Shedding light on the ‘dark side’ of phylogenetic comparative methods

Model Adequacy and the Macroevolution of Angiosperm Functional Traits

(2015) Matthew W. Pennell et al.   AMERICAN NATURALIST

A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies

(2015) Natalie Cooper et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

How much of the world is woody?

(2014) Richard G. FitzJohn et al.   JOURNAL OF ECOLOGY

The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters

(2014) Wayne P. Maddison et al.   SYSTEMATIC BIOLOGY

Correction to ‘Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary’, and a note on fitting macroevolutionary models to comparative paleontological data sets

(2014) Graham J. Slater   Methods in Ecology and Evolution

Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models

(2014) Lam Si Tung Ho et al.   Methods in Ecology and Evolution

Asymptotic theory with hierarchical autocorrelation: Ornstein–Uhlenbeck tree models

(2013) Lam Si Tung Ho et al.   ANNALS OF STATISTICS

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology

(2013) Matthew W. Pennell et al.   Annals of the New York Academy of Sciences

Early origin of viviparity and multiple reversions to oviparity in squamate reptiles

(2013) R. Alexander Pyron et al.   ECOLOGY LETTERS

Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae

(2013) Thomas J. Givnish et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations

(2013) D. L. Mahler et al.   SCIENCE

Evolutionary Inferences from Phylogenies: A Review of Methods

(2012) Brian C. O'Meara   Annual Review of Ecology Evolution and Systematics

IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS

(2012) Carl Boettiger et al.   EVOLUTION

MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION

(2012) Jeremy M. Beaulieu et al.   EVOLUTION

Heavy use of equations impedes communication among biologists

(2012) T. W. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tempo of trophic evolution and its impact on mammalian diversification

(2012) S. A. Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anatomical enablers and the evolution of C4photosynthesis in grasses

(2012) Pascal-Antoine Christin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interpreting the Evolutionary Regression: The Interplay Between Observational and Biological Errors in Phylogenetic Comparative Studies

(2012) Thomas F. Hansen et al.   SYSTEMATIC BIOLOGY

Independent Contrasts and PGLS Regression Estimators Are Equivalent

(2012) Simon P. Blomberg et al.   SYSTEMATIC BIOLOGY

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology

(2011) Jonathan B. Losos   AMERICAN NATURALIST

MOTMOT: models of trait macroevolution on trees

(2011) Gavin H. Thomas et al.   Methods in Ecology and Evolution

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Body Size Evolution in Mammals: Complexity in Tempo and Mode

(2010) Natalie Cooper et al.   AMERICAN NATURALIST

Niche conservatism as an emerging principle in ecology and conservation biology

(2010) John J. Wiens et al.   ECOLOGY LETTERS

Species Selection Maintains Self-Incompatibility

(2010) E. E. Goldberg et al.   SCIENCE

Quantitative Traits and Diversification

(2010) Richard G. FitzJohn   SYSTEMATIC BIOLOGY

The seven deadly sins of comparative analysis

(2009) R. P. FRECKLETON   JOURNAL OF EVOLUTIONARY BIOLOGY

Phylogenetic Logistic Regression for Binary Dependent Variables

(2009) Anthony R. Ives et al.   SYSTEMATIC BIOLOGY

Macroecology and extinction risk correlates of frogs

(2007) Natalie Cooper et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY