions of species.
Location Portugal, Western Europe.
Methods Probabilities of occurrence for 44 species of amphibians and reptiles in Portugal were modelled using seven modelling techniques: Gower metric, Ecological Niche Factor Analysis, classification trees, neural networks, generalized linear models, generalized additive models and spatial interpolators. Generalized linear and additive models were constructed with and without a term accounting for spatial autocorrelation. Model performance was measured using two methods: sensitivity and Kappa index. Species were grouped according to their spatial (area of occupancy and extent of occurrence) and environmental (marginality and tolerance) distributions. Two‐way comparison tests were performed to detect significant interactions between models and species groups.
Results Interaction between model and species groups was significant for both sensitivity and Kappa index. This indicates that model performance varied for species with different geographical and environmental distributions. Artificial neural networks performed generally better, immediately followed by generalized additive models including a covariate term for spatial autocorrelation. Non‐parametric methods were preferred to parametric approaches, especially when modelling distributions of species with a greater area of occupancy, a larger extent of occurrence, lower marginality and higher tolerance.
Main conclusions This is a first attempt to relate performance of modelling techniques with species spatial and environmental distributions. Results indicate a strong relationship between model performance and the kinds of species distributions being modelled. Some methods performed generally better, but no method was superior in all circumstances. A suggestion is made that choice of the appropriate method should be contingent on the goals and kinds of distributions being modelled.
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- Stefanie Gärtner, Albert Reif, Fotios Xystrakis, Uwe Sayer, Nawal Bendagha and Andreas Matzarakis, The drought tolerance limit of Fagus sylvatica forest on limestone in southwestern Germany, Journal of Vegetation Science, 19, 6, (757-768), (2009).
- MUIR D. EATON, JORGE SOBERÓN and A. TOWNSEND PETERSON, Phylogenetic perspective on ecological niche evolution in american blackbirds (Family Icteridae), Biological Journal of the Linnean Society, 94, 4, (869-878), (2008).
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- Philip J. Platts, Colin J. McClean, Jon C. Lovett and Rob Marchant, Predicting tree distributions in an East African biodiversity hotspot: model selection, data bias and envelope uncertainty, Ecological Modelling, 218, 1-2, (121), (2008).
- Christopher D. Lippitt, John Rogan, James Toledano, Florencia Sangermano, J. Ronald Eastman, Victor Mastro and Alan Sawyer, Incorporating anthropogenic variables into a species distribution model to map gypsy moth risk, Ecological Modelling, 210, 3, (339), (2008).
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- A. Townsend Peterson, Aimee Stewart, Kamal I. Mohamed, Miguel B. Araújo and Jerome Chave, Shifting Global Invasive Potential of European Plants with Climate Change, PLoS ONE, 3, 6, (e2441), (2008).
- Paul H. Evangelista, Sunil Kumar, Thomas J. Stohlgren, Catherine S. Jarnevich, Alycia W. Crall, John B. Norman III and David T. Barnett, Modelling invasion for a habitat generalist and a specialist plant species, Diversity and Distributions, 14, 5, (808-817), (2008).
- Heather M. Kharouba, Julie L. Nadeau, Eric Young and Jeremy T. Kerr, Using species distribution models to effectively conserve biodiversity into the future, Biodiversity, 9, 3-4, (39), (2008).
- Guangshun Jiang, Minghai Zhang and Jianzhang Ma, Habitat use and separation between red deer Cervus elaphus xanthopygus and roe deer Capreolus pygargus bedfordi in relation to human disturbance in the Wandashan Mountains, northeastern China, Wildlife Biology, 14, 1, (92), (2008).
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- Justin D. Hoffman, Sunil Narumalani, Deepak R. Mishra, Paul Merani and Robert G. Wilson, Predicting Potential Occurrence and Spread of Invasive Plant Species along the North Platte River, Nebraska, Invasive Plant Science and Management, 1, 04, (359), (2008).
- Arno Thomaes, Thierry Kervyn and Dirk Maes, Applying species distribution modelling for the conservation of the threatened saproxylic Stag Beetle (Lucanus cervus), Biological Conservation, 141, 5, (1400), (2008).
- Margaret F.J. Dolan, Anthony J. Grehan, Janine C. Guinan and Colin Brown, Modelling the local distribution of cold-water corals in relation to bathymetric variables: Adding spatial context to deep-sea video data, Deep Sea Research Part I: Oceanographic Research Papers, 55, 11, (1564), (2008).
- Ada Sánchez-Mercado, José R. Ferrer-Paris, Edgard Yerena, Shaenandhoa García-Rangel and Kathryn M. Rodríguez-Clark, Factors affecting poaching risk to Vulnerable Andean bears Tremarctos ornatus in the Cordillera de Mérida, Venezuela: space, parks and people, Oryx, 42, 03, (2008).
- Andy Jarvis, Annie Lane and Robert J. Hijmans, The effect of climate change on crop wild relatives, Agriculture, Ecosystems & Environment, 126, 1-2, (13), (2008).
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- Marta López-Darias, Jorge M. Lobo and Patrick Gouat, Predicting potential distributions of invasive species: the exotic Barbary ground squirrel in the Canarian archipelago and the west Mediterranean region, Biological Invasions, 10.1007/s10530-007-9181-2, 10, 7, (1027-1040), (2007).
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- Vasilis D. Valavanis, Graham J. Pierce, Alain F. Zuur, Andreas Palialexis, Anatoly Saveliev, Isidora Katara and Jianjun Wang, Modelling of essential fish habitat based on remote sensing, spatial analysis and GIS, Hydrobiologia, 10.1007/s10750-008-9493-y, 612, 1, (5-20), (2008).
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- Patrick E. Osborne, Giles M. Foody and Susana Suárez‐Seoane, Non‐stationarity and local approaches to modelling the distributions of wildlife, Diversity and Distributions, 13, 3, (313-323), (2007).
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- Lisa L. Manne, Paul H. Williams, Guy F. Midgley, Wilfried Thuiller, Tony Rebelo and Lee Hannah, Spatial and temporal variation in species‐area relationships in the Fynbos biological hotspot, Ecography, 30, 6, (852-861), (2007).
- Jana M. McPherson and Walter Jetz, Effects of species’ ecology on the accuracy of distribution models, Ecography, 30, 1, (135-151), (2007).
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- Christine N. Meynard and James F. Quinn, Predicting species distributions: a critical comparison of the most common statistical models using artificial species, Journal of Biogeography, 34, 8, (1455-1469), (2007).
- Richard G. Pearson, Christopher J. Raxworthy, Miguel Nakamura and A. Townsend Peterson, ORIGINAL ARTICLE: Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar, Journal of Biogeography, 34, 1, (102-117), (2006).
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- Agustín Estrada-peña and José M. Venzal, 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, 6, (1130), (2007).
- Fabio Attorre, Fabio Francesconi, Nadim Taleb, Paul Scholte, Ahmed Saed, Marco Alfo and Franco Bruno, Will dragonblood survive the next period of climate change? Current and future potential distribution of Dracaena cinnabari (Socotra, Yemen), Biological Conservation, 138, 3-4, (430), (2007).
- Mirkka M. Jones, Paulo Olivas Rojas, Hanna Tuomisto and David B. Clark, Environmental and neighbourhood effects on tree fern distributions in a neotropical lowland rain forest, Journal of Vegetation Science, 18, 1, (13-24), (2009).
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- Daniel W. McKenney, John H. Pedlar, Kevin Lawrence, Kathy Campbell and Michael F. Hutchinson, Beyond Traditional Hardiness Zones: Using Climate Envelopes to Map Plant Range Limits, BioScience, 10.1641/B571105, 57, 11, (929-937), (2007).
- Darren F. Ward, Modelling the potential geographic distribution of invasive ant species in New Zealand, Biological Invasions, 10.1007/s10530-006-9072-y, 9, 6, (723-735), (2006).
- Janine Bolliger, Felix Kienast, Reto Soliva and Gillian Rutherford, Spatial sensitivity of species habitat patterns to scenarios of land use change (Switzerland), Landscape Ecology, 10.1007/s10980-007-9077-7, 22, 5, (773-789), (2007).
- Li Zhu, Osbert J. Sun, Weiguo Sang, Zhenyu Li and Keping Ma, Predicting the spatial distribution of an invasive plant species (Eupatorium adenophorum) in China, Landscape Ecology, 10.1007/s10980-007-9096-4, 22, 8, (1143-1154), (2007).
- Irina Levinsky, Flemming Skov, Jens-Christian Svenning and Carsten Rahbek, Potential impacts of climate change on the distributions and diversity patterns of European mammals, Biodiversity and Conservation, 10.1007/s10531-007-9181-7, 16, 13, (3803-3816), (2007).
- Christopher J. Ellis, Brian J. Coppins and Terence P. Dawson, Predicted response of the lichen epiphyte Lecanora populicola to climate change scenarios in a clean-air region of Northern Britain, Biological Conservation, 10.1016/j.biocon.2006.10.036, 135, 3, (396-404), (2007).
- Christopher J. Ellis, Brian J. Coppins, Terence P. Dawson and Mark R.D. Seaward, Response of British lichens to climate change scenarios: Trends and uncertainties in the projected impact for contrasting biogeographic groups, Biological Conservation, 10.1016/j.biocon.2007.08.016, 140, 3-4, (217-235), (2007).
- Martin Kent, Biogeography and macroecology: now a significant component of physical geography, Progress in Physical Geography: Earth and Environment, 10.1177/0309133307087088, 31, 6, (643-657), (2016).
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- Graeme S. Cumming and Detlef P. Van Vuuren, Will climate change affect ectoparasite species ranges?, Global Ecology and Biogeography, 15, 5, (486-497), (2006).
- Jane Elith*, Catherine H. Graham*, Robert P. Anderson, Miroslav Dudík, Simon Ferrier, Antoine Guisan, Robert J. Hijmans, Falk Huettmann, John R. Leathwick, Anthony Lehmann, Jin Li, Lucia G. Lohmann, Bette A. Loiselle, Glenn Manion, Craig Moritz, Miguel Nakamura, Yoshinori Nakazawa, Jacob McC. M. Overton, A. Townsend Peterson, Steven J. Phillips, Karen Richardson, Ricardo Scachetti‐Pereira, Robert E. Schapire, Jorge Soberón, Stephen Williams, Mary S. Wisz and Niklaus E. Zimmermann, Novel methods improve prediction of species’ distributions from occurrence data, Ecography, 29, 2, (129-151), (2006).
- Marco Moretti, Marco Conedera, Ruben Moresi and Antoine Guisan, Modelling the influence of change in fire regime on the local distribution of a Mediterranean pyrophytic plant species (Cistus salviifolius) at its northern range limit, Journal of Biogeography, 33, 8, (1492-1502), (2006).
- M. B. Araújo, W. Thuiller and R. G. Pearson, Climate warming and the decline of amphibians and reptiles in Europe, Journal of Biogeography, 33, 10, (1712-1728), (2006).
- Richard G. Pearson, Wilfried Thuiller, Miguel B. Araújo, Enrique Martinez‐Meyer, Lluís Brotons, Colin McClean, Lera Miles, Pedro Segurado, Terence P. Dawson and David C. Lees, Model‐based uncertainty in species range prediction, Journal of Biogeography, 33, 10, (1704-1711), (2006).
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- Ramona Maggini, Anthony Lehmann, Niklaus E. Zimmermann and Antoine Guisan, Improving generalized regression analysis for the spatial prediction of forest communities, Journal of Biogeography, 33, 10, (1729-1749), (2006).
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- SIMON FERRIER and ANTOINE GUISAN, Spatial modelling of biodiversity at the community level, Journal of Applied Ecology, 43, 3, (393-404), (2006).
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- Kristen C. Ruegg, Robert J. Hijmans and Craig Moritz, Climate change and the origin of migratory pathways in the Swainson's thrush, Catharus ustulatus, Journal of Biogeography, 33, 7, (1172-1182), (2006).
- José Alexandre Felizola Diniz‐Filho, Modern processes drive macroecological patterns in North American avifauna, Journal of Biogeography, 33, 7, (1153-1154), (2006).
- Heather Schussman, Erika Geiger, Theresa Mau‐Crimmins and Judy Ward, Spread and current potential distribution of an alien grass, Eragrostis lehmanniana Nees, in the southwestern USA: comparing historical data and ecological niche models, Diversity and Distributions, 12, 5, (582-592), (2006).
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- Steven L. Chown and John S. Terblanche, Physiological Diversity in Insects: Ecological and Evolutionary Contexts, Advances in Insect Physiology Volume 33, 10.1016/S0065-2806(06)33002-0, (50-152), (2006).
- PHILIP E. HULME, Beyond control: wider implications for the management of biological invasions, Journal of Applied Ecology, 43, 5, (835-847), (2006).
- Xavier Santos, José C. Brito, Neftalí Sillero, Juan M. Pleguezuelos, Gustavo A. Llorente, Soumia Fahd and Xavier Parellada, Inferring habitat-suitability areas with ecological modelling techniques and GIS: A contribution to assess the conservation status of Vipera latastei, Biological Conservation, 130, 3, (416), (2006).
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- Ioannis N. Vogiatzakis and Geoffrey H. Griffiths, A GIS-based empirical model for vegetation prediction in Lefka Ori, Crete, Plant Ecology, 184, 2, (311), (2006).
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- P.M. Berry, M.D.A. Rounsevell, P.A. Harrison and E. Audsley, Assessing the vulnerability of agricultural land use and species to climate change and the role of policy in facilitating adaptation, Environmental Science & Policy, 9, 2, (189), (2006).
- Lise Tole, Choosing reserve sites probabilistically: A Colombian Amazon case study, Ecological Modelling, 194, 4, (344), (2006).
- Antje Burke, Savanna trees in Namibia—Factors controlling their distribution at the arid end of the spectrum, Flora - Morphology, Distribution, Functional Ecology of Plants, 201, 3, (189), (2006).
- Christophe Coudun and Jean-Claude Gégout, The derivation of species response curves with Gaussian logistic regression is sensitive to sampling intensity and curve characteristics, Ecological Modelling, 199, 2, (164), (2006).
- Christophe Coudun, Jean‐Claude Gégout, Christian Piedallu and Jean‐Claude Rameau, Soil nutritional factors improve models of plant species distribution: an illustration with Acer campestre (L.) in France, Journal of Biogeography, 33, 10, (1750-1763), (2006).
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- Marta Benito Garzón, Radim Blazek, Markus Neteler, Rut Sánchez de Dios, Helios Sainz Ollero and Cesare Furlanello, Predicting habitat suitability with machine learning models: The potential area of Pinus sylvestris L. in the Iberian Peninsula, Ecological Modelling, 197, 3-4, (383), (2006).
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- Luis M. Carrascal and Leticia Díaz, Winter bird distribution in abiotic and habitat structural gradients: A case study with mediterranean montane oakwoods, Ecoscience, 10.2980/1195-6860(2006)13[100:WBDIAA]2.0.CO;2, 13, 1, (100-110), (2006).
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