Using null model analysis of species co-occurrences to deconstruct biodiversity patterns and select indicator species

Diversity and Distributions

Volumn 15, Issue 6, 2009, Pages 958-971

  Azeria, Ermias T ^a,b   Fortin, Daniel ^a   Hébert, Christian ^b   Peres Neto, Pedro ^c   Pothier, David ^b   Ruel, Jean Claude ^b  

^a LAURENTIAN FORESTRY CENTRE   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

Biodiversity deconstruction; Boreal forest; Co occurrence; Indicator species; Null model analysis

Indexed keywords

BEETLE; BIODIVERSITY; BOREAL FOREST; CLUSTER ANALYSIS; ECOSYSTEM RESPONSE; HABITAT QUALITY; SPECIES DIVERSITY; SPECIES OCCURRENCE; SPECIES RICHNESS;

CANADA; NORTH AMERICA; QUEBEC [CANADA];

COLEOPTERA;

EID: 70349925236     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/j.1472-4642.2009.00613.x     Document Type: Article

References (51)

1. Azeria, E.T., Carlson, A., Pärt, T. Wiklund, C.G. (2006) Temporal dynamics and nestedness of an oceanic island bird fauna. Global Ecology and Biogeography, 15, 328 338.
2. Azeria, E.T., Sanmartín, I., Ås, S., Carlson, A. Burgess, N. (2007) Biogeographic patterns of the East African coastal forest vertebrate fauna. Biodiversity and Conservation, 16, 883 912.
3. Azeria, E.T., Fortin, D., Lemaître, J., Janssen, P., Hébert, C., Darveau, M. Cumming, S.G. (2009) Fine-scale structure and cross-taxon congruence of bird and beetle assemblages in an old-growth boreal forest mosaic. Global Ecology and Biogeography, 18, 333 345.
4. Batáry, P., Báldi, A., Szél, G., Podlussány, A., Rozner, I. Erdõs, S. (2007) Responses of grassland specialist and generalist beetles to management and landscape complexity. Diversity and Distributions, 13, 196 202.
5. Blamires, D., de Oliveira, G., de Souza Barreto, B. Diniz-Filho, J.A.F. (2008) Habitat use and deconstruction of richness patterns in Cerrado birds. Acta Oecologica, 33, 97 104.
6. Chust, G., Pretus, J.L., Ducrot, D. Ventura, D. (2004) Scale dependency of insect assemblages in response to landscape pattern. Landscape Ecology, 19, 41 57.
7. Colwell, R.K. (2005) Estimates: statistical estimation of species richness and shared species from samples, version 8.0. User's guide and application. Available at: http://purl.oclc.org/estimates (accessed 15 January 2009).
8. Efron, B. Tibshirani, R. (1997) Improvements on cross-validation: The.632+ bootstrap method. Journal of the American Statistical Association, 92, 548 560.
9. Ferrier, S. Guisan, A. (2006) Spatial modelling of biodiversity at the community level. Journal of Applied Ecology, 43, 393 404.
10. Fleishman, E. Mac Nally, R. (2002) Topographic determinants of faunal nestedness in Great Basin butterfly assemblages. Conservation Biology, 16, 422 429.
11. Fleishman, E., Noss, R.F. Noon, B.R. (2006) Utility and limitations of species richness metrics for conservation planning. Ecological Indicators, 6, 543 553.
12. Furnival, G.M. Wilson, R.W. (1974) Regression by leaps and bounds. Technometrics, 16, 499.
13. Giokas, S. Sfenthourakis, S. (2008) An improved method for the identification of areas of endemism using species co-occurrences. Journal of Biogeography, 35, 893 902.
14. Gotelli, N.J. (2000) Null model analysis of species co-occurrence patterns. Ecology, 81, 2606 2621.
15. Gotelli, N.J. Entsminger, G.L. (2006) EcoSim: null models software for ecology, version 7.0. Acquired Intelligence Inc. and Kesey-Bear, Jericho, VT. Available at: http://garyentsminger.com/ecosim/index.htm (accessed on 25 April 2007).
16. Guisan, A. Thuiller, W. (2005) Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8, 993 1009.
17. Guisan, A., Lehmann, A., Ferrier, S., Austin, M., Overton, J.M.C., Aspinall, R. Hastie, T. (2006) Making better biogeographical predictions of species' distributions. Journal of Applied Ecology, 43, 386 392.
18. Hoeting, J.A., Madigan, D., Raftery, A.E. Volinsky, C.T. (1999) Bayesian model averaging: a tutorial. Statistical Science, 14, 382 417.
19. Hubálek, Z. (1982) Coefficients of association and similarity, based on binary (presence-absence) data: an evaluation. Biological Reviews, 57, 669 689.
20. Janssen, P., Fortin, D. Hébert, C. (2009) Beetle diversity in a matrix of old-growth boreal forest: Influence of habitat heterogeneity at multiple scales. Ecography, 32, 423 432.
21. Karr, J.R. (1981) Assessment of biotic integrity using fish communities. Fisheries, 6, 21 27.
22. 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.
23. Lassau, S.A., Hochuli, D.F., Cassis, G. Reid, C.A.M. (2005) Effects of habitat complexity on forest beetle diversity: do functional groups respond consistently? Diversity and Distributions, 11, 73 82.
24. Legendre, P. Legendre, L. (1998) Numerical ecology, 2nd Edn, Elsevier Science B.V., Amsterdam, The Netherlands.
25. Lumley, T. Miller, A. (2004) leaps: Regression Subset Selection. R package version 2.7, Available at: http://CRAN.R-project.org/web/packages/leaps (accessed on 30 April 2008).
26. Mac Nally, R. Fleishman, E. (2004) A successful predictive model of species richness based on indicator species. Conservation Biology, 18, 646 654.
27. Mac Nally, R., Bennett, A.F., Brown, G., Lumsden, L.F., Yen, A.L., Hinkley, S., Lilywhite, P. Ward, D.F. (2002) How well do ecosystem-based planning units represent different components of biodiversity. Ecological Applications, 12, 900 912.
28. Mac Nally, R., Fleishman, E., Thomson, J.R. Dobkin, D.S. (2008) Use of guilds for modelling avian responses to vegetation in the Intermountain West (USA). Global Ecology and Biogeography, 17, 758 769.
29. MacArthur, R.H. (1972) Geographical ecology: patterns in the distribution of species, Princeton University Press, Princeton, NJ.
30. Marquet, P.A., Fernández, M., Navarrete, S.A. Valdovinos, C. (2004) Diversity emerging: toward a deconstruction of biodiversity patterns. In M. Lomolino L.R. Heaney (eds) Frontiers of biogeography: new directions in the geography of nature. pp. 191-209. Sinauer Associates Inc., Sunderland, MA.
31. McGeoch, M.A. (1998) The selection, testing and application of terrestrial insects as bioindicators. Biological Reviews, 73, 181 201.
32. Miller, A.J. (1990) Subset selection in regression, Chapman-Hall, New York.
33. Noss, R.F. (1990) Indicators for monitoring biodiversity: a hierarchical approach. Conservation Biology, 4, 355 364.
34. O'Connell, T.J., Jackson, L.E. Brooks, R.P. (2000) Bird guilds as indicators of ecological condition in the central Appalachians. Ecological Application, 10, 1706 1721.
35. Peres-Neto, P.R. (2004) Patterns in the co-occurrence of fish species in streams: the role of site suitability, morphology and phylogeny versus species interactions. Oecologia, 140, 352 360.
36. Peres-Neto, P.R. Olden, J.D. (2001) Assessing the robustness of randomization tests: examples from behavioural studies. Animal Behaviour, 61, 79 86.
37. Peres-Neto, P.R., Jackson, D.A. Somers, K.M. (2003) Giving meaningful interpretation to ordination axes: Assessing loading significance in principal component analysis. Ecology, 84, 2347 2363.
38. Pham, A.T., De Grandpré, L., Gauthier, S. Bergeron, Y. (2004) Gap dynamics and replacement patterns in gaps of the northeastern boreal forest of Quebec. Canadian Journal of Forest Research, 34, 353 364.
39. R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org (accessed on 24 November 2008)
40. Raftery, A.E., Hoeting, J.A., Volinsky, C.T. Painter, I. (2005) BMA: Bayesian model averaging, R package version 3.0. Available at: http://CRAN.R-project.org/web/packages/BMA (accessed on 30 April 2008).
41. Rejmánek, M. Lepš, J. (1996) Negative associations can reveal interspecific competition and reversal of competitive hierarchies during succession. Oikos, 76, 161 168.
42. Ricklefs, R.E. (2004) A comprehensive framework for global patterns in biodiversity. Ecology Letters, 7, 1 15.
43. Sanderson, J.G. (2004) Null model analysis of communities on gradients. Journal of Biogeography, 31, 879 883.
44. Sfenthourakis, S., Tzanatos, E. Giokas, S. (2006) Species co-occurrence: the case of congeneric species and a causal approach to patterns of species association. Global Ecology and Biogeography, 15, 39 49.
45. Similä, M., Kouki, J., Mönkkönen, M., Sippola, A.-.L. Huhta, E. (2006) Co-variation and indicators of species diversity: Can richness of forest-dwelling species be predicted in northern boreal forests? Ecological Indicators, 6, 686 700.
46. Tews, J., Brose, U., Grimm, V., Tielbörger, K., Wichmann, M.C., Schwager, M. Jeltsch, F. (2004) Animal species diversity driven by habitat heterogeneity/;diversity: the importance of keystone structures. Journal of Biogeography, 31, 79 92.
47. Thomson, J.R., Fleishman, E., Mac Nally, R. Dobkin, D.S. (2007) Comparison of predictor sets for species richness and the number of rare species of butterflies and birds. Journal of Biogeography, 34, 90 101. (Pubitemid 44952532)
48. White, D. (2009) Maptree: Mapping, pruning, and graphing tree models. R package version 1.4-5. Available at: http://cran.r-project.org/web/packages/ maptree (accessed on 30 June 2009).
49. Wiens, J.A., Hayward, G.D., Holthausen, R.S. Wisdom, M.J. (2008) Using surrogate species and groups for conservation planning and management. BioScience, 58, 241 252.
50. Wintle, B.A., McCarthy, M.A., Volinsky, C.T. Kavanagh, R.P. (2003) The use of Bayesian model averaging to better represent uncertainty in ecological models. Conservation Biology, 17, 1579 1590.
51. Wintle, B.A., Elith, J. Potts, J.M. (2005) Fauna habitat modelling and mapping: a review and case study in the Lower Hunter Central Coast region of NSW. Austral Ecology, 30, 719 738.