Quantifying phylogenetic beta diversity: Distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Leprieur, Fabien ^a   Albouy, Camille ^a   de Bortoli, Julien ^a   Cowman, Peter F ^b   Bellwood, David R ^b   Mouillot, David ^a,b  

^a UNIVERSITÉ MONTPELLIER 2   (France)

^b JAMES COOK UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; CORAL REEF; DECOMPOSITION; FISH; GENETIC VARIABILITY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; NONHUMAN; ORGANISM COMMUNITY; PHYLOGENY; PHYLOSOR INDEX; SIMULATION; UNIFRAC INDEX;

ANIMALS; COMPUTATIONAL BIOLOGY; CORAL REEFS; EVOLUTION, MOLECULAR; FISHES; GENETIC LINKAGE; GENETIC VARIATION; PHYLOGENY;

EID: 84865079509     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042760     Document Type: Article

References (55)

1. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ, (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33: 475-505.
2. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW, (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12: 693-715.
3. Graham CH, Parra JL, Rahbek C, McGuire JA, (2009) Phylogenetic structure in tropical hummingbird communities. Proc Natl Acad Sci U S A 106: 19673-19678.
4. Cadotte MW, Cardinale BJ, Oakley TH, (2008) Evolutionary history and the effect of biodiversity on plant productivity. Proc Natl Acad Sci U S A 105: 17012-17017.
5. Faith DP, Magallon S, Hendry AP, Conti E, Yahara T, et al. (2010) Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being. Current Opinion in Environmental Sustainability 2: 66-74.
6. Cadotte MW, Davies TJ, (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Divers Distrib 16: 376-385.
7. Mouillot D, Albouy C, Guilhaumon F, Lasram FBR, Coll M, et al. (2011) Protected and Threatened Components of Fish Biodiversity in the Mediterranean Sea. Curr Biol 21: 1044-1050.
8. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci U S A 105: 11505-11511.
9. Graham CH, Fine PVA, (2008) Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett 11: 1265-1277.
10. Morlon H, Schwilk DW, Bryant JA, Marquet PA, Rebelo AG, et al. (2011) Spatial patterns of phylogenetic diversity. Ecol Lett 14: 141-149.
11. Swenson NG, (2011) Phylogenetic Beta Diversity Metrics, Trait Evolution and Inferring the Functional Beta Diversity of Communities. PLoS One 6: e21264.
12. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
13. Faith DP, Lozupone CA, Nipperess D, Knight R, (2009) The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology's "Phylogenetic Beta Diversity" Framework. Int J Mol Sci 10: 4723-4741.
14. Gomez JP, Bravo GA, Brumfield RT, Tello JG, Cadena CD, (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.
15. Nipperess DA, Faith DP, Barton K, (2010) Resemblance in phylogenetic diversity among ecological assemblages. J Veg Sci 21: 809-820.
16. Koleff P, Gaston KJ, Lennon JJ, (2003) Measuring beta diversity for presence-absence data. J Anim Ecol 72: 367-382.
17. Baselga A, (2007) Disentangling distance decay of similarity from richness gradients: response to Soininenet al. 2007. Ecography 30: 838-841.
18. Leprieur F, Olden JD, Lek S, Brosse S, (2009) Contrasting patterns and mechanisms of spatial turnover for native and exotic freshwater fish in Europe. J Biogeogr 36: 1899-1912.
19. Baselga A, (2010) Partitioning the turnover and nestedness components of beta diversity. Glob Ecol Biogeogr 19: 134-143.
20. Svenning JC, Flojgaard C, Baselga A, (2011) Climate, history and neutrality as drivers of mammal beta diversity in Europe: insights from multiscale deconstruction. J Anim Ecol 80: 393-402.
21. Leprieur F, Tedesco PA, Hugueny B, Beauchard O, Durr HH, et al. (2011) Partitioning global patterns of freshwater fish beta diversity reveals contrasting signatures of past climate changes. Ecol Lett 14: 325-334.
22. Hortal J, Diniz JAF, Bini LM, Rodriguez MA, Baselga A, et al. (2011) Ice age climate, evolutionary constraints and diversity patterns of European dung beetles. Ecol Lett 14: 741-748.
23. Andrew ME, Wulder MA, Coops NC, Baillargeon G, (2012) Beta-diversity gradients of butterflies along productivity axes. Glob Ecol Biogeogr 21: 352-364.
24. Baselga A, Gómez-Rodríguez C, JM L, (2012) Historical legacies in world amphibian diversity revealed by the turnover and nestedness components of beta diversity. PLoS One 7: e32341.
25. Ives AR, Helmus MR, (2010) Phylogenetic Metrics of Community Similarity. Am Nat 176: E128-E142.
26. Baselga A, (2012) The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Glob Ecol Biogeogr In press.
27. Gaston KJ, Davies RG, Orme CDL, Olson VA, Thomas GH, et al. (2007) Spatial turnover in the global avifauna. Proc Biol Sci 274: 1567-1574.
28. Lennon JJ, Koleff P, Greenwood JJD, Gaston KJ, (2001) The geographical structure of British bird distributions: diversity, spatial turnover and scale. J Anim Ecol 70: 966-979.
29. McKnight MW, White PS, McDonald RI, Lamoreux JF, Sechrest W, et al. (2007) Putting beta-diversity on the map: Broad-scale congruence and coincidence in the extremes. PLoS Biology 5: 2424-2432.
30. Rodrigues ASL, Gaston KJ, (2002) Maximising phylogenetic diversity in the selection of networks of conservation areas. Biol Conserv 105: 103-111.
31. Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
32. Team RDC (2011) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
33. Mouchet MA, Mouillot D, (2011) Decomposing phylogenetic entropy into alpha, beta and gamma components. Biol Lett 7: 205-209.
34. Rosen DE, (1978) Vicariant patterns and historical explanation in biogeography. Syst Zool 27: 159-188.
35. Cunningham SA, (1995) Problems with null models in the study of phylogenetic radiation. Evolution 49: 1292-1294.
36. Yule GU, (1925) A mathemahcal theory of evolution, based on the conclusions of Dr J C Willis, F R S. Philos Trans R Soc Lond B Biol Sci 213: 21-87.
37. Mooers AO, Heard SB, (1997) Evolutionary process from phylogenetic tree shape. Q Rev Biol 72: 31-54.
38. Bortolussi N, Durand E, Blum M, Francois O, (2006) apTreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics 22: 363-364.
39. Schweiger O, Klotz S, Durka W, Kuhn I, (2008) A comparative test of phylogenetic diversity indices. Oecologia 157: 485-495.
40. Parenti P, Randall JE, (2011) Checklist of the species of the families Labridae and Scaridae: an update. Smithiana Bulletin 13: 29-44.
41. Bellwood DR, Wainwright PC (2002) The history and biogeography of fishes on coral reels. In: Sale PF, editor. Coral Reef Fishes: dynamic and diversity in a complex ecosystem. San Diego, CA, USA: Elsevier. pp. 5-32.
42. Bellwood DR, Hughes TP, Connolly SR, Tanner J, (2005) Environmental and geometric constraints on Indo-Pacific coral reef biodiversity. Ecol Lett 8: 643-651.
43. Cowman PF, Bellwood DR, (2011) Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots. J Evol Biol 24: 2543-2562.
44. Bellwood DR, Hughes TP, (2001) Regional-scale assembly rules and biodiversity of coral reefs. Science 292: 1532-1534.
45. O'Dea A, Jackson JBC, Fortunato H, Smith JT, D'Croz L, et al. (2007) Environmental change preceded Caribbean extinction by 2 million years. Proc Natl Acad Sci U S A 104: 5501-5506.
46. Swenson NG, Anglada-Cordero P, Barone JA, (2011) Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient. Proc Biol Sci 278: 877-884.
47. Gotelli NJ, Graves GR (1996) Null models in ecology. Washington, D.C.: Smithsonian Institution Press. 368 p.
48. Mouquet N, Devictor V, Meynard CN, Munoz F, Bersier LF, et al. (2012) Ecophylogenetics: advances and perspectives. Biol Rev In press.
49. Swenson NG, Erickson DL, Mi X, Bourg NA, Forero-Montana J, et al. (2012) Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities. Ecology In press.
50. Pommier T, Douzery EJP, Mouillot D, (2012) Environment drives high phylogenetic turnover among oceanic bacterial communities. Biol Lett In press.
51. Stevens RD, (2011) Relative effects of time for speciation and tropical niche conservatism on the latitudinal diversity gradient of phyllostomid bats. Proc Biol Sci 278: 2528-2536.
52. Davies TJ, Buckley LB, (2011) Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philos Trans R Soc Lond B Biol Sci 366: 2414-2425.
53. Kraft NJB, Comita LS, Chase JM, Sanders NJ, Swenson NG, et al. (2011) Disentangling the Drivers of beta Diversity Along Latitudinal and Elevational Gradients. Science 333: 1755-1758.
54. Chase JM, Kraft NJB, Smith KG, Vellend M, Inouye BD, (2011) Using null models to disentangle variation in community dissimilarity from variation in alpha-diversity. Ecosphere 2: Article 24.
55. Feng G, Zhang JL, Pei NC, Rao MD, Mi XC, et al. (2012) Comparison of phylobetadiversity indices based on community data from Gutianshan forest plot. Chin Sci Bull 57: 623-630.