Metrics and Models of Community Phylogenetics
Community phylogenetics combines ideas from community ecology and evolutionary biology, using species phylogeny to explore the processes underlying ecological community assembly. Here, we describe the development of the field’s comparative methods and their roots in conservation biology, biodiversity quantification, and macroevolution. Next, we review the multitude of community phylogenetic structure metrics and place each into one of four classes: shape, evenness, dispersion, and dissimilarity. Shape metrics examine the structure of an assemblage phylogeny, while evenness metrics incorporate species abundances. Dispersion metrics examine assemblages given a phylogeny of species that could occupy those assemblages (the source pool), while dissimilarity metrics compare phylogenetic structure between assemblages. We then examine how metrics perform in simulated communities that vary in their phylogenetic structure. We provide an example of model-based approaches and argue that they are a promising area of future research in community phylogenetics. Code to reproduce all these analyses is available in the Online Practical Material (http://www.mpcm-evolution.org). We conclude by discussing future research directions for the field as a whole.
- Darwin C (1859) On the origin of species. John Murray, LondonGoogle Scholar
- Ho LST, Ane C (2014). A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Syst Biol 63:397–408Google Scholar
- Jaccard P (1901) Etude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull de la Soc Vaudoise des Sci Nat 37:547–579Google Scholar
- Magurran AE (2004). Measuring biological diversity. Oxford University Press, OxfordGoogle Scholar
- R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
- Vellend M et al. (2011) “Measuring phylogenetic biodiversity”. In: Magurran AE, McGill BJ Biological Diversity, Oxford University Press, Oxford Chap. 14Google Scholar