Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components

Journal of Biogeography

Volumn 41, Issue 4, 2014, Pages 749-761

  Cardoso, Pedro ^a,b   Rigal, François ^b   Carvalho, José C ^b,c   Fortelius, Mikael ^a,d   Borges, Paulo A V ^b   Podani, Janos ^e,f   Schmera, Denes ^f,g  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF THE AZORES   (Portugal)

^c UNIVERSITY OF MINHO   (Portugal)

^d UNIVERSITY OF HELSINKI   (Finland)

^e EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^f INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^g UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Arthropods; Azores; Beta diversity metrics; Differentiation; Dissimilarity; European mammals; Functional diversity; Phylogenetic diversity; Taxonomic diversity; Turnover

Indexed keywords

ARTHROPOD; ASSEMBLY RULE; COMMUNITY ECOLOGY; EMPIRICAL ANALYSIS; FUNCTIONAL GROUP; MAMMAL; PHYLOGENETICS; SPECIES DIVERSITY; SPECIES RICHNESS; TAXONOMY; TURNOVER;

AZORES; EUROPE; PORTUGAL;

ARTHROPODA; MAMMALIA;

EID: 84896134838     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12239     Document Type: Article

References (60)

1. Agustí, J. (1990) The Miocene rodent succession in eastern Spain: a zoogeographical appraisal. European Neogene mammal chronology (ed. by E.H. Lindsay, V. Fahlbusch and P. Mein ), pp. 375-404. Plenum Press, New York.
2. Almeida-Neto, M., Frensel, D.M.B. & Ulrich, W. (2012) Rethinking the relationship between nestedness and beta diversity: a comment on Baselga (2011). Global Ecology and Biogeography, 21, 772-777.
3. Anderson, M.J., Crist, T.O., Chase, J.M., Vellend, M., Inouye, B.D., Freestone, A.L., Sanders, N.J., Cornell, H.V., Comita, L.S., Davies, K.F., Harrison, S.P., Kraft, N.J.B., Stegen, J.C. & Swenson, N.G. (2011) Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecology Letters, 14, 19-28.
4. Baiser, B., Olden, J.D., Record, S., Lockwood, J.L. & McKinney, M.L. (2012) Pattern and process of biotic homogenization in the New Pangaea. Proceedings of the Royal Society B: Biological Sciences, 279, 4772-4777.
5. Baselga, A. (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, 134-143.
6. Baselga, A. (2012) The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography, 21, 1223-1232.
7. Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., MacPhee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L. & Purvis, A. (2007) The delayed rise of present-day mammals. Nature, 446, 507-512.
8. Bryant, J.A., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J. & Green, J.L. (2008) Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences USA, 105, 11505-11511.
9. Cadotte, M.W., Davies, T.J., Regetz, J., Kembel, S.W., Cleland, E. & Oakley, T.H. (2010) Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13, 96-105.
10. Cardoso, P., Borges, P.A.V. & Veech, J.A. (2009) Testing the performance of beta diversity measures based on incidence data: the robustness to undersampling. Diversity and Distributions, 15, 1081-1090.
11. Cardoso, P., Rigal, F., Fattorini, S., Terzopoulou, S. & Borges, P.A.V. (2013) Integrating landscape disturbance and indicator species in conservation studies. PLoS ONE, 8, e63294.
12. Carvalho, J.C., Cardoso, P. & Gomes, P. (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, 760-771.
13. Carvalho, J.C., Cardoso, P., Borges, P.A.V., Schmera, D. & Podani, J. (2013) Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches. Oikos, 122, 825-834.
14. Casanovas-Vilar, I. & Agustí, J. (2007) Ecogeographical stability and climate forcing in the Late Miocene (Vallesian) rodent record of Spain. Palaeogeography, Palaeoclimatology, Palaeoecology, 248, 169-189.
15. Chao, A., Chiu, C.-H. & Jost, L. (2010) Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B: Biological Sciences, 365, 3599-3609.
16. Costeur, L. & Legendre, S. (2008) Spatial and temporal variation in European Neogene large mammals diversity. Palaeogeography, Palaeoclimatology, Palaeoecology, 261, 127-144.
17. Culver, D.C. & Pipan, T. (2009) Biology of caves and other subterranean habitats. Oxford University Press, Oxford.
18. Devictor, V., Mouillot, D., Meynard, C., Jiguet, F., Thuiller, W. & Mouquet, N. (2010) Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecology Letters, 13, 1030-1040.
19. Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
20. Feng, G., Zhang, J.-L., Pei, N.-C., Rao, M.-D., Mi, X.-C., Ren, H.-B. & Ma, K.-P. (2012) Comparison of phylobetadiversity indices based on community data from Gutianshan forest plot. Chinese Science Bulletin, 57, 623-630.
21. Gotelli, N.J. (2000) Null model analysis of species co-occurrence patterns. Ecology, 81, 2606-2621.
22. Gotelli, N.J., Buckley, N.J. & Wiens, J.A. (1997) Co-occurrence of Australian land birds: Diamond's assembly rules revisited. Oikos, 80, 311-324.
23. Graham, C. & Fine, P. (2008) Phylogenetic beta diversity: linking ecological and evolutionary processes across space and time. Ecology Letters, 11, 1265-1277.
24. Heikinheimo, H., Fortelius, M., Eronen, J. & Mannila, H. (2007) Biogeography of European land mammals shows environmentally distinct and spatially coherent clusters. Journal of Biogeography, 34, 1053-1064.
25. Helmus, M.R., Bland, T.J., Williams, C.K. & Ives, A.R. (2007) Phylogenetic measures of biodiversity. The American Naturalist, 169, E68-E83.
26. Jost, L. (2007) Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427-2439.
27. Kelley, L.A., Gardner, S.P. & Sutcliffe, M.J. (1996) An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Engineering, 9, 1063-1065.
28. Kluge, J. & Kessler, M. (2011) Phylogenetic diversity, trait diversity and niches: species assembly of ferns along a tropical elevational gradient. Journal of Biogeography, 38, 394-405.
29. Lande, R. (1996) Statistics and partitioning of species diversity, and similarity among multiple communities. Oikos, 76, 5-13.
30. Legendre, P. & Legendre, L. (2012) Numerical ecology, 3rd edn. Elsevier, Amsterdam.
31. Lennon, J.J., Koleff, P., Greenwood, J.J.D. & Gaston, K.J. (2001) The geographical structure of British bird distributions: diversity, spatial turnover and scale. Journal of Animal Ecology, 70, 966-979.
32. Leprieur, F., Albouy, C., De Bortoli, J., Cowman, P.F., Bellwood, D.R. & Mouillot, D. (2012) Quantifying phylogenetic beta diversity: distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients. PLoS ONE, 7, e42760.
33. Lozupone, C.A. & Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied Environmental Microbiology, 71, 8228-8235.
34. Maridet, O., Escarguel, G., Costeur, L., Mein, P., Hugueney, M. & Legendre, S. (2007) Small mammal (rodents and lagomorphs) European biogeography from the Late Oligocene to the mid Pliocene. Global Ecology and Biogeography, 16, 529-544.
35. Marini, L., Bertolli, A., Bona, E., Federici, G., Martini, F., Prosser, F. & Bommarco, R. (2013) Beta-diversity patterns elucidate mechanisms of alien plant invasion in mountains. Global Ecology and Biogeography, 22, 450-460.
36. van der Meulen, A.J., García-Paredes, I., Álvarez-Sierra, M.Á., van den Hoek Ostende, L.W., Hordijk, K., Oliver, A., López-Guerrero, P., Hernández-Ballarín, V. & Peláez-Campomanes, P. (2011) Biostratigraphy or biochronology? Lessons from the Early and Middle Miocene small mammal events in Europe. Geobios, 44, 309-321.
37. Meynard, C.N., Devictor, V., Mouillot, D., Thuiller, W., Jiguet, F. & Mouquet, N. (2011) Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France? Global Ecology and Biogeography, 20, 893-903.
38. Mitchell-Jones, A.J., Amori, G., Bogdanowicz, W., Krystufek, B., Reijnders, P.J.H., Spitzenberger, F., Stubbe, M., Thissen, J.B.M., Vohralík, V. & Zima, J. (1999) The atlas of European mammals. T. & A.D. Poyser and Academic Press, London.
39. Nipperess, D.A., Faith, D.P. & Barton, K. (2010) Resemblance in phylogenetic diversity among ecological assemblages. Journal of Vegetation Science, 21, 809-820.
40. Paradis, E., Claude, J. & Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
41. Petchey, O.L. & Gaston, K.J. (2002) Functional diversity (FD), species richness and community composition. Ecology Letters, 5, 402-411.
42. Petchey, O.L. & Gaston, K.J. (2006) Functional diversity: back to basics and looking forward. Ecology Letters, 9, 741-758.
43. Podani, J. & Schmera, D. (2011) A new conceptual and methodological framework for exploring and explaining pattern in presence-absence data. Oikos, 120, 1625-1638.
44. Podani, J., Ricotta, C. & Schmera, D. (2013) A general framework for analyzing beta diversity, nestedness and related community-level phenomena based on abundance data. Ecological Complexity, 15, 52-61.
45. R Development Core Team (2010) R: a language and environment for statistical computing. Version 2.13.0. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.r-project.org/.
46. Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24-43.
47. Ricotta, C. & Burrascano, S. (2008) Beta diversity for functional ecology. Preslia, 80, 61-71.
48. Ricotta, C., Bacaro, G., Marignani, M., Godefroid, S. & Mazzoleni, S. (2012) Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions? Oecologia, 170, 501-506.
49. Rook, L., Gallai, G. & Torre, D. (2006) Lands and endemic mammals in the Late Miocene of Italy: constraints for paleogeographic outlines of Tyrrhenian area. Palaeogeography, Palaeoclimatology, Palaeoecology, 238, 263-269.
50. Schmera, D. & Podani, J. (2011) Comments on the separating components of beta diversity. Community Ecology, 12, 153-160.
51. Silvertown, J., Ortega, J.F. & Carine, M. (2005) The monophyly of island radiations: an evaluation of niche pre-emption and some alternative explanations. Journal of Ecology, 93, 653-657.
52. Stegen, J.C. & Hurlbert, A.H. (2011) Inferring eco-evolutionary processes from taxonomic, phylogenetic and functional trait β-diversity. PLoS ONE, 6, e20906.
53. Swenson, N.G. (2011) Phylogenetic beta diversity metrics, trait evolution and inferring the functional beta diversity of communities. PLoS ONE, 6, e21264.
54. Tilman, D., Reich, P.B., Knops, J., Wedin, D., Mielke, T. & Lehman, C. (2001) Diversity and productivity in a long-term grassland experiment. Science, 294, 843-845.
55. Veech, J., Summerville, K., Crist, T. & Gering, J. (2002) The additive partitioning of species diversity: recent revival of an old idea. Oikos, 99, 3-9.
56. Villéger, S., Miranda, J.R., Hernandez, D.F. & Mouillot, D. (2012) Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities. PLoS ONE, 7, e40679.
57. Villéger, S., Grenouillet, G. & Brosse, S. (2013) Decomposing functional β-diversity reveals that low functional β-diversity is driven by low functional turnover in European fish assemblages. Global Ecology and Biogeography, 22, 671-681.
58. Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology, Evolution, and Systematics, 33, 475-505.
59. Whittaker, R.H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279-338.
60. Whittaker, R.J. & Fernández-Palacios, J.M. (2007) Island biogeography: ecology, evolution, and conservation, 2nd edn. Oxford University Press, Oxford.