Phylogenetic diversity metrics for ecological communities: Integrating species richness, abundance and evolutionary history

Ecology Letters

Volumn 13, Issue 1, 2010, Pages 96-105

  Cadotte, Marc W ^a,b   Jonathan Davies, T ^a   Regetz, James ^a   Kembel, Steven W ^c,d   Cleland, Elsa ^a,e   Oakley, Todd H ^f  

^a NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF OREGON   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Abundance distribution; Biodiversity; Ecophylogenetic diversity; Evenness; Evolutionary history; Jasper Ridge biological preserve; Null models; Shannon Index

Indexed keywords

ABUNDANCE; BIODIVERSITY; COMMUNITY ECOLOGY; EVOLUTIONARY THEORY; PHYLOGENETICS; SPECIES CONSERVATION; SPECIES DIVERSITY; SPECIES EVENNESS; SPECIES RICHNESS;

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; ECOLOGY; EVOLUTION; PHYLOGENY; PHYSIOLOGY; POACEAE; POPULATION DYNAMICS; SPECIES DIFFERENTIATION; STATISTICAL MODEL; UNITED STATES;

BIODIVERSITY; CALIFORNIA; ECOLOGY; EVOLUTION; GENETIC SPECIATION; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PHYLOGENY; POACEAE; POPULATION DYNAMICS;

CALIFORNIA; JASPER RIDGE BIOLOGICAL PRESERVE; UNITED STATES;

EID: 72949108886     PISSN: 1461023X     EISSN: 14610248     Source Type: Journal    
DOI: 10.1111/j.1461-0248.2009.01405.x     Document Type: Article

References (49)

1. Agapow, P.M. Purvis, A. (2002). Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst. Biol., 51, 866 872.
2. Allen, B., Kon, M. Bar-Yam, Y. (2009). A new phylogenetic diversity measure generalizing the Shannon index and its application to Phyllostomid bats. Am. Nat., 174, 236 243.
3. Cadotte, M.W., Cardinale, B.J. Oakley, T.H. (2008). Evolutionary history and the effect of biodiversity on plant productivity. Proc. Natl Acad. Sci. USA, 105, 17012 17017.
4. Cadotte, M.W., Hamilton, M.A. Murray, B.R. (2009). Phylogenetic relatedness and plant invader success across two spatial scales. Divers. Distrib., 15, 481 488.
5. Cavender-Bares, J. Wilczek, A. (2003). Integrating micro- and macroevolutionary processes in community ecology. Ecology, 84, 592 597.
6. Cavender-Bares, J., Keen, A. Miles, B. (2006). Phylogenetic structure of floridian plant communities depends on taxonomic and spatial scale. Ecology, 87, S109 S122.
7. Cavender-Bares, J., Kozak, K., Fine, P.V.A. Kembel, S.W. (2009). The merging of community ecology and phylogenetic biology. Ecol. Lett., 12, 693 715.
8. Chesson, P. (2000). Mechanism of maintenance of species diversity. Annu. Rev. Ecol. Syst., 31, 343 366.
9. Cingolani, A.M., Cabido, M., Gurvich, D.E., Renison, D. Diaz, S. (2007). Filtering processes in the assembly of plant communities: are species presence and abundance driven by the same traits? J. Veg. Sci., 18, 911 920.
10. Crozier, R.H. (1997). Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annu. Rev. Ecol. Syst., 28, 243 268.
11. Crozier, R.H., Dunnett, L.J. Agapow, P.M. (2005). Phylogenetic biodiversity assessment based on systematic nomenclature. Evol. Bioinform., 1, 11 36.
12. Davies, T.J., Barraclough, T.G., Chase, M.W., Soltis, P.S., Soltis, D.E. Savolainen, V. (2004). Darwin's abominable mystery: insights from a supertree of the angiosperms. Proc. Natl Acad. Sci. USA, 101, 1904 1909.
13. Davies, T.J., Fritz, S.A., Grenyer, R., Orme, C.D.L., Bielby, J., Bininda- Emonds, O.R.P. et al. (2008). Phylogenetic trees and the future of mammalian biodiversity. Proc. Natl Acad. Sci. USA, 105, 11556 11563.
14. Dukes, J.S., Chiariello, N.R., Cleland, E.E., Moore, L.A., Shaw, M.R., Thayer, S. et al. (2005). Responses of grassland production to single and multiple global environmental changes. PLoS Biol., 3, 1829 1837.
15. Faith, D.P. (1992). Conservation evaluation and phylogenetic diversity. Biol. Conserv., 61, 1 10.
16. Faith, D.P. (2006). The role of the phylogenetic diversity measure, PD, in bioinformaatics: getting the definition right. Evol. Bioinform., 2, 277 283.
17. Felsenstein, J. (1985). Phylogenies and the comparative method. Am. Nat., 125, 1 15.
18. Fisher, R.H., Corbet, A.S. Williams, C.B. (1943). The relation between the number of species and the number of individuals in a random sample of animal population. J. Anim. Ecol., 12, 42 58.
19. Hardy, O.J. Senterre, B. (2007). Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. J. Ecol., 95, 493 506.
20. Harvey, P.H. Pagel, M. (1991). The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford.
21. Helmus, M.R., Bland, T.J., Williams, C.K. Ives, A.R. (2007). Phylogenetic measures of biodiversity. Am. Nat., 169, E68 E83.
22. Hillebrand, H., Bennett, D. Cadotte, M.W. (2008). The consequences of dominance: a review of the effects of evenness on local and regional ecosystem processes. Ecology, 89, 1510 1520.
23. Hubbell, S.P. (2001). The Unified Neutral Theory of Biodiveristy and Biogeography. Princeton University Press, Princeton, NJ.
24. Hughes, A.R., Inouye, B.D., Johnson, M.T.J., Underwood, N. Vellend, M. (2008). Ecological consequences of genetic diversity. Ecol. Lett., 11, 609 623.
25. Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. Baillie, J.E.M. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.
26. Johnson, M.T.J. Stinchcombe, J.R. (2007). An emerging synthesis between community ecology and evolutionary biology. Trends Ecol. Evol., 22, 250 257.
27. Losos, J.B. (2008). Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett., 11, 995 1007.
28. MacArthur, R.H. (1957). On the relative abundance of bird species. Proc. Natl Acad. Sci. USA, 43, 293 295.
29. Mace, G.M., Gittleman, J.L. Purvis, A. (2003). Preserving the tree of life. Science, 300, 1707 1709.
30. Magurran, A.E. (2003). Measuring Biological Diversity. Blackwell Science, Oxford.
31. Pardi, F. Goldman, N. (2007). Resource-aware taxon selection for maximizing phylogenetic diversity. Syst. Biol., 56, 431 444.
32. Pavoine, S., Ollier, S. Dufour, A.-B. (2005). Is the originality of a species measurable? Ecol. Lett., 8, 579 586.
33. Petchey, O.L. Gaston, K.J. (2002). Functional diversity (FD), species richness and community composition. Ecol. Lett., 5, 402 411.
34. Preston, F.W. (1948). The commonness and rarity of species. Ecology, 29, 254 283.
35. Pybus, O. Harvey, P.H. (2000). Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. B Biol. Sci., 267, 2267 2272.
36. R Development Core Team (2009). R: A Language and Environment for Statistical Computing. In. R Foundation for Statistical Computing Vienna, Austria.
37. Redding, D.W. Mooers, A.O. (2006). Incorporating evolutionary measures into conservation prioritization. Conserv. Biol., 20, 1670 1678.
38. Redding, D.W., Hartmann, K., Mimoto, A., Bokal, D., DeVos, M. Mooers, A.O. (2008). Evolutionarily distinctive species often capture more phylogenetic diversity than expected. J. Theor. Biol., 251, 606 615.
39. Sanderson, M.J. (1997). A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol., 14, 1218 1231.
40. Sherwin, W.B., Jabot, F., Rush, R. Rossetto, M. (2006). Measurement of biological information with applications from genes to landscapes. Mol. Ecol., 15, 2857 2869.
41. Silvertown, J., Dodd, M., Gowing, D., Lawson, C. McConway, K. (2006). Phylogeny and the hierarchical organization of plant diversity. Ecology, 87, S39 S49.
42. Vanewright, R.I., Humphries, C.J. Williams, P.H. (1991). What to protect - systematics and the agony of choice. Biol. Conserv., 55, 235 254.
43. Vile, D., Shipley, B. Garnier, E. (2006). Ecosystem productivity can be predicted from potential relative growth rate and species abundance. Ecol. Lett., 9, 1061 1067.
44. Villeger, S., Mason, N.W.H. Mouillot, D. (2008). New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology, 89, 2290 2301.
45. Webb, C.O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat., 156, 145 155.
46. Webb, C.O. Donoghue, M.J. (2005). Phylomatic: tree assembly for applied phylogenetics. Mol. Ecol. Notes, 5, 181 183.
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. Webb, C.O., Losos, J.B. Agrawal, A.A. (2006). Integrating phylogenies into community ecology. Ecology, 87, S1 S2.
49. Webb, C.O., Ackerly, D.D. Kembel, S.W. (2008). Phylocom: software for the anlaysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 2098 2100.