Linking patterns in phylogeny, traits, abiotic variables and space: A novel approach to linking environmental filtering and plant community assembly

Journal of Ecology

Volumn 99, Issue 1, 2011, Pages 165-175

  Pavoine, Sandrine ^a,b   Vela, Errol ^c   Gachet, Sophie ^d   De Bélair, Gérard ^e   Bonsall, Michael B ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b SORBONNE UNIVERSITÉ   (France)

^c UNIV MONTPELLIER   (France)

^d AVIGNON UNIVERSITÉ   (France)

^e St Peter's College ^*  (Algeria)

Author keywords

Coastal marsh plain; Community ecology; Determinants of plant community diversity and structure; Functional traits; Phylogenetic clustering; Phylogenetic signal; RLQ analysis; Spatial analysis; Species assemblage; Statistical graphics

Indexed keywords

ABUNDANCE; COMMUNITY ECOLOGY; GENETIC ANALYSIS; LIFE HISTORY TRAIT; PERENNIAL PLANT; PHYLOGENETICS; PHYLOGENY; PLANT COMMUNITY; SALINITY TOLERANCE; SOLAR RADIATION; SPATIAL ANALYSIS; SPECIES DIVERSITY;

ALGERIA;

AMARANTHACEAE; CYPERACEAE; DICOTYLEDONEAE; JUNCACEAE;

EID: 78650395430     PISSN: 00220477     EISSN: 13652745     Source Type: Journal    
DOI: 10.1111/j.1365-2745.2010.01743.x     Document Type: Article

References (77)

1. APG III Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. Botanical Journal of the Linnean Society, 161, 105-121.
2. Beche, L.A. & Statzner, B. (2009) Richness gradients of stream invertebrates across the USA: taxonomy- and trait-based approaches. Biodiversity and Conservation, 18, 3909-3930.
3. de Bélair, G. (1981) Biogéographie et aménagement: la plaine de La Mafragh (Annaba, Algérie). PhD Thesis, Université Paul Valéry, Montpellier.
4. Blondel, J. & Aronson, J. (1999) Biology and Wildlife of the Mediterranean Regions. Oxford University Press, Oxford.
5. de Bolòs, O. & Vigo, J. (19842001) Flora dels països catalans. Barcino, Barcelona.
6. de Bolòs, O., Vigo, J., Masalles, R. & Ninot, J.M. (1993) Flora manual dels països catalans, 2nd edn. Editorial Portic, Barcelona.
7. Braun-Blanquet, J., Fuller, G.D. & Conrad, H.S. (1932) Plant Sociology-The Study of Plant Communities (Authorized English Translation of Planzensoziologie). McGraw-Hill Book Company, Inc., New York and London.
8. Brooks, D.R. (1985) Historical ecology: a new approach to studying the evolution of ecological associations. Annals of the Missouri Botanical Garden, 72, 660-680.
9. Brooks, D.R. & McLennan, D.A. (1993) Historical ecology: examining phylogenetic components of community evolution. Species Diversity in Ecological Communities: Historical and Geographical Perspectives (eds R.E. Ricklefs & D. Schluter ), pp. 267-280. University of Chicago Press, Chicago.
10. Castroviejo, S. (19842010) Flora Iberica: plantes vasculares de la Peninsula iberica e Islas Baleares. Real Jardín Botánico, CSIC, Madrid, Spain.
11. Cavender-Bares, J., Keen, A. & Miles, B. (2006) Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology, 87, S109-S122.
12. Cavender-Bares, J., Ackerly, D., Baum, D. & Bazzaz, F. (2004) Phylogenetic overdispersion in Floridian oak communities. American Naturalist, 163, 823-843.
13. Chase, J.M., Amarasekare, P., Cottenie, K., Gonzalez, A., Holt, R.D., Holyoak, M., Hoopes, M.F., Leibold, M.A., Loreau, M., Mouquet, N., Shurin, J.B. & Tilman, D. (2005) Competing theories for competitive metacommunities. Metacommunities: Spatial Dynamics and Ecological Communities (eds M. Holyoak, M.A. Leibold & R.D. Holt ), pp. 335-354. The University of Chicago Press, Chicago.
14. Cleveland, W.S. (1994) The Elements of Graphing Data. AT&T Bell Laboratories, Murray Hill, New Jersey.
15. Cliff, A.D. & Ord, J.K. (1973) Spatial Autocorrelation. Pion, London.
16. Cornelissen, J.H.C., Lavorel, S., Garnier, E., Diaz, S., Buchmann, N., Gurvich, D.E., Reich, P.B., Steege, H., Morgan, H.D., Van-der-Heijden, M.G.A., Pausas, J.G. & Poorter, H. (2003) A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Australian Journal of Botany, 51, 335-380.
17. Cuenod, A., Pottier-Alapetite, G. & Labbe, A. (1954) Flore analytique et synoptique de la la Tunisie-cryptogames vasculaires, gymnospermes et monocotyledones. S.E.F.A.N., Tunis, Tunisia.
18. Desdevises, Y., Legendre, P., Azouzi, L. & Morand, S. (2003) Quantifying phylogenetically structured environmental variation. Evolution, 57, 2647-2652.
19. Diniz-Filho, J.A.F. & Bini, L.M. (2008) Macroecology, global change and the shadow of forgotten ancestors. Global Ecology and Biogeography, 17, 11-17.
20. Diniz-Filho, J.A.F., Bini, L.M., Rodriguez, M.A., Rangel, T.F.L.V.B. & Hawkins, B.A. (2007) Seeing the forest for the trees: partitioning ecological and phylogenetic components of Bergmann's rule in European Carnivora. Ecography, 30, 598-608.
21. Dolédec, S., Chessel, D., Ter Braak, C.J.F. & Champely, S. (1996) Matching species traits to environmental variables: a new three-table ordination method. Environmental and Ecological Statistics, 3, 143-166.
22. Dray, S., Chessel, D. & Thioulouse, J. (2003) Co-inertia analysis and the linking of ecological data tables. Ecology, 84, 3078-3089.
23. Dray, S. & Dufour, A.B. (2007) The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical Software, 22, 1-20.
24. Dray, S. & Legendre, P. (2008) Testing the species traits-environment relationships: the fourth-corner problem revisited. Ecology, 89, 3400-3412.
25. Dray, S., Legendre, P. & Peres-Neto, P.R. (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecological Modelling, 196, 483-493.
26. Elton, J. (1946) Competition and the structure of ecological communities. Animal Ecology, 15, 54-68.
27. Emberger, L. (1955) Une classification biogéographique des climats. Recueil des travaux des laboratoires de botanique, de géologie et zoologie de la faculté des sciences de Montpellier, 7, 3-43.
28. Emberger, L. (1966) Place de la région méditerranéenne française dans l'ensemble méditerranéen. Bulletins de l'APGB, 2, 153-165.
29. Escofier, B. & Pagès, J. (1994) Multiple factorial analysis (AFMULT package). Computational Statistics & Data Analysis, 19, 121-140.
30. Fortin, M.-J. & Dale, M. (2005) Spatial Analysis: a Guide for Ecologists. Cambridge University Press, Cambridge.
31. Freckleton, R.P. & Jetz, W. (2009) Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proceedings of the Royal Society of London Series B - Biological Sciences, 276, 21-30.
32. Gachet, S., Véla, E. & Tatoni, T. (2005) BASECO: a floristic and ecological database of Mediterranean French flora. Biodiversity and Conservation, 14, 1023-1034.
33. Gerhold, P., Pärtel, M., Liira, J., Zobel, K. & Prinzing, A. (2008) Phylogenetic structure of local communities predicts the size of the regional species pool. Journal of Ecology, 96, 709-712.
34. Giannini, N.P. (2003) Canonical phylogenetic ordination. Systematic Biology, 52, 684-695.
35. Gower, J.C. (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53, 325-338.
36. Gower, J.C. (1971) A general coefficient of similarity and some of its properties. Biometrics, 27, 857-874.
37. Greenacre, M.J. (1984) Theory and Applications of Correspondence Analysis. Academic Press, London.
38. Hedges, S.B. & Kumar, S., eds. (2009) The TimeTree of Life, pp. 551. Oxford University Press, New York.
39. Hill, M.O. & Smith, A.J.E. (1976) Principal component analysis of taxonomic data with multi-state discrete characters. Taxon, 25, 249-255.
40. Hubbell, S.P. (2005) Neutral theory in community ecology and the hypothesis of functional equivalence. Functional Ecology, 19, 166-172.
41. Hubbell, S.P. (2006) Neutral theory and the evolution of ecological equivalence. Ecology, 87, 1387-1398.
42. Ingram, T. & Shurin, J.B. (2009) Trait-based assembly and phylogenetic structure in northeast Pacific rockfish assemblages. Ecology, 90, 2444-2453.
43. Jauzein, P. (1995) Flore des champs cultivés. I.N.R.A. Eds, Sopra, Paris.
44. Jauzein, P. & Tison, J.M. (In Press) Flore de France méditerranéenne continentale. Conservatoire Botanique National Méditerranéen de Porquerolles, Hyères.
45. Jeanmonod, D. & Gamisans, J. (2007) Flora Corsica. Edisud, Aix-en-Provence.
46. Jetz, W., Sekercioglu, C.H. & Böhning-Gaese, K. (2008) The worldwide variation in avian clutch size across species and space. PloS Biology, 6, e303.
47. Julve, P. (19982008) Baseflor: index botanique, écologique et chorologique de la flore de France (Version 8 décembre 2008).
48. Kühn, I., Nobis, M.P. & Durka, W. (2009) Combining spatial and phylogenetic eigenvector filtering in trait analysis. Global Ecology & Biogeography, 481, 745-758.
49. Lacourse, T. (2009) Environmental change controls postglacial forest dynamics through interspecific differences in life-history traits. Ecology, 90, 2149-2160.
50. Legendre, L., Desdevises, Y. & Bazin, E. (2002) A statistical test for host-parasite coevolution. Systematic Biology, 51, 217-234.
51. Legendre, P. & Legendre, L. (1998) Numerical ecology, 2nd English edn. Elsevier Science BV, Amsterdam.
52. LeViol, I., Julliard, R., Kerbiriou, C., Redon, L.d., Carnino, N., Machon, N. & Porcher, E. (2008) Plant and spider communities benefit differently from the presence of planted hedgerows in highway verges. Biological conservation, 141, 1581-1590.
53. Losos, J.B. (1996) Phylogenetic perspectives on community ecology. Ecology, 77, 1344-1354.
54. Losos, J.B. (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters, 11, 995-1007.
55. Mayfield, M.M., Boni, M.F. & Ackerly, D.D. (2009) Traits, habitats, and clades: identifying traits of potential importance to environmental filtering. American Naturalist, 174, E1-E22.
56. Méot, A., Legendre, P. & Borcard, D. (1998) Partialling out the spatial component of ecological variation: questions and propositions in the linear modelling framework. Environmental and Ecological Statistics, 5, 1-27.
57. Moretti, M. & Legg, C. (2009) Combining plant and animal traits to assess community functional responses to disturbance. Ecography, 32, 299-309.
58. Ollier, S. (2004) Tools for the integration of spatial, temporal and evolutionary constraints in ecological data analysis - Des outils pour l'intégration des contraintes spatiales, temporelles et évolutives en analyse des données écologiques. PhD thesis, University of Lyon, Lyon, France.
59. Ollier, S., Couteron, P. & Chessel, D. (2006) Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree. Biometrics, 62, 417-477.
60. Pavoine, S., Baguette, M. & Bonsall, M.B. (2010) Decomposition of trait diversity among the nodes of a phylogenetic tree. Ecological Monographs, 80, 485-507.
61. Pavoine, S., Love, M. & Bonsall, M.B. (2009) Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages: application to rockfish (genus: Sebastes) in the Southern California Bight. Ecology letters, 12, 898-908.
62. Pavoine, S., Vallet, J., Dufour, A.-B., Gachet, S. & Daniel, H. (2009) On the challenge of treating various types of variables: application for improving the measurement of functional diversity. Oikos, 118, 391-402.
63. Pignatti, S. (1982) Flora d'Italia. Edagricole, Bologna.
64. Pottier-Alapetite, G. (19791981) Flore de la Tunisie - dicotyledones. Imprimerie Officielle de la République Tunisienne, Tunis, Tunisia.
65. R Development Core Team (2010) R: a Language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
66. Rao, C.R. (1964) The use and interpretation of principal component analysis in applied research. Sankhya, A, 26, 329-359.
67. Sabatier, R., Lebreton, J.D. & Chessel, D. (1989) Principal component analysis with instrumental variables as a tool for modelling composition data. Multiway Data Analysis (eds R. Coppi & S. Bolasco ), pp. 341-352. Elsevier Science Publishers B.V., North-Holland.
68. Silvertown, J., McConway, K., Gowing, D., Dodd, M., Fay, M.F., Joseph, J.A. & Dolphin, K. (2006) Absence of phylogenetic signal in the niche structure of meadow plant communities. Proceedings of the Royal Society of London Series B-Biological Sciences, 273, 39-44.
69. Simberloff, D. (1970) Taxonomic diversity of island biotas. Evolution, 24, 23-47.
70. 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.
71. Thioulouse, J., Chessel, D. & Champely, S. (1995) Multivariate analysis of spatial patterns: a unified approach to local and global structures. Environmental and Ecological Statistics, 2, 1-14.
72. Tukey, J. (1977) Exploratory Data Analysis. Addison-Wesley Publishing company, Reading, MA.
73. Valdés, B., Rejdali, M., Achhal, A., Jury, S.L. & Montserrat, J.M. (2002) Catalogue des plantes vasculaires du nord du Maroc, incluant des clés d'identification. CSIC, Madrid.
74. Webb, C.O. (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist, 156, 145-155.
75. Webb, C.O., Ackerly, D.D. & Kembel, S.W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 18, 2098-2100.
76. Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33, 475-505.
77. Wold, S., Esbensen, K. & Geladi, P. (1987) Principal component analysis. Chemometrics and Intelligent Laboratory Systems, 2, 37-52.