author={Carl Boettiger and Graham M. Coop and Peter L. Ralph},
Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a… 

Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model.

An extensive simulation study is conducted to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes, and identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled.

Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

  • D. Bapst
  • Environmental Science
  • 2014
Abstract Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

This paper shows how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well‐known phylogenetic generalized least squares (PGLS) framework, and shows its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.

Phylogenies, the Comparative Method, and the Conflation of Tempo and Mode.

Investigation of the efficacy of phylogenetic comparative methods to distinguish between models that represent different evolutionary processes in a phylogenetic context found that evolutionary inference is straightforward when phenotypic patterns are generated by simple evolutionary processes that are represented by modifying a single model parameter at a time.

How Well Can We Detect Shifts in Rates of Lineage Diversification? A Simulation Study of Sequential AIC Methods

An extensive simulation study is performed demonstrating that MEDUSA has an extremely high Type I error rate, and provides severely biased parameter estimates, and the source(s) of these pathologies are revealed.

A standardized effect size for evaluating and comparing the strength of phylogenetic signal

A non‐parametric, permutation test for the log‐likelihood of an evolutionary model, plus a standardized statistic, Z, from this test, which can be considered a phylogenetic signal effect size, can be used in two‐sample tests to compare the strength of phylogenetics signal for multiple traits.

Intrinsic inference difficulties for trait evolution with Ornstein‐Uhlenbeck models

T theoretical properties of the maximum‐likelihood (ML) estimators for these parameters, including their non‐uniqueness and inaccuracy, are reported, and it is shown that theoretical expectations indeed apply to real trees.

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

It is shown that the Ornstein Uhlenbeck model is frequently incorrectly favoured over simpler models when using Likelihood ratio tests, and that many studies fitting this model use datasets that are small and prone to this problem.

Model Adequacy and the Macroevolution of Angiosperm Functional Traits

This work presents a general statistical framework for assessing the adequacy of phylogenetic trait models and uses this approach to evaluate the statistical performance of commonly used trait models on 337 comparative datasets covering three key Angiosperm functional traits.

How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods

An extensive simulation study is performed demonstrating that MEDUSA has a high false-discovery rate, and provides biased estimates of diversification-rate parameters.



Phylogenies and the Comparative Method

A method of correcting for the phylogeny has been proposed, which specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies.

Statistical tests of models of DNA substitution

  • N. Goldman
  • Biology
    Journal of Molecular Evolution
  • 2004
A test statistics suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsentein.

Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence

Simulations show λ to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses.

A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal

A novel likelihood ratio test is described that compares different topologies (each estimated from a different data partition for the same taxa) to determine if they are significantly different, and indicates that different genes provide significantly different phylogenies for amniotes, supporting earlier suggestions based on less direct tests.


Analysis of variance of log K for all 121 traits indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits, and this work presents new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models.

Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects

Statistics and a null model for estimating phylogenetic effects in comparative data are proposed and a model-independent measure of autocorrelation (Moran's I) is applied for estimating whether cross-taxonomic trait variation is related to phylogeny.

Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

This article explains and develops a method based on the Ornstein‐Uhlenbeck (OU) process, first proposed by Hansen, that allows to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum‐likelihood‐based model selection techniques, and to infer details of the evolutionary process.

Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters

  • M. Pagel
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1994
I present a new statistical method for analysing the relationship between two discrete characters that are measured across a group of hierarchically evolved species or populations. The method

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

  • J. Losos
  • Biology
    The American Naturalist
  • 2011
The best way to fully understand the past is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process, because phylogenies are much more informative about pattern than they are about process.

Phylogenetic Analysis of the Evolutionary Correlation Using Likelihood

The approach presented herein is the first to allow for the explicit testing of how and when the evolutionary covariances between characters have changed in the history of a group.