Inferring the parameters of the neutral theory of biodiversity using phylogenetic information and implications for tropical forests

Ecology Letters

Volumn 12, Issue 3, 2009, Pages 239-248

  Jabot, Franck ^a   Chave, Jérôme ^a  

^a CNRS   (France)

Author keywords

Approximate Bayesian computation; Community phylogenetics; Dispersal limitation; Neutral theory; Parameter inference; Phylogenetic imbalance; Regional species pool

Indexed keywords

BAYESIAN ANALYSIS; BIODIVERSITY; DISPERSAL; DIVERSITY INDEX; PHYLOGENETICS; PHYLOGENY; SPECIES EVENNESS; TREE; TROPICAL FOREST;

ARTICLE; BIODIVERSITY; COMPUTER SIMULATION; GENETICS; PHYLOGENY; STATISTICAL MODEL; TREE; TROPIC CLIMATE;

BIODIVERSITY; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; PHYLOGENY; TREES; TROPICAL CLIMATE;

EID: 60649110912     PISSN: 1461023X     EISSN: 14610248     Source Type: Journal    
DOI: 10.1111/j.1461-0248.2008.01280.x     Document Type: Article

References (48)

1. Allen, A.P. Savage, V.M. (2007). Setting the absolute tempo of biodiversity dynamics. Ecol. Lett., 10, 637 646.
2. Alonso, D., Etienne, R.S. McKane, A.J. (2006). The merits of neutral theory. Trends Ecol. Evol., 21, 451 457.
3. Beaumont, M.A., Zhang, W.Y. Balding, D.J. (2002). Approximate Bayesian computation in population genetics. Genetics, 162, 2025 2035.
4. Chave, J., Alonso, D. Etienne, R.S. (2006). Theoretical biology - comparing models of species abundance. Nature, 441, E1.
5. Clark, J.S. (2005). Why environmental scientists are becoming Bayesians. Ecol. Lett., 8, 2 14.
6. Condit, R., Pitman, N., Leigh, E.G. Jr., Chave, J., Terborgh, J., Foster, R.B. et al. (2002). Beta-diversity in tropical forest trees. Science, 295, 666 669.
7. Condit, R., Ashton, P., Bunyavejchewin, S., Dattaraja, H.S., Davies, S., Esufali, S. et al. (2006). The importance of demographic niches to tree diversity. Science, 313, 98 101.
8. Dick, C.W., Hardy, O.J., Jones, F.A. Petit, R.J. (2008). Spatial scales of pollen and seed-mediated gene flow in tropical rain forest trees. Trop. Plant Biol., 1, 20 33.
9. Etienne, R.S. (2005). A new sampling formula for neutral biodiversity. Ecol. Lett., 8, 253 260.
10. Etienne, R.S., Latimer, A.M., Silander, J.A. Cowling, R.M. (2006). Comment on "Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot". Science, 311, 610b.
11. Ewens, W.J. (1972). The sampling theory of selectively neutral alleles. Theor. Popul. Biol., 3, 87 112.
12. Ewens, W.J. (2004). Mathematical Population Genetics. I. Theoretical Introduction, 2nd edn. Springer, New York, 417 pp.
13. Fine, P.V.A. Ree, R.H. (2006). Evidence for a time-integrated species-area effect on the latitudinal gradient in tree diversity. Am. Nat., 168, 796 804.
14. Gentry, A.H. (1988). Changes in plant community diversity and floristic composition on environmental and geographical gradients. Ann. Miss. Bot. Gard., 75, 1 34.
15. Hardy, O.J. Senterre, B. (2007). Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. J. Ecol., 95, 493 506.
16. Heard, S.B. Cox, G.H. (2007). The shapes of phylogenetic trees of clades, faunas, and local assemblages: exploring spatial pattern in differential diversification. Am. Nat., 169, E107 E118.
17. Hubbell, S.P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ.
18. Hutchinson, G.E. (1959). Homage to Santa Rosalia or why are there so many kinds of animals? Am. Nat., 93, 145 159.
19. Jabot, F., Etienne, R.S. Chave, J. (2008). Reconciling neutral community models and environmental filtering: theory and an empirical test. Oikos, 117, 1308 1320.
20. Lande, R., Engen, S. Saether, B.-E. (2003). Stochastic Population Dynamics in Ecology and Conservation, Oxford Series in Ecology and Evolution. Oxford University Press, Oxford UK, 212 pp.
21. Latimer, A.M., Silander, J.A. Jr. Cowling, R.M. (2005). Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot. Science, 309, 1722 1725.
22. Lavin, M., Schrire, B.P., Lewis, G., Pennington, R.T., Delgado-Salinas, A., Thulin, M. et al. (2004). Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philos. Trans. R. Soc. Lond. B, 359, 1509 1522.
23. Leigh, E.G. Jr. (2007). Neutral theory: a historical perspective. J. Evol. Biol., 20, 2075 2091.
24. Losos, J.B. (1992). The evolution of convergent structure in Caribbean anolis communities. Syst. Biol., 41, 403 420.
25. Losos, E.C. Leigh, E.G. Jr. (2004). Tropical Forest Diversity and Dynamism. Findings from a Large-Scale Plot Network. University of Chicago Press, Chicago, IL.
26. MacArthur, R.H. Wilson, E.O. (1967). The Theory of Island Biogeography. Princeton University Press, Princeton, NJ, 224 pp.
27. Magurran, A.E. (2004). Measuring Biological Diversity. Blackwell, Oxford, UK, 256 pp.
28. Marjoram, P. Tavaré, S. (2006). Modern computational approaches for analyzing molecular genetic variation data. Nat. Rev. Gen., 7, 759 770.
29. Marjoram, P., Molitor, J., Plagnol, V. Tavaré, S. (2003). Markov chain Monte Carlo without likelihoods. Proc. Natl Acad. Sci. USA, 100, 15324 15328.
30. McGill, B.J., Etienne, R.S., Gray, J.S., Alonso, D., Anderson, M.J., Benecha, H.K. et al. (2007). Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol. Lett., 10, 995 1015.
31. Mooers, A.O. Heard, S.B. (1997). Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol., 72, 31 54.
32. Mooers, A.O., Harmon, L.J., Blum, M.G.B., Wong, D.H.J. Heard, S.B. (2007). Some models of phylogenetic tree shape. In : Reconstructing Evolution: New Mathematical and Computational Advances (eds Gascuel, O. Steel, M.). Oxford University Press, Oxford, pp. 149 170.
33. Nathan, R. (2006). Long-distance dispersal of plants. Science, 313, 786 788.
34. Pennington, R.T. Dick, C.W. (2004). The role of immigrants in the assembly of the American rainforest tree flora. Philos. Trans. R. Soc. B, 359, 1611 1622.
35. Pennington, R.T., Richardson, J.E. Lavin, M. (2006). Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure. New Phytol., 172, 605 616.
36. Richardson, J.E., Pennington, R.T., Pennington, T.C. Hollingsworth, P.M. (2001). Rapid diversification of a species-rich genus of neotropical rainforest trees. Science, 293, 2242 2245.
37. Ricklefs, R.E. (2004). A comprehensive framework for global patterns in biodiversity. Ecol. Lett., 7, 1 15.
38. Ricklefs, R.E. (2006). The unified neutral theory of biodiversity: do the numbers add up? Ecology, 87, 1424 1431.
39. Shao, K.T. Sokal, R.R. (1990). Tree balance. Syst. Zool., 39, 266 276.
40. Swenson, N.G., Enquist, B.J., Pither, J., Thompson, J. Zimmerman, J.K. (2006). The problem and promise of scale dependency in community phylogenetics. Ecology, 87, 2418 2424.
41. Tavaré, S., Balding, D.J., Griffiths, R.C. Donnelly, P. (1997). Inferring coalescence times from DNA sequence data. Genetics, 145, 505 518.
42. Wakeley, J. (2007). Coalescent Theory. An Introduction. Roberts & Company Publishers, Greenwood Village, CO.
43. Webb, C.O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat., 156, 145 155.
44. Webb, C.O. Donoghue, M.J. (2005). Phylomatic: tree assembly for applied phylogenetics. Mol. Ecol. Notes, 5, 181 183.
45. Webb, C.O. Pitman, N.C.A. (2002). Phylogenetic balance and ecological evenness. Syst. Biol., 51, 898 907.
46. Webb, C.O., Ackerly, D.D., McPeek, M.A. Donoghue, M.J. (2002). Phylogenies and community ecology. Annu. Rev. Ecol. Syst., 33, 475 505.
47. Wiens, J.J. Donoghue, M.J. (2004). Historical biogeography, ecology and species richness. Trends Ecol. Evol., 19, 639 644.
48. Yule, G.U. (1924). A mathematical theory of evolution based on the conclusions of Dr. J.C. Willis. Philos. Trans. R. Soc. Lond. B, 213, 21 87.