Metrics and Models of Community Phylogenetics

  • William D. PearseEmail author
  • Andy Purvis
  • Jeannine Cavender-Bares
  • Matthew R. Helmus


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 ( We conclude by discussing future research directions for the field as a whole.


Phylogenetic Community Phylogenetic Structure Dissimilarity Metric Source Pool Phylogenetic Metrics 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We would like to thank László Zsolt Garamszegi for inviting us to contribute this chapter, and three anonymous reviewers for their valuable suggestions and feedback. Marc Cadotte and Gustavo Carvalho shared code for calculating metrics, and A. David and L. McInnes provided useful feedback on this chapter.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • William D. Pearse
    • 1
    Email author
  • Andy Purvis
    • 2
  • Jeannine Cavender-Bares
    • 1
  • Matthew R. Helmus
    • 3
  1. 1.Department Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulUSA
  2. 2.Department of Life SciencesNatural History MuseumLondonUK
  3. 3.Amsterdam Global Change Institute, Department of Animal EcologyVrije UniversiteitAmsterdamThe Netherlands

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