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.
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.
This is a preview of subscription content, log in to check access.
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.
Ackerly DD, Schwilk DW, Webb CO (2006) Niche evolution and adaptive radiation: testing the order of trait divergence. Ecology 87:S50–S61CrossRefGoogle Scholar
Agapow P-M, Purvis A (2002) Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst Biol 51(6):866–872CrossRefGoogle Scholar
Fritz SA, Purvis A (2010) Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conserv Biol 24(4):1042–1051CrossRefGoogle Scholar
Graham CH, Fine PVA (2008) Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett 11(12):1265–1277CrossRefGoogle Scholar
Haegeman B, Loreau M (2008) Limitations of entropy maximization in ecology. Oikos 117:1700–1710CrossRefGoogle Scholar
Heard SB, Cox GH (2007) The shapes of phylogenetic trees of clades, faunas, and local assemblages: exploring spatial pattern in differential diversification. Am Nat 169(5):E107–E118CrossRefGoogle Scholar
Mayfield MM, Levine JM (2010) Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol Lett 13(9):1085–1093CrossRefGoogle Scholar
Mooers AØ, Heard SB (1997) Inferring evolutionary process from phylogenetic tree shape. Q Rev Biol 72(1):31–54CrossRefGoogle Scholar
Mouquet N et al (2012) Ecophylogenetics: advances and perspectives. Biol Rev 87(4):769–785CrossRefGoogle Scholar
Pagel M (1999) Inferring the historical patterns of biological evolution. Nature 401(6756):877–884CrossRefGoogle Scholar
Parra JL, McGuire JA, Graham CH (2010) Incorporating clade identity in analyses of phylogenetic community structure: an example with hummingbirds. Am Nat 176(5):573–587CrossRefGoogle Scholar
Pavoine S, Bonsall MB (2011) Measuring biodiversity to explain community assembly: a unified approach. Biol Rev 86(4):792–812CrossRefGoogle Scholar
Pavoine S, Ollier S, Dufour A-B (2005) Is the originality of a species measurable? Ecol Lett 8(6):579–586CrossRefGoogle Scholar
Pearse WD, Jones A, Purvis A (2013) Barro Colorado Island’s phylogenetic assemblage structure across fine spatial scales and among clades of different ages. Ecology 94(12):2861–2872CrossRefGoogle Scholar
Peres-Neto PR, Leibold MA, Dray S (2012) Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics. Ecology 93:S14–S30CrossRefGoogle Scholar
Pillar VD, Duarte LS (2010) A framework for metacommunity analysis of phylogenetic structure. Ecol Lett 13(5):587–596CrossRefGoogle Scholar
Pybus OG, Harvey PH (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc Roy Soc B Biol Sci 267(1459):2267–2272CrossRefGoogle Scholar
R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar