Phylogenetic uncertainty revisited: Implications for ecological analyses
2015/03/20 by Thiago F. Rangel, Robert K. Colwell, Gary R. Graves +4 · 141 citations
Earth and Planetary Sciences · Environmental Science · #Biology #Clade #Computer science #Ecology #Ecology and Vegetation Dynamics Studies #Evolution and Paleontology Studies #Evolutionary biology #Extant taxon #Genetics #Phylogenetic comparative methods #Phylogenetic tree #Phylogenetics #Taxon #Trait #Wildlife Ecology and Conservation
paper · pdf · doi:10.1111/evo.12644
published in Evolution 69(5), 1301-1312 (Oxford University Press)
openalex publication_date 2015/03/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/27
Abstract
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade-wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.
Citations
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