Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

pp 451-464


Metrics and Models of Community Phylogenetics

  • William D. PearseAffiliated withDepartment Ecology, Evolution, and Behavior, University of Minnesota Email author 
  • , Andy PurvisAffiliated withDepartment of Life Sciences, Natural History Museum
  • , Jeannine Cavender-BaresAffiliated withDepartment Ecology, Evolution, and Behavior, University of Minnesota
  • , Matthew R. HelmusAffiliated withAmsterdam Global Change Institute, Department of Animal Ecology, Vrije Universiteit

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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.