Using species richness and functional traits predictions to constrain assemblage predictions from stacked species distribution models

Journal of Biogeography

Volumn 42, Issue 7, 2015, Pages 1255-1266

  D'Amen, Manuela ^a   Dubuis, Anne ^a   Fernandes, Rui F ^a   Pottier, Julien ^b   Pellissier, Loïc ^a,c   Guisan, Antoine ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b French National Institute of Agricultural Research   (France)

^c UNIVERSITY OF FRIBOURG   (Switzerland)

Author keywords

Community ecology; Functional ecology; Macroecological models; MEM; SDM; SESAM framework; Species distribution models; Stacked SDM; Swiss Alps

Indexed keywords

COMMUNITY ECOLOGY; ECOSYSTEM FUNCTION; ECOSYSTEM MODELING; FUNCTIONAL CHANGE; FUNCTIONAL MORPHOLOGY; GLOBAL CHANGE; GRASSLAND; MACROECOLOGY; POPULATION MODELING; SPATIAL DISTRIBUTION; SPECIES RICHNESS;

ALPS; WESTERN ALPS;

EID: 84931573209     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12485     Document Type: Article

References (70)

1. Albert, C.H., Thuiller, W., Yoccoz, N.G., Soudant, A., Boucher, F., Saccone, P. & Lavorel, S. (2010) Intraspecific functional variability: extent, structure and sources of variation. Journal of Ecology, 98, 604-613.
2. Albouy, C., Guilhaumon, F., Araújo, M.B., Mouillot, D. & Leprieur, F. (2012) Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages. Global Change Biology, 18, 2995-3003.
3. Algar, A.C., Kharouba, H.M., Young, E.R. & Kerr, J.T. (2009) Predicting the future of species diversity: macroecological theory, climate change, and direct tests of alternative forecasting methods. Ecography, 32, 22-33.
4. Allouche, O., Tsoar, A. & Kadmon, R. (2006) Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). Journal of Applied Ecology, 43, 1223-1232.
5. Aranda, S.C. & Lobo, J.M. (2011) How well does presence-only-based species distribution modelling predict assemblage diversity? A case study of the Tenerife flora. Ecography, 34, 31-38.
6. Araújo, M.B., Rozenfeld, A., Rahbek, C. & Marquet, P.A. (2011) Using species co-occurrence networks to assess the impacts of climate change. Ecography, 34, 897-908.
7. Austin, M.P. & Van Niel, K.P. (2010) Improving species distribution models for climate change studies: variable selection and scale. Journal of Biogeography, 38, 1-8.
8. Baselga, A. & Araújo, M.B. (2009) Individualistic vs community modelling of species distributions under climate change. Ecography, 32, 55-65.
9. Baselga, A. & Araújo, M.B. (2010) Do community-level models describe community variation effectively? Journal of Biogeography, 37, 1842-1850.
10. Calabrese, J.M., Certain, G., Kraan, C. & Dormann, C.F. (2014) Stacking species distribution models and adjusting bias by linking them to macroecological models. Global Ecology and Biogeography, 23, 99-112.
11. Clark, J.S. (2009) Beyond neutral science. Trends in Ecology and Evolution, 24, 8-15.
12. Cornelissen, J.H.C., Lavorel, S., Garnier, E., Díaz, S., Buchmann, N., Gurvich, D.E., Reich, P.B., ter Steege, H., Morgan, H.D., van der Heijden, M.G.A., Pausas, J.G. & Poorter, H. (2003) A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Australian Journal of Botany, 51, 335-380.
13. Currie, D.J. (1991) Energy and large-scale patterns of animal- and plant-species richness. The American Naturalist, 137, 27-49.
14. Dornelas, M., Connolly, S.R. & Hughes, T.P. (2006) Coral reef diversity refutes the neutral theory of biodiversity. Nature, 440, 80-82.
15. Douma, J.C., Witte, J.-P.M., Aerts, R., Bartholomeus, R.P., Ordoñez, J.C., Venterink, H.O., Wassen, M.J. & van Bodegom, P.M. (2012) Towards a functional basis for predicting vegetation patterns; incorporating plant traits in habitat distribution models. Ecography, 35, 294-305.
16. Dubuis, A., Pottier, J., Rion, V., Pellissier, L., Theurillat, J.-P. & Guisan, A. (2011) Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches. Diversity and Distributions, 17, 1122-1131.
17. Dubuis, A., Giovanettina, S., Pellissier, L., Pottier, J., Vittoz, P. & Guisan, A. (2012) Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables. Journal of Vegetation Science, 24, 593-606.
18. Dubuis, A., Rossier, L., Pottier, J., Pellissier, L. & Guisan, A. (2013) Predicting current and future community patterns of plant functional traits. Ecography, 36, 1158-1168.
19. Dunstan, P.K., Foster, S.D. & Darnell, R. (2011) Model based grouping of species across environmental gradients. Ecological Modelling, 222, 955-963.
20. Faleiro, F.V., Machado, R.B. & Loyola, R.D. (2013) Defining spatial conservation priorities in the face of land-use and climate change. Biological Conservation, 158, 248-257.
21. Fernandes, J.A., Cheung, W.W., Jennings, S., Butenschon, M., de Mora, L., Frolicher, T.L. & Grant, A. (2013) Modelling the effects of climate change on the distribution and production of marine fishes: accounting for trophic interactions in a dynamic bioclimate envelope model. Global Change Biology, 19, 2596-2607.
22. Ferrier, S. & Guisan, A. (2006) Spatial modelling of biodiversity at the community level. Journal of Applied Ecology, 43, 393-404.
23. Francis, A.P. & Currie, D.J. (2003) A globally consistent richness-climate relationship for angiosperms. The American Naturalist, 161, 523-536.
24. Gilman, S.E., Urban, M.C., Tewksbury, J., Gilchrist, G.W. & Holt, R.D. (2010) A framework for community interactions under climate change. Trends in Ecology and Evolution, 25, 325-331.
25. Gotelli, N.J., Buckley, N.J. & Wiens, J.A. (1997) Co-occurrence of Australian land birds: Diamond's assembly rules revisited. Oikos, 80, 311-324.
26. Gotelli, N.J., Anderson, M.J., Arita, H.T. et al. (2009) Patterns and causes of species richness: a general simulation model for macroecology. Ecology Letters, 12, 873-886.
27. Götzenberger, L., De Bello, F., Anne Bråthen, K., Davison, J., Dubuis, A., Guisan, A., Lepš, J., Lindborg, R., Moora, M., Pärtel, M., Pellissier, L., Pottier, J., Vittoz, P., Zobel, K. & Zobel, M. (2012) Ecological assembly rules in plant communities-approaches, patterns and prospects. Biological Reviews, 87, 111-127.
28. Guisan, A. & Rahbek, C. (2011) SESAM - a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages. Journal of Biogeography, 38, 1433-1444.
29. Guisan, A., Tingley, R., Baumgartner, J.B. et al. (2013) Predicting species distributions for conservation decisions. Ecology Letters, 16, 1424-1435.
30. Hawkins, B.A., Field, R., Cornell, H.V., Currie, D.J., Guégan, J.F., Kaufman, D.M., Kerr, J.T., Mittelbach, G.G., Oberdorff, T., O'Brien, E.M., Porter, E.E. & Turner, J.R.G. (2003) Energy, water, and broad-scale geographic patterns of species richness. Ecology, 84, 3105-3117.
31. Hooper, D.U., Chapin, F.S., III, Ewel, J.J., Hector, A., Inchausti, P., Lavorel, S., Lawton, J.H., Lodge, D.M., Loreau, M., Naeem, S., Schmid, B., Setälä, H., Symstad, A.J., Vandermeer, J. & Wardle, D.A. (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs, 75, 3-35.
32. Hortal, J., De Marco, P., Santos, A.M.C. & Diniz-Filho, J.A.F. (2012) Integrating biogeographical processes and local community assembly. Journal of Biogeography, 39, 627-628.
33. Hubbell, S.P. (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.
34. Hui, F.C.K., Warton, D.I., Foster, S.D. & Dunstan, P.K. (2013) To mix or not to mix: comparing the predictive performance of mixture models vs. separate species distribution models. Ecology, 94, 1913-1919.
35. Keddy, P.A. (1992a) A pragmatic approach to functional ecology. Functional Ecology, 6, 621-626.
36. Keddy, P.A. (1992b) Assembly and response rules: two goals for predictive community ecology. Journal of Vegetation Science, 3, 157-164.
37. Kissling, W.D., Dormann, C.F., Groeneveld, J., Hickler, T., Kühn, I., McInerny, G.J., Montoya, J.M., Römermann, C., Schiffers, K., Schurr, F.M., Singer, A., Svenning, J.-C., Zimmermann, N.E. & O'Hara, R.B. (2012) Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents. Journal of Biogeography, 39, 2163-2178.
38. Laughlin, D.C., Joshi, C., van Bodegom, P.M., Bastow, Z.A. & Fulé, P.Z. (2012) A predictive model of community assembly that incorporates intraspecific trait variation. Ecology Letters, 15, 1291-1299.
39. Le Roux, P.C., Lenoir, J., Pellissier, L., Wisz, M.S. & Luoto, M. (2013) Horizontal, but not vertical, biotic interactions affect fine-scale plant distribution patterns in a low-energy system. Ecology, 94, 671-682.
40. Leach, K., Zalat, S. & Gilbert, F. (2013) Egypt's Protected Area network under future climate change. Biological Conservation, 159, 490-500.
41. Liu, C.R., Berry, P.M., Dawson, T.P. & Pearson, R.G. (2005) Selecting thresholds of occurrence in the prediction of species distributions. Ecography, 28, 385-393.
42. Mateo, R.G., Felicísimo, Á.M., Pottier, J., Guisan, A. & Muñoz, J. (2012) Do stacked species distribution models reflect altitudinal diversity patterns? PLoS ONE, 7, e32586.
43. McGill, B.J., Enquist, B.J., Weiher, E. & Westoby, M. (2006) Rebuilding community ecology from functional traits. Trends in Ecology and Evolution, 21, 178-185.
44. Mokany, K., Harwood, T.D., Overton, J.M., Barker, G.M. & Ferrier, S. (2011) Combining α- and β-diversity models to fill gaps in our knowledge of biodiversity. Ecology Letters, 14, 1043-1051.
45. Mokany, K., Harwood, T.D., Williams, K.J. & Ferrier, S. (2012) Dynamic macroecology and the future for biodiversity. Global Change Biology, 18, 3149-3159.
46. Moles, A.T. & Westoby, M. (2006) Seed size and plant strategy across the whole life cycle. Oikos, 113, 91-105.
47. Moser, D., Dullinger, S., Englisch, T., Niklfeld, H., Plutzar, C., Sauberer, N., Zechmeister, H.G. & Grabherr, G. (2005) Environmental determinants of vascular plant species richness in the Austrian Alps. Journal of Biogeography, 32, 1117-1127.
48. Ovaskainen, O., Hottola, J. & Siitonen, J. (2010) Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions. Ecology, 91, 2514-2521.
49. Ozinga, W.A., Schaminée, J.H.J., Bekker, R.M., Bonn, S., Poschlod, P. & Tackelberg, O. (2005) Predictability of plant species composition from environmental conditions is constrained by dispersal limitation. Oikos, 108, 555-561.
50. Pakeman, R.J. & Quested, H.M. (2007) Sampling plant functional traits: what proportion of the species need to be measured? Applied Vegetation Science, 10, 91-96.
51. Pellissier, L., Fournier, B., Guisan, A. & Vittoz, P. (2010) Plant traits co-vary with altitude in grasslands and forests in the European Alps. Plant Ecology, 211, 351-365.
52. Pellissier, L., Pradervand, J.-N., Pottier, J., Dubuis, A., Maiorano, L. & Guisan, A. (2012) Climate-based empirical models show biased predictions of butterfly communities along environmental gradients. Ecography, 35, 684-692.
53. Pellissier, L., Rohr, R.P., Ndiribe, C., Pradervand, J.-N., Salamin, N., Guisan, A. & Wisz, M. (2013) Combining food web and species distribution models for improved community projections. Ecology and Evolution, 3, 4572-4583.
54. Peres-Neto, P.R., Olden, J.D. & Jackson, D.A. (2001) Environmentally constrained null models: site suitability as occupancy criterion. Oikos, 93, 110-120.
55. Pottier, J., Dubuis, A., Pellissier, L., Maiorano, L., Rossier, L., Randin, C.F., Vittoz, P. & Guisan, A. (2013) The accuracy of plant assemblage prediction from species distribution models varies along environmental gradients. Global Ecology and Biogeography, 22, 52-63.
56. Pradervand, J.-N., Dubuis, A., Pellissier, L., Guisan, A. & Randin, C.F. (2014) Very high-resolution environmental predictors in species distribution models: moving beyond topography? Progress in Physical Geography, 38, 79-96.
57. Randin, C.F., Vuissoz, G., Liston, G.E., Vittoz, P. & Guisan, A. (2009) Introduction of snow and geomorphic disturbance variables into predictive models of alpine plant distribution in the western Swiss Alps. Arctic, Antarctic, and Alpine Research, 41, 347-361.
58. Shipley, B. (2010) Community assembly, natural selection and maximum entropy models. Oikos, 119, 604-609.
59. Shipley, B., Vile, D. & Garnier, E. (2006) From plant traits to plant communities: a statistical mechanistic approach to biodiversity. Science, 314, 812-814.
60. Shipley, B., Laughlin, D.C., Sonnier, G. & Ottinowski, R. (2011) A strong test of a maximum entropy model of trait-based community assembly. Ecology, 92, 507-517.
61. Sonnier, G., Shipley, B. & Navas, M. (2010a) Plant traits, species pools and the prediction of relative abundance in plant communities : a maximum entropy approach. Journal of Vegetation Science, 21, 318-331.
62. Sonnier, G., Shipley, B. & Navas, M.L. (2010b) Quantifying relationships between traits and explicitly measured gradients of stress and disturbance in early successional plant communities. Journal of Vegetation Science, 21, 318-331.
63. Swets, J.A. (1988) Measuring the accuracy of diagnostic systems. Science, 240, 1285-1293.
64. Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M.B. (2009) BIOMOD - a platform for ensemble forecasting of species distributions. Ecography, 32, 369-373.
65. Thuiller, W., Albert, C.H., Dubuis, A., Randin, C. & Guisan, A. (2010) Variation in habitat suitability does not always relate to variation in species' plant functional traits. Biology Letters, 6, 120-123.
66. Webb, C.T., Hoeting, J.A., Ames, G.M., Pyne, M.I. & LeRoy Poff, N. (2010) A structured and dynamic framework to advance traits-based theory and prediction in ecology. Ecology Letters, 13, 267-283.
67. Wennekes, P., Rosindell, J. & Etienne, R. (2012) The neutral-niche debate: a philosophical perspective. Acta Biotheoretica, 60, 257-271.
68. Westoby, M. (1998) A leaf-height-seed (LHS) plant ecology strategy scheme. Plant and Soil, 199, 213-227.
69. Wisz, M.S., Pottier, J., Kissling, W.D. et al. (2013) The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling. Biological Reviews of the Cambridge Philosophical Society, 88, 15-30.
70. Wright, D.H. (1983) Species-energy theory: an extension of species-area theory. Oikos, 41, 496-506.