A new dynamic null model for phylogenetic community structure

Ecology Letters

Volumn 18, Issue 2, 2015, Pages 153-163

  Pigot, Alex L ^a,b   Etienne, Rampal S ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Colonisation; Community assembly; Extinction; Null model; Phylogeny; Speciation; Traits

Indexed keywords

AVES; PRIMATES;

ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIRD; CLASSIFICATION; PHYLOGENY; PHYSIOLOGY; PRIMATE; SOUTH AMERICA; SPECIES DIFFERENTIATION; SPECIES EXTINCTION;

ALGORITHMS; ANIMALS; BIRDS; EXTINCTION, BIOLOGICAL; GENETIC SPECIATION; MODELS, BIOLOGICAL; PHYLOGENY; PRIMATES; SOUTH AMERICA;

EID: 84934094960     PISSN: 1461023X     EISSN: 14610248     Source Type: Journal    
DOI: 10.1111/ele.12395     Document Type: Article

References (48)

1. Allen, G.E. & Dytham, C. (2009). An efficient method for stochastic simulation of biological populations in continuous time. Biosystems, 98, 37-42.
2. Barnagaud, J.Y., Kissling, W.D., Sandel, B., Eiserhardt, W.L., Sekercioglu, C.H., Enquist, B.J. et al. (2014). Ecological traits influence the phylogenetic structure of bird species co-occurrences worldwide. Ecol. Lett., 17, 811-820. doi:10.1111/ele.12285.
3. Bell, G. (2001). Neutral macroecology. Science, 293, 2413-2418.
4. Belmaker, J. & Jetz, W. (2013). Spatial scaling of functional structure in bird and mammal assemblages. Am. Nat., 181, 464-478.
5. Blomberg, S.P., Garland, T. & Ives, A.R. (2003). Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717-745.
6. Bolnick, D.I. & Fitzpatrick, B.M. (2007). Sympatric speciation: models and empirical evidence. Annu. Rev. Ecol. Evol. S., 38, 459-487.
7. Cadotte, M., Albert, C.H. & Walker, S.C. (2013). The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecol. Lett., 16, 1234-1244.
8. Cavender-Bares, J., Ackerly, D.D., Baum, D.A. & Bazzaz, F.A. (2004). Phylogenetic overdispersion in floridian oak communities. Am. Nat., 163, 823-843.
9. Cavender-Bares, J., Kozak, K.H., Fine, P.V.A. & Kembel, S.W. (2009). The merging of community ecology and phylogenetic biology. Ecol. Lett., 12, 693-715.
10. Colwell, R.K. & Winkler, D.W. (1984). A null model for null models in biogeography In: Ecological Communities: Conceptual Issues and the Evidence (eds Strong, D.L., Simberloff, D., Abele, L.G. & Thistle, A.B.). Princeton University Press, Princeton, pp. 1603.
11. Connor, E.F. & Simberloff, D. (1979). The assembly of species communities - chance or competition. Ecology, 60, 1132-1140.
12. Cooper, N., Rodriguez, J. & Purvis, A. (2008). A common tendency for phylogenetic overdispersion in mammalian assemblages. Proc. Biol. Sci., 275, 2031-2037.
13. Derryberry, E.P., Claramunt, S., Derryberry, G., Chesser, R.T., Cracraft, J., Aleixo, A. et al. (2011). Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: furnariidae). Evolution, 65, 2973-2986.
14. Diamond, J.M. (1975). Assembly of species communities. In: Ecology and Evolution of Communities (eds Cody, M.L. & Diamond, J.M.). Belknap, Cambridge, MA, pp. 342-444.
15. Eklof, A., Jacob, U., Kopp, J., Bosch, J., Castro-Urgal, R., Chacoff, N.P. et al. (2013). The dimensionality of ecological networks. Ecol. Lett., 16, 577-583.
16. Gillespie, D.T. (1977). Exact stochastic simulation of coupled chemical-reactions. J. Phys. Chem-Us, 81, 2340-2361.
17. Goldberg, E.E., Lancaster, L.T. & Ree, R.H. (2011). Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst. Biol., 60, 451-465.
18. Gomez, J.P., Bravo, G.A., Brumfield, R.T., Tello, J.G. & Cadena, C.D. (2010). A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of neotropical forest birds. J. Anim. Ecol., 79, 1181-1192.
19. Gotelli, N.J. & Graves, G.R. (1996). Null Models in Ecology. Smithsonian Institution Press, Washington.
20. Gotelli, N.J. & McGill, B.J. (2006). Null versus neutral models: what's the difference? Ecography, 29, 793-800.
21. Graham, C.H. & Fine, P.V.A. (2008). Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol. Lett., 11, 1265-1277.
22. Graham, C.H., Parra, J.L., Tinoco, B.A., Stiles, F.G. & McGuire, J.A. (2012). Untangling the influence of ecological and evolutionary factors on trait variation across hummingbird assemblages. Ecology, 93, S99-S111.
23. Hardy, O.J. (2008). Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. J. Ecol., 96, 914-926.
24. HilleRisLambers, J., Adler, P.B., Harpole, W.S., Levine, J.M. & Mayfield, M.M. (2012). Rethinking community assembly through the lens of coexistence theory. Annu. Rev. Ecol. Evol. Syst., 43, 227-248.
25. Hubbell, S.P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton.
26. Ingram, T. & Shurin, J.B. (2009). Trait-based assembly and phylogenetic structure in northeast pacific rockfish assemblages. Ecology, 90, 2444-2453.
27. Kembel, S.W. (2009). Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol. Lett., 12, 949-960.
28. Kembel, S.W. & Hubbell, S.P. (2006). The phylogenetic structure of a neotropical forest tree community. Ecology, 87, S86-S99.
29. Kisel, Y. & Barraclough, T.G. (2010). Speciation has a spatial scale that depends on levels of gene flow. Am. Nat., 175, 316-334.
30. Kraft, N.J.B., Cornwell, W.K., Webb, C.O. & Ackerly, D.D. (2007). Trait evolution, community assembly, and the phylogenetic structure of ecological communities. Am. Nat., 170, 271-283.
31. Kraft, N.J.B., Valencia, R. & Ackerly, D.D. (2008). Functional traits and niche-based tree community assembly in an amazonian forest. Science, 322, 580-582.
32. MacArthur, J.W. & Wilson, E.O. (1967). The Theory of Island Biogeography. Princeton University Press, Princeton.
33. Mayfield, M.M. & Levine, J.M. (2010). Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett., 13, 1085-1093.
34. McGuire, J.A., Witt, C.C., Remsen, J.V., Corl, A., Rabosky, D.L., Altshuler, D.L. et al. (2014). Molecular phylogenetics and the diversification of hummingbirds. Curr. Biol., 24, 910-916.
35. Morlon, H. (2014). Phylogenetic approaches for studying diversification. Ecol. Lett., 17, 508-525.
36. Revell, L.J. (2012). Phytools: an r package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
37. Ricklefs, R.E. (1987). Community diversity - relative roles of local and regional processes. Science, 235, 167-171.
38. Solari, S., Pacheco, V., Luna, L., Velazco, P.M. & Patterson, B.D. (2006). Mammals of the manu biosphere reserve. Fieldiana Zoo., 110, 13-22.
39. Springer, M.S., Meredith, R.W., Gatesy, J., Emerling, C.A., Park, J., Rabosky, D.L. et al. (2012). Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE, 7, 1-23.
40. Stadler, T. (2013). Treesim in R-simulating trees under the birth-death model. Available from: Http://cran.R-project.Org/web/packages/treesim/index.Html.
41. Swenson, N.G., Enquist, B.J., Pither, J., Kerkhoff, A.J., Boyle, B., Weiser, M.D. et al. (2012). The biogeography and filtering of woody plant functional diversity in north and south america. Global Ecol. Biogeogr., 21, 798-808.
42. Vamosi, S.M., Heard, S.B., Vamosi, J.C. & Webb, C.O. (2009). Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol., 18, 572-592.
43. Vellend, M. (2010). Conceptual synthesis in community ecology. Q. Rev. Biol., 85, 183-206.
44. Walker, B., Stotz, D.F., Pequeno, T. & Fitzpatrick, J.W. (2006). Birds of the manu biosphere reserve. Fieldiana Zoo., 110, 23-46.
45. Warren, D.L., Cardillo, M., Rosauer, D.F. & Bolnick, D.I. (2014). Mistaking geography for biology: inferring processes from species distributions. Trends Ecol. Evol. 29, 572-580.
46. Webb, C.O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat., 156, 145-155.
47. Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002). Phylogenies and community ecology. Annu. Rev. Ecol. Syst., 33, 475-505.
48. Williams, C.B. (1947). The generic relations of species in small ecological communities. J. Anim. Ecol., 16, 11-18.