Analyzing tropical forest tree species abundance distributions using a nonneutral model and through approximate Bayesian inference

American Naturalist

Volumn 178, Issue 2, 2011, Pages

  Jabot, Franck ^a,b   Chave, Jérôme ^a  

^a CNRS   (France)

^b Cemagref   (France)

Author keywords

Approximate Bayesian computation; Community modeling; Environmental filtering; Neutral theory

Indexed keywords

ABUNDANCE; BAYESIAN ANALYSIS; COMMUNITY COMPOSITION; DATA SET; DISPERSAL; ECOLOGICAL MODELING; EMPIRICAL ANALYSIS; NICHE; NUMERICAL MODEL; POPULATION DISTRIBUTION; POPULATION MODELING; TROPICAL FOREST;

ARTICLE; BAYES THEOREM; BIODIVERSITY; BIOLOGICAL MODEL; BIOTA; CLASSIFICATION; ECOLOGY; EVALUATION; METHODOLOGY; PANAMA; PHYSIOLOGY; POPULATION DYNAMICS; SPECIES DIFFERENCE; TREE; TROPIC CLIMATE;

BAYES THEOREM; BIODIVERSITY; BIOTA; ECOLOGY; MODELS, BIOLOGICAL; PANAMA; POPULATION DYNAMICS; SPECIES SPECIFICITY; TREES; TROPICAL CLIMATE;

EID: 79960209593     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/660829     Document Type: Article

References (66)

1. Adler, P. B., J. HilleRisLambers, and J. M. Levine. 2007. A niche for neutrality. Ecology Letters 10:95-104.
2. Alonso, D., A. Ostling, and R. S. Etienne. 2008. The implicit assumption of symmetry and the species abundance distribution. Ecology Letters 11:93-105.
3. Bazzaz, F. A. 1991. Habitat selection in plants. American Naturalist 137(suppl.):S116-S130.
4. Beaumont, M. A., W. Y. Zhang, and D. J. Balding. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
5. Bell, G. 2003. The interpretation of biological surveys. Proceedings of the Royal Society B: Biological Sciences 270:2531-2542.
6. Chase, J. M., and M. A. Leibold. 2003. Ecological niches: linking classical and contemporary approaches. University of Chicago Press, Chicago.
7. Chave, J., H. Muller-Landau, and S. Levin. 2002. Comparing classical community models: theoretical consequences for patterns of diversity. American Naturalist 159:1-23.
8. Chave, J., D. Alonso, and R.S. Etienne. 2006. Theoretical biology: comparing models of species abundance. Nature 441:E1.
9. Chesson, P. L. 2000. Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics 31:343-366.
10. Clark, J. S. 2007. Models for ecological data: an introduction. Princeton University Press, Princeton, NJ.
11. Clobert, J., E. Danchin, A. A. Dhondt, and J. D. Nichols. 2001. Dispersal. Oxford University Press, Oxford.
12. Comita, L. S., H. C. Muller-Landau, S. Aguilar, and S. P. Hubbell. 2010. Asymmetric density dependence shapes species abundances in a tropical tree community. Science 329:330-332.
13. Condit, R., N. Pitman, E. G. Leigh Jr., J. Chave, J. Terborgh, R. B. Foster, P. Núñez, et al. 2002. Beta-diversity in tropical forest trees. Science 295:666-669.
14. Condit, R., P. Ashton, S. Bunyavejchewin, H. S. Dattaraja, S. Davies, S. Esufali, C. Ewango, et al. 2006. The importance of demographic niches to tree diversity. Science 313:98-101.
15. Connell, J. H. 1971. On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. Pages 298-312 in P. J. den Boer, and G. Gradwell, eds. Dynamics of populations. Center for Agricultural Publishing and Documentation, Wageningen.
16. Csilléry, K., M. G. B. Blum, O. E. Gaggiotti, and O. François. 2010. Approximate Bayesian computation (ABC) in practice. Trends in Ecology & Evolution 25:410-418.
17. Diamond, J. M. 1975. Assembly of species communities. Pages 342-444 in M. L. Cody, and J. M. Diamond, eds. Ecology and evolution of communities. Harvard University Press, Cambridge, MA.
18. Engelbrecht, B. M. J., L. S. Comita, R. Condit, T. A. Kursar, M. T. Tyree, B. L. Turner, and S. P. Hubbell. 2007. Drought sensitivity shapes species distribution patterns in tropical forests. Nature 447:80-82.
19. Engen, S., R. Lande, T. Walla, and P. J. DeVries. 2002. Analyzing spatial structure of communities using the two-dimensional Poisson lognormal species abundance model. American Naturalist 160:60-73.
20. Etienne, R. S. 2005. A new sampling formula for neutral biodiversity. Ecology Letters 8:253-260.
21. Etienne, R. S. 2007. A neutral sampling formula for multiple samples and an "exact" test of neutrality. Ecology Letters 10:608-618.
22. Etienne, R. S., and D. Alonso. 2005. A dispersal-limited sampling theory for species and alleles. Ecology Letters 8:1147-1156.
23. Etienne, R. S., and H. Olff. 2005. Confronting different models of community structure to species-abundance data: a Bayesian model comparison. Ecology Letters 8:493-504
24. Ewens, W. J. 2004. Mathematical population genetics. Springer, New York.
25. Gonzalez, M. A., E. A. Roger, E. A. Courtois, F. Jabot, N. Norden, C. E. T. Paine, C. Baraloto, et al. 2010. Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest. Journal of Ecology 98:137-146.
26. Gravel, D., C. D. Canham, M. Beaudet, and C. Messier. 2006. Reconciling niche and neutrality: the continuum hypothesis. Ecology Letters 9:399-409.
27. Harms, K. E., S. J. Wright, O. Calderon, A. Hernandez, and E. A. Herre. 2000. Pervasive density-dependent recruitment enhances seedling diversity in a tropical forest. Nature 404:493-495.
28. Hillebrand, H., D. S. Gruner, E. T. Borer, M. E. S. Bracken, E. E. Cleland, J. J. Elser, W. S. Harpole, et al. 2007. Consumer versus resource control of producer diversity depends on ecosystem type and producer community structure. Proceedings of the National Academy of Sciences of the USA 104:10904-10909.
29. Holyoak, M., M. A. Leibold, and R. D. Holt. 2005. Metacommunities: spatial dynamics and ecological communities. University of Chicago Press, Chicago.
30. Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.
31. Jabot, F. 2010. A stochastic dispersal-limited trait-based model of community dynamics. Journal of Theoretical Biology 262:650-661.
32. Jabot, F., and J. Chave. 2009. Inferring the parameters of the neutral theory of biodiversity using phylogenetic information, and implications for tropical forests. Ecology Letters 12:239-248.
33. Jabot, F., R. S. Etienne, and J. Chave. 2008. Reconciling neutral community models and environmental filtering: theory and an empirical test. Oikos 117:1308-1320.
34. Janzen, D. H. 1970. Herbivores and the number of tree species in tropical forests. American Naturalist 104:501-528.
35. John, R., J. W. Dalling, K. E. Harms, J. B. Yavitt, R. F. Stallard, M. Mirabello, S. P. Hubbell, et al. 2007. Soil nutrients influence spatial distributions of tropical tree species. Proceedings of the National Academy of Sciences of the USA 104:864-869.
36. Keddy, P. A. 1992. Assembly and response rules: two goals for predictive community ecology. Journal of Vegetation Science 3:157-164.
37. Latimer, A. M., J. A. Silander, and R. M. Cowling. 2005. Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot. Science 309:1722-1725.
38. Lawton, J. H. 1999. Are there general laws in ecology? Oikos 84:177-192.
39. Leigh, E. G., Jr. 2007. Neutral theory: a historical perspective. Journal of Evolutionary Biology 20:2075-2091.
40. Losos, E. C., and E. G. Leigh Jr. 2004. Tropical forest diversity and dynamism: findings from a large-scale plot network. University of Chicago Press, Chicago.
41. MacArthur, R. H. 1972. Geographical ecology: patterns in the distribution of species. Princeton University Press, Princeton, NJ.
42. MacArthur, R. H., and E. O. Wilson. 1967. The theory of island biogeography. Princeton University Press, Princeton, NJ.
43. Marjoram, P., and S. Tavaré. 2006. Modern computational approaches for analyzing molecular genetic variation data. Nature Reviews Genetics 7:759-770.
44. McGill, B. J., B. A. Maurer, and M. D. Weiser. 2006. Empirical evaluation of neutral theory. Ecology 87:1411-1423.
45. McGill, B. J., R. S. Etienne, J. S. Gray, D. Alonso, M. J. Anderson, H. Kassa Benecha, M. Dornelas, et al. 2007. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10:995-1015.
46. McGuire, K. L. 2007. Common ectomycorrhizal networks may maintain monodominance in a tropical rain forest. Ecology 88:567-574.
47. Mueller-Dombois, D., and H. Ellenberg. 1974. Aims and methods of vegetation ecology. Wiley, New York.
48. Norden, N., J. Chave, P. Belbenoit, A. Caubère, P. Châtelet, P.-M. Forget, B. Riéra, et al. 2009. Interspecific variation in seedling responses to seed limitation and habitat conditions for 14 Neotropical woody species. Journal of Ecology 97:186-197.
49. Pitman, N. C. A., J. W. Terborgh, M. R. Silman, P. Núñez, D. A. Neill, C. E. Ceron, W. A. Palacios, et al. 2001. Dominance and distribution of tree species in upper Amazonian terra firme forests. Ecology 82:2101-2117.
50. Plotkin, J. B., M. D. Potts, N. Leslie, N. Manokaran, J. LaFrankie, and P. S. Ashton. 2000. Species-area curves, spatial aggregation, and habitat specialization in tropical forests. Journal of Theoretical Biology 207:81-99.
51. Pyke, C. R., R. Condit, S. Aguilar, and S. Lao. 2001. Floristic composition across a climatic gradient in a Neotropical lowland forest. Journal of Vegetation Science 12:553-566.
52. R Development Core Team. 2009. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org.
53. Simberloff, D. 2004. Community ecology: is it time to move on? American Naturalist 163:787-799.
54. Sugihara, G., and R. M. May. 1990. Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series. Nature 344:734-741.
55. Svenning, J. C., D. A. Kinner, R. F. Stallard, B. M. J. Engelbrecht, and S. J. Wright. 2004. Ecological determinism in plant community structure across a tropical forest landscape. Ecology 85:2526-2538.
56. Tilman, D. 1982. Resource competition and community structure. Princeton University Press, Princeton, NJ.
57. Tilman, D. 2004. Niche trade-offs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. Proceedings of the National Academy of Sciences of the USA 101:10854-10861.
58. Torti, S. D., P. D. Coley, and T. A. Kursar. 2001. Causes and con sequences of monodominance in tropical lowland forests. American Naturalist 157:141-153.
59. Tuomisto, H., K. Ruokolainen, M. Aguilar, and A. Sarmiento. 2003. Floristic patterns along a 43-km long transect in an Amazonian rain forest. Journal of Ecology 91:743-756.
60. Valencia, R., R. B. Foster, G. Villa, R. Condit, J.-C. Svenning, C. Hernandez, K. Romoleroux, et al. 2004. Tree species distributions and local habitat variation in the Amazon: large forest plot in eastern Ecuador. Journal of Ecology 92:214-229.
61. Vallade, M., and B. Houchmandzadeh. 2003. Analytical solution of a neutral model of biodiversity. Physical Review E 68:061902.
62. Volkov, I., J. R. Banavar, S. P. Hubbell, and A. Maritan. 2003. Neutral theory and relative species abundance in ecology. Nature 424:1035-1037.
63. Volkov, I., J. R. Banavar, F. L. He, S. P. Hubbell, and A. Maritan. 2005. Density dependence explains tree species abundance and diversity in tropical forests. Nature 438:658-661.
64. Watterson, G. A. 1978. Homozygosity test of neutrality. Genetics 88:405-417.
65. Wills, C., K. E. Harms, R. Condit, D. King, J. Thompson, F. He, H. C. Muller-Landau, et al. 2006. Nonrandom processes maintain diversity in tropical forests. Science 27:527-531.
66. Zobel, M. 1997. The relative of species pools in determining plant species richness: an alternative explanation of species coexistence? Trends in Ecology & Evolution 12:266-269.