title: Phylogenetic uncertainty revisited: Implications for ecological analyses.
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.
authors: Departmento de Ecologia, Universidade Federal de Goiás, CP 131, Goiânia, GO, Brasil, 74.001-970. thiago.rangel@ufg.br.
authors: Thiago F
authors: TF
authors: Rangel
authors: Departmento de Ecologia, Universidade Federal de Goiás, CP 131, Goiânia, GO, Brasil, 74.001-970.|Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, Connecticut, 06269-3043.|Museum of Natural History, University of Colorado, Boulder, Colorado, 80309.
authors: Robert K
authors: RK
authors: Colwell
authors: Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013.|Department of Biology, Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen O, Denmark.
authors: Gary R
authors: GR
authors: Graves
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, Connecticut, 06269-3043.
authors: Karolina
authors: K
authors: Fučíková
authors: Department of Biology, Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen O, Denmark.
authors: Carsten
authors: C
authors: Rahbek
authors: Departmento de Ecologia, Universidade Federal de Goiás, CP 131, Goiânia, GO, Brasil, 74.001-970.
authors: José Alexandre F
authors: JA
authors: Diniz-Filho
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D004463:Ecology / Q000379:methods; D017753:Ecosystem; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny; D012984:Software; D035501:Uncertainty
keywords: Hummingbirds; sensitivity analysis; uncertainty quantification