treeNODF: nestedness to phylogenetic, functional and other tree-based diversity metrics
Article first published online: 17 APR 2014
© 2014 The Authors. Methods in Ecology and Evolution © 2014 British Ecological Society
Methods in Ecology and Evolution
Volume 5, Issue 6, pages 563–572, June 2014
How to Cite
Melo, A. S., Cianciaruso, M. V., Almeida-Neto, M. (2014), treeNODF: nestedness to phylogenetic, functional and other tree-based diversity metrics. Methods in Ecology and Evolution, 5: 563–572. doi: 10.1111/2041-210X.12185
- Issue published online: 11 JUN 2014
- Article first published online: 17 APR 2014
- Accepted manuscript online: 15 MAR 2014 07:57AM EST
- Manuscript Accepted: 6 MAR 2014
- Manuscript Received: 12 MAY 2013
- Conselho Nacional de Desenvolvimento Científico e Tecnológico. Grant Numbers: 307479/2011-0, 306843/2012-9, 306870/2012-6, 558187/2009-9
- community phylogenetics;
- functional diversity;
- nested overlap based on decreasing fill;
- NODF ;
- phylogenetic diversity
- Available measures of nestedness consider descriptor variables (e.g. species) as equally associated, ignoring evolutionary or ecological dissimilarities. Here, we introduce treeNODF, a new class of nestedness that takes into account the resemblance of descriptor variables.
- The method is an extension of the NODF index and can be applied to systems in which the resemblance of descriptor variables is described by a tree-like object. Computation of treeNODF is similar to NODF, but uses branch lengths instead of the sum of species occurrences. In this way, we can calculate a phyloNODF for metacommunities if a phylogeny is used to account for differences in phylogenetic diversity (PD) and traitNODF if a functional dendrogram constructed from species ecological traits is used to account for the functional diversity (FD) of communities. Similar to NODF, treeNODF can also be used to assess nestedness among species. In this case, envNODF uses a dendrogram describing the resemblance among the environmental conditions of different sites, to test whether rare species occur in a subset of the environmental conditions in the habitats occupied by frequent species.
- treeNODF is a composite metric that can be additively partitioned into compositional (S.fraction) and tree-topology (topoNODF = treeNODF – S.fraction) components of the descriptor variables. Tests of treeNODF and its components can be carried out using null models and, if a hypothetical factor is used to order metacommunity data, permutation tests. We show that treeNODF is robust for matrix size and fill, as well as for tree topology.
- Finally, we illustrate the use of treeNODF by analysing data on Caribbean bats using phyloNODF, traitNODF and envNODF, as well as their composition and tree-topology components.