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Metrics and Models of Community Phylogenetics

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Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Abstract

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

The original version of this chapter was revised: Online Practical Material website has been updated. The erratum to this chapter is available at https://doi.org/10.1007/978-3-662-43550-2_23

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Acknowledgments

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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Authors and Affiliations

  1. Department Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, Saint Paul, MN, 55108, USA

    William D. Pearse & Jeannine Cavender-Bares

  2. Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK

    Andy Purvis

  3. Amsterdam Global Change Institute, Department of Animal Ecology, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands

    Matthew R. Helmus

Authors
  1. William D. Pearse
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  2. Andy Purvis
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  3. Jeannine Cavender-Bares
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  4. Matthew R. Helmus
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Corresponding author

Correspondence to William D. Pearse .

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Editors and Affiliations

  1. Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Sevilla, Spain

    László Zsolt Garamszegi

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Pearse, W.D., Purvis, A., Cavender-Bares, J., Helmus, M.R. (2014). Metrics and Models of Community Phylogenetics. In: Garamszegi, L. (eds) Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-43550-2_19

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