Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

Ecology

Volumn 91, Issue 9, 2010, Pages 2514-2521

  Ovaskainen, Otso ^a   Hottola, Jenni ^a,b   Shtonen, Juha ^b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Bayesian inference; Dead wood; Logistic regression; Multivariate model; Polypore; Species community; Species interaction; Wood decaying fungi

Indexed keywords

BAYESIAN ANALYSIS; COEXISTENCE; DEAD WOOD; EXPERIMENTAL STUDY; FUNGUS; HABITAT SELECTION; LOGISTICS; MULTIVARIATE ANALYSIS;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; ECOSYSTEM; FUNGUS; MICROBIOLOGY; MULTIVARIATE ANALYSIS; PHYSIOLOGY; POPULATION DYNAMICS; STATISTICAL MODEL; WOOD;

ECOSYSTEM; FUNGI; LOGISTIC MODELS; MODELS, BIOLOGICAL; MULTIVARIATE ANALYSIS; POPULATION DYNAMICS; WOOD;

FUNGI;

EID: 77956572723     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/10-0173.1     Document Type: Article

References (27)

1. Barnard, J., R. McCulloch, and X. L. Meng. 2000. Modeling covariance matrices in terms of standard deviations and correlations, with, application to shrinkage. Statistica Sinica 10:1281-1311.
2. Boddy, L. 2000. Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiology Ecology 31:185-194.
3. Clark, J. S. 2005. Why environmental scientists are becoming Bayesians. Ecology Letters 8:2-14. (Pubitemid 40172132)
4. Connor, E. F., and D. Simberloff. 1979. The assembly of species communities: chance or competition. Ecology 60: 1132-1140.
5. Cressie, N., C. A. Calder, J. S. Clark, J. M. V. Hoef, and. C. K. Wikle. 2009. Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling. Ecological Applications 19:553-570.
6. Diamond, J. M. 1975. Assembly of species communities. Pages 342-444 in M. Cody and J. Diamond, editors. Ecology and evolution of communities. Harvard University Press, Cambridge, Massachusetts, USA.
7. Diez, J. M., and H. R. Pulliam. 2007. Hierarchical analysis of species distributions and abundance across environmental, gradients. Ecology 88:3144-3152.
8. Ferrier, S., and A. Guisan. 2006. Spatial, modelling of biodiversity at the community level, Journal of Applied Ecology 43:393-404. (Pubitemid 43725544)
9. Gotelli, N. J, 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606-2621.
10. Gotelli, N. J., and. D. J. McCabe. 2002. Species co-occurrence: a meta-analysis of J. M. Diamond's assembly rules model. Ecology 83:2091-2096.
11. Hastings, A. 1987. Can. competition be detected using species co-occurrence data? Ecology 68:117-123.
12. Heilmann-Clausen, J., and L. Boddy. 2005. Inhibition and stimulation effects in. communities of wood decay fungi: exudates from colonized wood influence growth by other species. Microbial Ecology 49:399-406. (Pubitemid 41130751)
13. Holmes, C. C, and. H. Leonhard. 2006. Bayesian auxiliary variable models for binary and multinomial regression, Bayesian Analysis 1:145-168.
14. Jonsson, B. G., N. Kruys, and T. Ranius. 2005. Ecology of species living on dead wood: lessons for dead wood management. Silva Fennica 39:289-309. (Pubitemid 41542765)
15. Kelt, D. A., M. L. Taper, and. P. L. Meserve. 1995. Assessing the impact of competition on community assembly: a case study using small mammals. Ecology 76:1283-1296.
16. Latimer, A. M., S. Banerjee, H, Sang, E. S. Mosher, and J. A. Silander. 2009. Hierarchical models facilitate spatial analysis of large data sets: a case study on invasive plant species in the northeastern United States. Ecology Letters 12:144-154.
17. Leathwick, J. R., J. Elith, and T. Hastie. 2006. Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. Ecological Modelling 199:188-196.
18. Lilja, S., and T. Kuuluvainen. 2005. Structure of old Pinus sylvestris dominated forest stands along a geographic and human, impact gradient in mid-boreal Fennoscandia. Silva Fennica 39:407-428.
19. Lonsdale, D., M. Pautasso, and O. Holdenrieder. 2008. Wooddecaying fungi in the forest: conservation needs and management options. European Journal of Forest Research 127:1-22. (Pubitemid 50011017)
20. Niemelä, T. 2005. Polypores, lignicolous fungi. Helsinki University Press, Helsinki, Finland.
21. Niemelä, T., P. Renvall, and R. Penttilä. 1995. Interactions of fungi at late stages of wood decomposition. Annales Botanici Fennici 32:141-152. (Pubitemid 26469685)
22. O'Brien, S. M., and D. B. Dunson. 2004. Bayesian multivariate logistic regression, Biometrics 60:739-746.
23. Ovaskainen, O., J. Nokso-Koivisto, J. Hottola, T. Rajala, T. Pennanen, H. Ali-Kovero, O. Miettinen, P. Oinonen, P. Auvinen, L. Paulin, K.-H. Larsson, and R. Mäkipää. 2010. Identifying wood-inhabiting fungi with 454 sequencing: what is the probability that BLAST gives the correct species? Fungal Ecology, in press, [doi: 10.1016/j.funeco.2010.01.001]
24. Peres-Neto, P. R., J. D. Olden, and D. A. Jackson. 2001. Environmentally constrained null models: site suitability as occupancy criterion. Oikos 93:110-120.
25. Renvall, P. 1995. Community structure and dynamics of woodrotting Basidiomycetes on decomposing conifer trunks in northern Finland, Karstenia 35:1-51.
26. Rouvinen, S., T. Kuuluvainen, and L. Karjalainen. 2002. Coarse woody debris in old Pinus sylvestris dominated forests along a geographic and human impact gradient in boreal Fennoscandia. Canadian Journal of Forest Research 32: 2184-2200.
27. Siitonen, J. 2001. Forest management, coarse woody debris and saproxylic organisms: Fennoscandian boreal forests as an example. Ecological Bulletins 49:11-41.