Fit-for-Purpose: Species Distribution Model Performance Depends on Evaluation Criteria - Dutch Hoverflies as a Case Study

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Aguirre Gutiérrez, Jesús ^a,b   Carvalheiro, Luísa G ^a,c   Polce, Chiara ^c   van Loon, E Emiel ^b   Raes, Niels ^a,d   Reemer, Menno ^a,e   Biesmeijer, Jacobus C ^a,b  

^a NATURALIS BIODIVERSITY CENTER   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c UNIVERSITY OF LEEDS   (United Kingdom)

^d UNIVERSITEIT LEIDEN BRANCH   (Netherlands)

^e European Invertebrate Survey Nederland   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CLIMATE CHANGE; DIPTERA; DUTCH HOVERFLIES; ECOLOGY; ENVIRONMENTAL IMPACT; GEOGRAPHIC DISTRIBUTION; NONHUMAN; PREDICTION; SPECIES CONSERVATION; SPECIES DISTRIBUTION; SPECIES DISTRIBUTION MODEL;

ALGORITHMS; ANIMALS; AREA UNDER CURVE; DIPTERA; ECOLOGICAL AND ENVIRONMENTAL PROCESSES; ENVIRONMENT; GEOGRAPHY; MODELS, THEORETICAL;

EID: 84877775562     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063708     Document Type: Article

References (72)

1. Guisan A, Thuiller W, (2005) Predicting species distribution: offering more than simple habitat models. Ecol. Lett. 8: 993-1009 doi:10.1111/j.1461-0248.2005.00792.x.
2. Elith J, Leathwick JR, (2009) Species Distribution Models: Ecological Explanation and Prediction Across Space and Time. Annu. Rev. Ecol. Evol. S. 40: 677-697 doi:10.1146/annurev.ecolsys.110308.120159.
3. McInerny GJ, Etienne RS, (2012) Ditch the niche- is the niche a useful concept in ecology or species distribution modelling? Journal of Biogeography 39: 2096-2102 doi:10.1111/jbi.12033.
4. Peterson AT, Soberón J, (2012) Species Distribution Modeling and Ecological Niche Modeling?: Getting the Concepts Right. Natureza & Conservação 10: 1-6.
5. Warren DL, (2012) In defense of "niche modeling". Trends in ecology & evolution 27: 497-500 doi:10.1016/j.tree.2012.03.010.
6. Higgins SI, O'Hara RB, Römermann C, (2012) A niche for biology in species distribution models. Journal of Biogeography 39: 2091-2095 doi:10.1111/jbi.12029.
7. Soberón J, Nakamura M, (2009) Niches and distributional areas: Concepts, methods, and assumptions. Proc. Nat. Acad. Sci. 106: 19644-19650.
8. Franklin J (2009) Mapping species distributions- spatial inference and prediction. Cambridge: Cambridge University Press.
9. Peterson AT, Soberon J, Pearson RG, Anderson RP, Martinez-Meyer E, et al. (2011) Ecological Niches and Geographic Distributions. New Jersey: Princeton University Press.
10. Thuiller W, Lafourcade B, Engler R, Araújo MB (2009) BIOMOD- a platform for ensemble forecasting of species distributions. Ecography 32: 369-373 (Version 1.1-7.00). doi:10.1111/j.1600-0587.2008.05742.x.
11. Guo Q, Liu Y, (2010) ModEco: an integrated software package for ecological niche modeling. Ecography 33: 637-642.
12. Souza Muñoz ME, Giovanni R, Siqueira MF, Sutton T, Brewer P, et al. (2009) openModeller: a generic approach to species' potential distribution modelling. GeoInformatica 15: 111-135 doi:10.1007/s10707-009-0090-7.
13. Elith J, Graham CH, Anderson PR, Dudík M, Ferrier S, et al. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography 29: 129-151 doi:10.1111/j.2006.0906-7590.04596.x.
14. Elith J, Graham CH, (2009) Do they? How do they? Why do they differ? On finding reasons for differing performances of species distribution models. Ecography 32: 66-77 doi:10.1111/j.1600-0587.2008.05505.x.
15. Pearson RG, Thuiller W, Araújo MB, Martinez-Meyer E, Brotons L, et al. (2006) Model-based uncertainty in species range prediction. J. Biogeogr. 33: 1704-1711 doi:10.1111/j.1365-2699.2006.01460.x.
16. Segurado P, Araujo MB, Kunin WE, (2006) Consequences of spatial autocorrelation for niche-based models. J. Appl. Ecol. 43: 433-444 doi:10.1111/j.1365-2664.2006.01162.x.
17. Buisson L, Thuiller W, Casajus N, Lek S, Grenouillet G, (2010) Uncertainty in ensemble forecasting of species distribution. Glob. Change Biol. 16: 1145-1157 doi:10.1111/j.1365-2486.2009.02000.x.
18. Barve N, Barve V, Jiménez-Valverde A, Lira-Noriega A, Maher SP, et al. (2011) The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological Modelling 222: 1810-1819 doi:10.1016/j.ecolmodel.2011.02.011.
19. Bidinger K, Lötters S, Rödder D, Veith M, (2012) Species distribution models for the alien invasive Asian Harlequin ladybird (Harmonia axyridis). J Appl. Entomol. 136: 109-123.
20. Machado-Machado EA, (2012) Empirical mapping of suitability to dengue fever in Mexico using species distribution modeling. Appl. Geogr. 33: 82-93 doi:10.1016/j.apgeog.2011.06.011.
21. Raes N, Roos MC, Slik JWF, Van Loon EE, Steege HT, (2009) Botanical richness and endemicity patterns of Borneo derived from species distribution models. Ecography 32: 180-192 doi:10.1111/j.1600-0587.2009.05800.x.
22. Rodríguez-Soto C, Monroy-Vilchis O, Maiorano L, Boitani L, Faller JC, et al. (2011) Predicting potential distribution of the jaguar (Panthera onca) in Mexico: identification of priority areas for conservation. Divers. Distrib. 17: 350-361 doi:10.1111/j.1472-4642.2010.00740.x.
23. Beale CM, Lennon JJ, Gimona A, (2008) Opening the climate envelope reveals no macroscale associations with climate in European birds. Proc. Nat. Acad. Sci. 105: 14908-14912 doi:10.1073/pnas.0803506105.
24. Veloz SD, Williams JW, Blois JL, He F, Otto-Bliesner B, et al. (2012) No-analog climates and shifting realized niches during the late quaternary: implications for 21st-century predictions by species distribution models. Glob. Change Biol. 18: 1698-1713 doi:10.1111/j.1365-2486.2011.02635.x.
25. Saupe EE, Barve V, Myers CE, Soberón J, Barve N, et al. (2012) Variation in niche and distribution model performance: The need for a priori assessment of key causal factors. Ecological Modelling 237-238: 11-22 doi:10.1016/j.ecolmodel.2012.04.001.
26. Araújo MB, Peterson AT, (2012) Uses and misuses of bioclimatic envelope modeling. Ecology 93: 1527-1539 doi:10.1890/11-1930.1.
27. Wisz MS, Hijmans RJ, Li J, Peterson AT, Graham CH, et al. (2008) Effects of sample size on the performance of species distribution models. Divers. Distrib. 14: 763-773 doi:10.1111/j.1472-4642.2008.00482.x.
28. Araújo MB, Guisan A, (2006) Five (or so) challenges for species distribution modelling. J. Biogeogr. 33: 1677-1688 doi:10.1111/j.1365-2699.2006.01584.x.
29. Marmion M, Parviainen M, Luoto M, Heikkinen RK, Thuiller W, (2009) Evaluation of consensus methods in predictive species distribution modelling. Divers. Distrib. 15: 59-69 doi:10.1111/j.1472-4642.2008.00491.x.
30. Zimmermann NE, Edwars TC, Graham CH, Pearman PB, Svenning J, (2010) New trends in species distribution modelling. Ecography 33: 985-989 doi:10.1111/j.1600-0587.2010.06953.x.
31. EIS-European Invertebrate Survey - The Netherlands. Postbus 9517, 2300 RA Leiden, The Netherlands. Available: http://www.eis-nederland.nl. Accessed 2013 April 11.
32. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25: 1965-1978.
33. Ripley BD (1996) Pattern recognition and neural networks. Cambridge, UK.: Cambridge University Press.
34. Ridgeway G (1999) 2 Boosting for classification. Bernoulli: 172-181.
35. Friedman BJH, (2001) 1999 Reitz Lecture. 29: 1189-1232.
36. Breiman L, (2001) Random Forests. Mach. Learn. 45: 5-32 doi:10.1023/a:1010933404324.
37. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecol. Model. 190: 231-259.
38. Hastie TJ (1990) Generalized Additive Models. Chapman and Hall.
39. McCullagh (1989) Generalized linear models. Chapman and Hall.
40. Mateo RG, Croat TB, Felicísimo ÁM, Muñoz J, (2010) Profile or group discriminative techniques? Generating reliable species distribution models using pseudo-absences and target-group absences from natural history collections. Divers. Distrib. 16: 84-94 doi:10.1111/j.1472-4642.2009.00617.x.
41. R Development Core Team. (2011) R: A language and environment for statistical computing. Available: http://www.r-project.org. Accessed 2013 April 11.
42. Thuiller W, Lafourcade B, Araújo MB (2010) Presentation Manual for BIOMOD. In: Thuiller W, Lafourcade B, Engler R, Araújo MB (2009) BIOMOD- a platform for ensemble forecasting of species distributions. Ecography 32: 369-373 (Version 1.1-7.00). doi:10.1111/j.1600-0587.2008.05742.x.
43. Phillips SJ, Dudik M, (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31: 161.
44. Scarnati L, Attorre F, Farcomeni A, Francesconi F, Sanctis M, (2009) Modelling the spatial distribution of tree species with fragmented populations from abundance data. Community Ecology 10: 215-224.
45. Garzón BM, Sánchez de Dios R, Sainz Ollero H, (2008) Effects of climate change on the distribution of Iberian tree species. Applied Vegetation Science 11: 169-178.
46. Lawler JJ, White D, Neilson RP, Blaustein AR, (2006) Predicting climate-induced range shifts: model differences and model reliability. Global Change Biology 12: 1568-1584.
47. Araújo MB, New M, (2007) Ensemble forecasting of species distributions. TREE 22: 42-47 doi:10.1016/j.tree.2006.09.010.
48. Hanley JA, McNeil BJ, (1982) The Meaning and Use of the Area under a Receiver Operating (ROC) Curvel Characteristic. Radiology 143: 29-36.
49. Jiménez-Valverde A, Lobo JM, (2007) Threshold criteria for conversion of probability of species presence to either-or presence-absence. Acta Oecol. 31: 361-369.
50. Phillips SJ, Dudík M, Elith J, Graham CH, Lehmann A, et al. (2009) Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecol. Appl. 19: 181-197.
51. Barbet-Massin M, Jiguet F, Albert CH, Thuiller W, (2012) Selecting pseudo-absences for species distribution models: how, where and how many? Methods in Ecology and Evolution 3: 327-338.
52. Raes N, ter Steege H, (2007) A null-model for significance testing of presence-only species distribution models. Ecography 30: 727-736 doi:10.1111/j.2007.0906-7590.05041.x.
53. Elith J, Phillips SJ, Hastie T, Dudík M, Chee YE, et al. (2011) A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17: 43-57 doi:10.1111/j.1472-4642.2010.00725.x.
54. Austin M, (2007) Species distribution models and ecological theory: A critical assessment and some possible new approaches. Ecol. Model. 200: 1-19 doi:10.1016/j.ecolmodel.2006.07.005.
55. Jiménez-Valverde A, (2012) Insights into the area under the receiver operating characteristic curve (AUC) as a discrimination measure in species distribution modelling. Glob. Ecol. Biogeogr. 21: 498-507 doi:10.1111/j.1466-8238.2011.00683.x.
56. Borcard D, Legendre P, Avois-Jacquet C, Tuomisto H, (2004) Dissecting the spatial structure of ecological data at multiple scales. Ecology 85: 1826-1832.
57. Kraft NJB, Ackerly DD, (2010) Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest. Ecological Monographs 80: 401-422.
58. Addicott JF, Aho JM, Antolin MF, Padilla DK, Richardson JS, et al. (1987) Ecological neighborhoods: scaling environmental patterns. Oikos 49: 340-346.
59. Wiens JA, (1989) Spatial scaling in ecology. Functional Ecology 3: 385-397.
60. Díaz S, Cabido M, (2001) Vive la différence: plant functional diversity matters to ecosystem processes. Trends in Ecology & Evolution 16 (11): 646-655.
61. de Bello F, Lavorel S, Díaz S, Harrington R, Cornelissen JHC, et al. (2010) Towards an assessment of multiple ecosystem processes and services via functional traits. Biodiversity and Conservation 19: 2873-2893 doi:10.1007/s10531-010-9850-9.
62. Visser H, T. de Nijs, (2006) The Map Comparison Kit. Environ. Modell. Softw. 21: 346-358.
63. Cohen J, (1960) A Coefficient of Agreement for Nominal Scales. Educ. Psychol. Meas. 20: 37-46 doi:10.1177/001316446002000104.
64. Hagen-Zanker A, (2009) An improved Fuzzy Kappa statistic that accounts for spatial autocorrelation. Int. J. Geogr. Inf. Sci. 23: 61-73 doi:10.1080/13658810802570317.
65. Hagen-Zanker A, (2006) Map comparison methods that simultaneously address overlap and structure. J. Geogr. Syst. 8: 165-185 doi:10.1007/s10109-006-0024-y.
66. Bolker BM, Brooks ME, Clark CJ, Geange SW, Poulsen JR, et al. (2009) Generalized linear mixed models: a practical guide for ecology and evolution. TREE 24: 127-135 doi:10.1016/j.tree.2008.10.008.
67. Pinheiro J, Bates D, DebRoy S, Sarkar D, Team the R development core (2012) nlme: Linear and Nonlinear Mixed Effects Models: R package version 3.1-103.
68. Bean WT, Stafford R, Brashares JS, (2012) The effects of small sample size and sample bias on threshold selection and accuracy assessment of species distribution models. Ecography 35: 250-258 doi:10.1111/j.1600-0587.2011.06545.x.
69. Lomba A, Pellissier L, Randin C, Vicente J, Moreira F, et al. (2010) Overcoming the rare species modelling paradox: A novel hierarchical framework applied to an Iberian endemic plant. Biol. Conserv. 143: 2647-2657 doi:10.1016/j.biocon.2010.07.007.
70. Ng AY, Jordan MI, (2002) On discriminative vs. generative classifiers: A comparison of logistic regression and naive bayes. Neural Information Processing Systems 2: 841-848 doi:10.1.1.19.9829.
71. Ponder WF, Carter GA, Flemons P, Chapman RR, (2010) Evaluation of Museum Collection Data for Use in Biodiversity Assessment. Conserv. Biol. 15: 648-657.
72. Oliver TH, Gillings S, Girardello M, Rapacciuolo G, Brereton TM, et al. (2012) Population density but not stability can be predicted from species distribution models. J. Appl. Ecol. 49: 581-590 doi:10.1111/j.1365-2664.2012.02138.x.