10.5061/DRYAD.H5G85
Rangel, Thiago Fernando
Universidade Federal de Goiás
Colwell, Robert K.
University of Colorado Boulder
University of Connecticut
Universidade Federal de Goiás
Graves, Gary R.
Smithsonian Institution
University of Copenhagen
Fučíková, Karolina
University of Connecticut
Rahbek, Carsten
University of Copenhagen
Diniz-Filho, José Alexandre F.
Universidade Federal de Goiás
Data from: Phylogenetic uncertainty revisited: implications for ecological
analyses
Dryad
dataset
2015
Uncertainty quantification
Sensitivity Analysis
2015-03-16T15:22:38Z
2015-03-16T15:22:38Z
en
https://doi.org/10.1111/evo.12644
7590708 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 maximizes 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.
Phylogenetic Uncertain TaxaList of missing species in the backbone
phylogenyHummingbirds Phy - 158 PUT.txtHummingbirds Phylogeny, with Most
Derived Consensus Clades for each Phylogenetic Uncertain TaxaHummingbirds
Phylogeny, with Most Derived Consensus Clades for each Phylogenetic
Uncertain TaxaHummingbirds Phy - MDCC Standard.txt25000 Phylogenies of
McGuire et al. 2007, with MDCCs defined25000 Phylogenies of McGuire et al.
2007, with MDCCs definedHummingbirds Phy - 25000 trees 146spp
MDCC.rarGeographic Grid, with 2868 cells, describing New WorldWH2868 - Geo
Coords.txtPresence/Absence matrix of 304Spp Hummingbird in the Western
Hemisphere GridWH2868 - 304Spp Hummingbird PresAbsMat.txtBodySize of 304
species of HummingbirdsHummingbirds - 304spp BodySize.txtElevational range
of 304 species of hummingbirdsHummingbirds - 304spp ElevRange.txt
South America