Impact of model complexity on cross-temporal transferability in Maxent species distribution models: An assessment using paleobotanical data

Ecological Modelling

Volumn 312, Issue , 2015, Pages 308-317

  Moreno Amat, Elena ^a   Mateo, Rubén G ^a,b   Nieto Lugilde, Diego ^c,d   Morueta Holme, Naia ^d,e   Svenning, Jens Christian ^d   García Amorena, Ignacio ^a  

^a UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c UNIVERSITY OF GRANADA   (Spain)

^d AARHUS UNIVERSITY   (Denmark)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alnus glutinosa; Corylus avellana; Model validation; Pollen fossil; Species distribution model; Multiplier

Indexed keywords

ALGORITHMS; CLIMATE CHANGE; ECONOMIC AND SOCIAL EFFECTS; FORECASTING; PLANTS (BOTANY); POPULATION DISTRIBUTION; UNCERTAINTY ANALYSIS;

CORYLUS AVELLANA; GLUTINOSA; MODEL VALIDATION; POLLEN FOSSIL; SPECIES DISTRIBUTION MODELING;

CLIMATE MODELS;

CLIMATE CONDITIONS; FOSSIL RECORD; GEOGRAPHICAL DISTRIBUTION; MAXIMUM ENTROPY ANALYSIS; NUMERICAL MODEL; PALEOBOTANY; PLANT COMMUNITY; SPATIOTEMPORAL ANALYSIS; SPECIES OCCURRENCE;

SPAIN;

ALNUS GLUTINOSA; CORYLUS AVELLANA;

EID: 84934968239     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2015.05.035     Document Type: Article

References (60)

1. Anderson R.P., González I. Species-specific tuning increases robustness to sampling bias in models of species distributions: an implementation with Maxent. Ecol. Model. 2011, 222:2796-2811. 10.1016/j.ecolmodel.2011.04.011.
2. Araújo M.B., Alagador D., Cabeza M., Nogués-Bravo D., Thuiller W. Climate change threatens European conservation areas. Ecol. Lett. 2011, 14:484-492. 10.1111/j.1461-0248.2011.01610.x.
3. Araújo M., Pearson R., Thuiller W., Erhard M. Validation of species-climate impact models under climate change. Glob. Change Biol. 2005, 11:1504-1513. 10.1111/j.1365-2486.2005.01000.x.
4. Araújo M.B., Peterson A.T. Uses and misuses of bioclimatic envelope modeling. Ecology 2012, 93(7):1527-1539.
5. Austin M. Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecol. Model. 2007, 200:1-19. 10.1016/j.ecolmodel.2006.07.005.
6. Beck J., Böller M., Erhardt A., Schwanghart W. Spatial bias in the GBIF database and its effect on modeling species' geographic distributions. Ecol. Inform. 2014, 19:10-15. 10.1016/j.ecoinf.2013.11.002.
7. Cao Y., DeWalt R.E., Robinson J.L., Tweddale T., Hinz L., Pessino M. Using Maxent to model the historic distributions of stonefly species in Illinois streams: the effects of regularization and threshold selections. Ecol. Model. 2013, 259:30-39. 10.1016/j.ecolmodel.2013.03.012.
8. Carrión J.S. Paleoflora ibérica: Plioceno-Cuaternario. Ministerio de Economía y Competitividad, Madrid 2013, Universidad de Murcia y Fundación Séneca, Murcia, (Coord).
9. Castroviejo S. Flora ibérica 1-8, 10-15, 17-18, 21 1986-2012, Real Jardín Botánico, CSIC, Madrid, (Coord).
10. Elith J., Graham C.H., Anderson R.P., Dudík 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., Soberón J., Williams S., Wisz M.S., Zimmermann N.E. Novel methods improve prediction of species' distributions from occurrence data. Ecography 2006, 29:129-151. 10.1111/j.2006.0906-7590.04596.x.
11. Elith J., Kearney M., Phillips S. The art of modelling range-shifting species. Methods Ecol. Evol. 2010, 1:330-342. 10.1111/j.2041-210X.2010.00036.x.
12. Elith J., Leathwick J.R. Species distribution models: ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. Syst. 2009, 40:677-697. 10.1146/annurev.ecolsys.110308.120159.
13. Erdtman G., Sarjeant W.A.S., Praglowski J., Nilsson S., Dunbar A. Handbook of Palynology: Morphology, Taxonomy, Ecology: An Introduction to the Study of Pollen Grains and Spores 1969, 486. Munksgaard, Copenhagen.
14. European Pollen Database 2007-2015, 〈http://www.europeanpollendatabase.net/〉 [accessed 23.01.12].
15. Fielding A.H., Bell J.F. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environ. Conserv. 1997, 24:38-49. 10.1017/S0376892997000088.
16. GBIF. Global Biodiversity Information Facility. URL: [accessed 23.01.12]. http://www.gbif.org/.
17. Guisan A., Zimmermann N.E. Predictive habitat distribution models in ecology. Ecol. Model. 2000, 135:147-186. 10.1016/S0304-3800(00)00354-9.
18. GRASS Development Team Geographic Resources Analysis Support System (GRASS) Software. Open Source Geospatial Foundation Project 2012, GRASS Development Team, 〈http://grass.osgeo.org〉 [accessed 05.03.12].
19. Halvorsen R., Mazzoni S., Bryn A., Bakkestuen V. Opportunities for improved distribution modelling practice via a strict maximum likelihood interpretation of MaxEnt. Ecography 2015, 38:172-183. 10.1111/ecog.00565.
20. Harris R.M.B., Porfirio L.L., Hugh S., Lee G., Bindoff N.L., Mackey B. To be or not to be? Variable selection can change the projected fate of a threatened species under future climate. Ecol. Manage. Restor. 2013, 14:230-234. 10.1111/emr.12055.
21. Hijmans R.J., Cameron S.E., Parra J.L., Jones P.G., Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 2005, 25:1965-1978. 10.1002/joc.1276.
22. Hijmans R.J., Elith J. Species Distribution Modeling with R. R CRAN Project 2013, 〈http://cran.r-project.org/web/packages/dismo/vignettes/sdm.pdf〉 [accessed 14.01.13].
23. Hijmans R.J., Graham C.H. The ability of climate envelope models to predict the effect of climate change on species distributions. Global Change Biol. 2006, 12:2272-2281. 10.1111/j.1365-2486.2006.01256.x.
24. Jalas J., Suominen, J., (Eds) 1972-1994. Atlas Florae Europaeae: Distribution of Vascular Plants in Europe, Vol. 1-10. The Committee for Mapping the Flora of Europe and Societas Biologica Fennica Vanamo. Helsinki.
25. Johnson J.B., Omland K.S. Model selection in ecology and evolution. Trends Ecol. Evol. 2004, 19:101-108. 10.1016/j.tree.2003.10.013.
26. Kajba D., Gračan J. Euforgen Technical Guidelines for Genetic Conservation and Use for Black Alder (Alnus glutinosa) 2003, 4. International Plant Genetic Resources Institute, Rome, Italy.
27. Kearney M.R., Wintle B.A., Porter W.P. Correlative and mechanistic models of species distribution provide congruent forecasts under climate change. Conserv. Lett. 2010, 3(3):203-213. 10.1111/j.1755-263X.2010.00097.x.
28. Kiehl J.T., Gent P.R. The community climate system model, version 2. J. Clim. 2004, 17:3666-3682. 10.1175/15200442(2004)017<3666:TCCSMV>2.0.CO;2.
29. Kumar S., Stohlgren T.J. Maxent modeling for predicting suitable habitat for threatened and endangered tree Canacomyrica monticola in New Caledonia. J. Ecol. Nat. Environ. 2009, 1:94-98.
30. Lawson C.R., Hodgson J.A., Wilson R.J., Richards S.A. Prevalence, thresholds and the performance of presence-absence models. Methods Ecol. Evol. 2014, 5:54-64. 10.1111/2041-210X.12123.
31. Lima-Ribeiro M.S., Nogués-Bravo D., Terribile L.C., Batra P., Diniz-Filho J.A.F. Climate and humans set the place and time of proboscidean extinction in late quaternary of South America. Palaeogeogr. Palaeoclimatol. Palaeoecol. 2013, 392:546-556. 10.1016/j.palaeo.2013.10.008.
32. Lisitsyna O.V., Giesecke T., Hicks S. Exploring pollen percentage threshold values as an indication for the regional presence of major European trees. Rev. Palaeobot. Palynol. 2011, 166:311-324. 10.1016/j.revpalbo.2011.06.004.
33. Lobo J.M., Jiménez-Valverde A., Real R. AUC: a misleading measure of the performance of predictive distribution models. Global Ecol. Biogeogr. 2008, 17:145-151. 10.1111/j.1466-8238.2007.00358.x.
34. Mateo R.G., Vanderpoorten A., Muñoz J., Laenen B., Désamoré A. Modeling species distributions from heterogeneous data for the biogeographic regionalization of the European bryophyte flora. PLoS ONE 2013, 8:e55648. 10.1371/journal.pone.0055648.
35. Merow C., Smith M.J., Edwards T.C., Guisan A., McMahon S.M., Normand S., Thuiller W., Wüest R.O., Zimmermann N.E., Elith J. What do we gain from simplicity versus complexity in species distribution models?. Ecography 2014, 37:1267-1281. 10.1111/ecog.00845.
36. Merow C., Smith M.J., Silander J.A. A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter. Ecography 2013, 36:1058-1069. 10.1111/j.1600-0587.2013.07872.x.
37. Morin X., Thuiller W. Comparing niche-and process-based models to reduce prediction uncertainty in species range shifts under climate change. Ecology 2009, 90(5):1301-1313.
38. Morueta-Holme N., Fløjgaard C., Svenning J.C. Climate change risks and conservation implications for a threatened small-range mammal species. PLoS ONE 2010, 5:e10360. 10.1371/journal.pone.0010360.
39. Muscarella R., Galante P.J., Soley-Guardia M., Boria R.A., Kass J.M., Uriarte M., Anderson R.P. ENMeval: an R package for conductiong spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods Ecol. Evol. 2014, 10.1111/2041-210X.12261.
40. Nieto-Lugilde D., Maguire K.C., Blois J.L., Williams J.W., Fitzpatrick M.C. Close agreement between pollen-based and forest inventory-based models of vegetation turnover. Global Ecol. Biogeogr. 2015, 10.1111/geb.12300.
41. Paleodiversitas Sistema de información sobre Paleoflora y Paleovegetación de la Península ibérica 2011, 〈http://www.paleodiversitas.org/〉 [accessed 23.01.12].
42. Pearman P.B., Randin C.F., Broennimann O., Vittoz P., van der Knaap W.O., Engler R., Le Lay G., Zimmermann N.E., Guisan A. Prediction of plant species distributions across six millennia. Ecol. Lett. 2008, 11:357-369. 10.1111/j.1461-0248.2007.01150.x.
43. Pearson R.G., Raxworthy C.J., Nakamura M., Townsend Peterson A. Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. J. Biogeogr. 2007, 34:102-117. 10.1111/j.1365-2699.2006.01594.x.
44. Phillips S.J., Anderson R.P., Schapire R.E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 2006, 190:231-259. 10.1016/j.ecolmodel.2005.03.026.
45. Phillips S.J., Dudík M. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 2008, 31:161-175. 10.1111/j.0906-7590.2008.5203.x.
46. Prentice I.C., Cramer W., Harrison S.P., Leemans R., Monserud R.A., Solomon A.M. A global biome model based on plant physiology and dominance, soil properties and climate. J. Biogeogr. 1992, 19:117-134. 10.2307/2845499.
47. Radosavljevic A., Anderson R.P. Making better Maxent models of species distributions: complexity, overfitting and evaluation. J. Biogeogr. 2014, 41:629-643. 10.1111/jbi.12227.
48. Record S., Fitzpatrick M.C., Finley A.O., Veloz S., Ellison A.M. Should species distribution models account for spatial autocorrelation? A test of model projections across eight millennia of climate change. Global Ecol. Biogeogr. 2013, 22:760-771. 10.1111/geb.12017.
49. Reimer P.J., Baillie M.G.L., Bard E., Bayliss A., Beck J.W., Blackwell P.G., Bronk Ramsey C., Buck C.E., Burr G.S., Edwards R.L., Friedrich M., Grootes P.M., Guilderson T.P., Hajdas I., Heaton T.J., Hogg A.G., Hughen K.A., Kaiser K.F., Kromer B., McCormac F.G., Manning S.W., Reimer R.W., Richards D.A., Southon J.R., Talamo S., Turney C.S.M., van der Plicht J., Weyhenmeyer E. IntCal09 and Marine09 radiocarbon age calibration curves, 0-50,000 years cal BP. Radiocarbon 2009, 51:1111-1150.
50. Renner I.W., Warton D.I. Equivalence of MAXENT and Poisson point process models for species distribution modeling in ecology. Biometrics 2013, 69:274-281. 10.1111/j.1541-0420.2012.01824.x.
51. Shcheglovitova M., Anderson R.P. Estimating optimal complexity for ecological niche models: a jackknife approach for species with small sample sizes. Ecol. Model. 2013, 269:9-17. 10.1016/j.ecolmodel.2013.08.011.
52. Stuiver M., Reimer P.J., Reimer R. Calib 6.0 2012, 〈http://radiocarbon.pa.qub.ac.uk/calib/calib.html〉 [accessed 23.01.12].
53. Svenning J.C., Fløjgaard C., Marske K.A., Nogués-Bravo D., Normand S. Applications of species distribution modeling to paleobiology. Quat. Sci. Rev. 2011, 30:2930-2947. 10.1016/j.quascirev.2011.06.012.
54. Syfert M.M., Smith M.J., Coomes D.A. The effects of sampling bias and model complexity on the predictive performance of MaxEnt species distribution models. PLoS ONE 2013, 8:e55158. 10.1371/journal.pone.0055158.
55. Synes N.W., Osborne P.E. Choice of predictor variables as a source of uncertainty in continental-scale species distribution modelling under climate change. Global Ecol. Biogeogr. 2011, 20:904-914. 10.1111/j.1466-8238.2010.00635.x.
56. Szczepanek K., Tobolski K., Nalepka D. Alnus Mill. Alder. Late Glacial and Holocene History of Vegetation in Poland Based on Isopollen Maps 2004, 47-55. W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków. M. Ralska-Jasiewiczowa, M. Latałowa, K. Wasylikowa, K. Tobolski, E. Madeyska, H.E. Wright, C. Turner (Eds.).
57. Warren D.L., Glor R.E., Turelli M. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 2010, 1:607-611. 10.1111/j.1600-0587.2009.06142.x.
58. Warren D.L., Seifert S.N. Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecol. Appl. 2011, 21:335-342. 10.1890/10-1171.1.
59. Warren D.L., Wright A.N., Seifert S.N., Shaffer H.B. Incorporating model complexity and spatial sampling bias into ecological niche models of climate change risks faced by 90 California vertebrate species of concern. Divers. Distrib. 2014, 20:334-343. 10.1111/ddi.12160.
60. Yackulic C.B., Chandler R., Zipkin E.F., Royle J.A., Nichols J.D., Campbell Grant E.H., Veran S. Presence-only modelling using MAXENT: when can we trust the inferences?. Methods Ecol. Evol. 2013, 4:236-243. 10.1111/2041210x.12004.