A new modeling approach estimates the relative importance of different community assembly processes

Ecology

Volumn 96, Issue 6, 2015, Pages 1502-1515

  Van Der Plas, Fons ^a   Janzen, Thijs ^b   Ordonez, Alejandro ^c   Fokkema, Wimke ^b   Reinders, Josephine ^b   Etienne, Rampal S ^b   Olff, Han ^b  

^a UNIVERSITY OF BERN   (Switzerland)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Abiotic filters; Approximate Bayesian Computation; Community assembly; Dispersal; Functional traits; Hluhluwe iMfolozi Park; Limiting similarity; Neutral theory; Savanna; South Africa; Stochasticity; Trees

Indexed keywords

ASSEMBLY RULE; BAYESIAN ANALYSIS; BIODIVERSITY; BIOME; COEXISTENCE; COMMUNITY COMPOSITION; DATA SET; DISPERSAL; ECOLOGICAL MODELING; FUNCTIONAL MORPHOLOGY; NATURE RESERVE; NICHE PARTITIONING; POPULATION DISTRIBUTION; SAVANNA; STOCHASTICITY; TREE;

SOUTH AFRICA;

EID: 84930827048     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/14-0454.1     Document Type: Article

References (63)

1. Abrams, P. A. 1983. The theory of limiting similarity. Annual Reviews in Ecology and Systematics 14:359-376.
2. Adler, P. B., A. Fajardo, A. R. Kleinhesselink, and N. J. B. Kraft. 2013. Trait-based tests of coexistence mechanisms. Ecology Letters 16:1294-1306.
3. Adler, P. B., J. HilleRisLambers, and J. M. Levine. 2007. A niche for neutrality. Ecology Letters 10:95-104.
4. Akima, H., A. Gebhardt, T. Petzoldt, and M. Maechler. 2009. Akima: interpolation of irregularity spaced data. R package version 0.5-4. http://cran.r-project.org/web/packages/akima/index.html
5. Balfour, D. A., and O. E. Howison. 2002. Spatial and temporal variation in a mesic savanna fire regime: responses to variation in annual rainfall. African Journal of Range and Forage Science 19:45-53.
6. Beaumont, M. A. 2010. Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics 41:379-406.
7. Beaumont, M. A., W. Zhang, and D. J. Balding. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
8. Bond, W. J., and B. W. Wilgen. 1996. Fire and plants. Chapman and Hall, London, UK.
9. Bray, J. R., and J. T. Curtis. 1957. An ordination of upland forest communities of southern Wisconsin. Ecological Monographs 27:325-349.
10. Brown, V. K., and J. H. Lawton. 1991. Herbivory and the evolution of leaf size and shape. Philosophical Transactions of the Royal Society B 333:265-272.
11. Bryant, J. P., P. J. Kuropat, S. M. Cooper, K. Frisby, and N. Owensmith. 1989. Resource availability hypothesis of plant antiherbivore defense tested in a South African savanna ecosystem. Nature 340:227-229.
12. Caswell, H. 1976. Community structure: neutral model analysis. Ecological Monographs 46:327-354.
13. Chase, J. M., and M. A. Leibold. 2003. Ecological niches: linking classical and contemporary approaches. University Press, Chicago, Illinois, USA.
14. Cornwell, W. K., and D. D. Ackerly. 2009. Community assembly and shifts in plant trait distributions across an environmental gradient in coastal California. Ecological Monographs 79:109-126.
15. Cornwell, W. K., D. W. Schwilk, and D. D. Ackerly. 2006. A trait-based test for habitat filtering: convex hull volume. Ecology 87:1465-1471.
16. Cramer, M. D., A. van Cauter, and W. J. Bond. 2010. Growth of N2-fixing savanna Acacia species is constrained by below-ground competition with grass. Journal of Ecology 98:156-167.
17. Csillery, K., M. G. M. Blum, O. E. Gaggiotti, and O. Francois. Approximate Bayesian Computation (ABC) in practice. 2010. Trends in Ecology and Evolution 25:410-418.
18. Garzon-Lopez, C. X., P. A. Jansen, S. A. Bohlman, A. Ordonez, and H. Olff. 2014. Effects of sampling scale on patterns of habitat association in tropical trees. Journal of Vegetation Science 25:349-362.
19. Gotelli, N. J., and G. L. Entsminger. 2001. Swap and fill algorithms in null model analysis: rethinking the Knight's Tour. Oecologia 129:281-291.
20. Gotelli, N. J., and G. R. Graves. 1996. Null models in ecology. Smithsonian Institution Press, Washington, D.C., USA.
21. Hacke, U. G., J. S. Sperry, W. T. Pockman, S. D. Davis, and K. A. McCulloch. 2001. Trends in wood density and structure are linked to prevention of xylem implosion by negative pressure. Oecologia 126:457-461.
22. Hartig, F., J. M. Calabrese, B. Reineking, T. Wiegand, and A. Huth. 2011. Statistical inference for stochastic simulation models-theory and application. Ecology Letters 14:816-827.
23. Helmus, M. R., K. Savage, M. W. Diebel, J. T. Maxted, and A. R. Ives. 2007. Separating the determinants of phylogenetic tree community structure. Ecology Letters 10:917-925.
24. Higgins, S. I., et al. 2007. Effects of four decades of fire manipulation on woody vegetation structure in savanna. Ecology 88:1119-1125.
25. HilleRisLambers, J., P. B. Adler, W. S. Harpole, J. M. Levine, and M. M. Mayfield. 2012. Rethinking community assembly through the lens of coexistence theory. Annual Review of Ecology, Evolution, and Systematics 43:224-248.
26. Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, New Jersey, USA.
27. Hubbell, S. P. 2006. Neutral theory and the evolution of functional equivalence. Ecology 87:1387-1398.
28. Hutchinson, G. E. 1959. Homage to Santa Rosalia or why are there so many kinds of animals? American Naturalist 870: 145-159.
29. Janzen, T., and F. van der Plas. 2014. STEPCAM: ABC-SMC inference of the STEPCAM model. R package version 1.0. http://CRAN.R-project.org/packageSTEPCAM
30. Keddy, P. A. 1992. Assembly and response rules: 2 goals for predictive community ecology. Journal of Vegetation Science 3:157-164.
31. Kembel, S. W. 2009. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecology Letters 12: 949-960.
32. Kraft, N. J. B., W. K. Cornwell, C. O. Webb, and D. D. Ackerly. 2007. Trait evolution, community assembly, and the phylogenetic structure of ecological communities. American Naturalist 170:271-283.
33. Laliberte, E., and B. Shipley. 2011. FD: measuring functional diversity from multiple traits, and other tools for functional ecology. R package version 1.0-11. http://cran.r-project.org/web/packages/FD/index.html
34. Laughlin, D. C., J. Chaitanya, P. M. van Bodegom, Z. A. Bastow, and P. Z. Fule. 2012. A predictive model of community assembly that incorporates intraspecific trait variation. Ecology Letters 15:1291-1299.
35. Laughlin, D. C., and D. E. Laughlin. 2013. Advances in modeling trait-based plant community assembly. Trends in Plant Science 18:584-593.
36. MacArthur, R., and R. Levins. 1967. The limiting similarity, convergence, and divergence of coexisting species. American Naturalist 101:377-385.
37. Marks, C. O., and M. J. Lechowicz. 2006. Alternative designs and the evolution of functional diversity. American Naturalist 167:55-66.
38. Marschner, H. 1995. Mineral nutrition of higher plants. Second edition. Academic Press, London, UK.
39. Martorell, C., and R. P. Freckleton. 2014. Testing the roles of competition, facilitation and stochasticity on community structure in a species-rich assemblage. Journal of Ecology 102:75-85.
40. Mayfield, M. M., and J. M. Levine. 2010. Opposing effects on competitive exclusion of the phylogenetic structure of communities. Ecology Letters 13:1085-1093.
41. McGill, B. J., B. J. McEnquist, E. Weiher, and M. Westoby. 2006. Rebuilding community ecology from functional traits. Trends in Ecology and Evolution 21:178-185.
42. Oksanen, J., et al. 2013. vegan: community ecology package. Package version 2.0-2. http://CRAN.R-project.org/packagevegan
43. Parmentier, I., M. Rejou-Mechain, J. Chave, J. Vleminckx, D. W. Thomas, D. Kenfack, G. B. Chuyong, and O. J. Hardy. 2014. Prevalence of phylogenetic clustering at multiple scales in an African rain forest community. Journal of Ecology 102:1008-1016.
44. Pooley, E. 1997. The complete field guide to trees of Natal, Zululand and Transkei. Third edition. Natal Flora Publications Trust, Durban, South Africa.
45. R Development Core Team. 2011. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.r-project.org
46. Reed, D. N., T. M. Anderson, J. Dempewolf, K. Metzger, and S. Serneels. 2009. The spatial distribution of vegetation types in the Serengeti ecosystem: the influence of rainfall and topographic relief on vegetation characteristics. Journal of Biogeography 36:770-782.
47. Rosindell, J., S. P. Hubbell, and R. S. Etienne. 2011. The unified neutral theory of biodiversity and biogeography at age ten. Trends in Ecology and Evolution 26:340-348.
48. Scholes, R. J., P. R. Dowty, K. Caylor, D. A. B. Parsons, P. G. H. Frost, and H. H. Shugart. 2002. Trends in savanna structure and composition along an aridity gradient in the Kalahari. Journal of Vegetation Science 13:419-428.
49. Shipley, B., C. E. T. Paine, and C. Baraloto. 2012. Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly. Ecology 93:760-769.
50. Tilman, D. 1982. Resource competition and community structure. Princeton University Press, Princeton, New Jersey, USA.
51. Toni, T., D. Welch, N. Strelkowa, A. Ipsen, and M. P. H. Stumpf. 2009. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface 6:187-202.
52. Van Buuren, S., and K. Groothuis-Oudshoorn. 2011. Mice: multivariate imputation by chained equations in R. Journal of Statistical Software 45:1-67.
53. van der Plas, F., T. M. Anderson, and H. Olff. 2012. Trait similarity patterns within grass and grasshopper communities: multitrophic community assembly at work. Ecology 93: 836-846.
54. van der Plas, F., R. Howison, J. Reinders, W. Fokkema, and H. Olff. 2013. Functional traits of trees on and off termite mounds: understanding the origin of biotically-driven heterogeneity in savannas. Journal of Vegetation Science 24: 227-238.
55. Vellend, M. 2010. Conceptual synthesis in community ecology. Quarterly Review of Biology 85:193-206.
56. Villeger, S., N. W. H. Mason, and D. Mouillot. 2008. New multidimensional functional diversity indices for a multifac-eted framework in functional ecology. Ecology 89:2290-2301.
57. Violle, C., D. R. Nemergut, Z. C. Pu, and L. Jiang. 2011. Phylogenetic limiting similarity and competitive exclusion. Ecology Letters 14:782-787.
58. Weiher, E., D. Freund, T. Bunton, A. Stefanski, T. Lee, and S. Bentivenga. 2011. Advances, challenges and a developing synthesis of ecological community assembly theory. Philosophical Transactions of the Royal Society B 366:2403-2413.
59. Weiher, E., and P. A. Keddy. 1995a. Assembly rules, null models, and trait dispersion: new questions from old patterns. Oikos 74:159-164.
60. Weiher, E., and P. A. Keddy. 1995b. The assembly of experimental wetland communities. Oikos 73:323-335.
61. Weiher, E., A. van der Werf, K. Thompson, M. Roderick, E. Garnier, and O. Eriksson. 1999. Challenging Theophrastus: a common core list of plant traits for functional ecology. Journal of Vegetation Science 10:609-620.
62. Westoby, M., D. S. Falster, A. T. Moles, P. A. Vesk, and I. J. Wright. 2002. Plant ecological strategies: some leading dimensions of variation between species. Annual Review of Ecology and Systematics 33:125-159.
63. Whately, A., and R. N. Porter. 1983. The woody vegetation communities in the Hluhluwe-Corridor-Umfolozi Game Reserve Complex. Bothalia 14:745-758.