Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

@article{Butler2004PhylogeneticCA,
  title={Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution},
  author={Marguerite A Butler and Aaron A. King},
  journal={The American Naturalist},
  year={2004},
  volume={164},
  pages={683 - 695}
}
Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein‐Uhlenbeck (OU) process, first proposed by Hansen. Ornstein‐Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion… Expand

Topics from this paper

Stochastic Models in Phylogenetic Comparative Methods: Analytical Properties and Parameter Estimation
TLDR
This thesis addresses the problem of correlated measurement errors on a phylogenetic regression by developing a multivariate Ornstein-Uhlenbeck model combined with a maximum-likelihood estimation package in R, and explores questions concerning “time since hybridization”. Expand
Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model.
TLDR
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. Expand
Inferring Bounded Evolution in Phenotypic Characters from Phylogenetic Comparative Data.
TLDR
A new model for the evolution of continuous characters on phylogenies: Brownian motion between two reflective bounds, or Bounded Brownian Motion (BBM), which should enable researchers to elucidate whether the phenotypic traits they study are evolving under hard constraints between bounds. Expand
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION
TLDR
The OU model of adaptive evolution is expanded to include models that variously relax the assumption of a constant rate and strength of selection, and can assign each selective regime a separate trait optimum, a rate of stochastic motion parameter, and a parameter for the strength ofselection. Expand
SIMULATION‐BASED LIKELIHOOD APPROACH FOR EVOLUTIONARY MODELS OF PHENOTYPIC TRAITS ON PHYLOGENY
TLDR
A flexible and comprehensive framework for estimating evolutionary parameters through simulation‐based likelihood computations that can be easily implemented in more computationally effective frameworks such as approximate Bayesian computation (ABC), which will enhance the use of computationally intensive methods in the study of phenotypic evolution. Expand
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data.
TLDR
It is argued that Bayesian model fitting of OU models to comparative data provides a framework for integrating of multiple sources of biological data-such as microevolutionary estimates of selection parameters and paleontological timeseries-allowing inference of adaptive landscape dynamics with explicit, process-based biological interpretations. Expand
Models and methods for analyzing phenotypic evolution in lineages and clades
TLDR
Methods for analyzing continuous traits, with an emphasis on those approaches that rely on explicit statistical models of evolution and incorporate genealogical information (ancestor–descendant or phylogenetic relationships), are discussed. Expand
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data
TLDR
It is argued that Bayesian model-fitting of Ornstein-Uhlenbeck models to comparative data provides a framework for integrating of multiple sources of biological data—such as microevolutionary estimates of selection parameters and paleontological timeseries—allowing inference of adaptive landscape dynamics with explicit, process-based biological interpretations. Expand
Intrinsic inference difficulties for trait evolution with Ornstein‐Uhlenbeck models
TLDR
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. Expand
A NEW BAYESIAN METHOD FOR FITTING EVOLUTIONARY MODELS TO COMPARATIVE DATA WITH INTRASPECIFIC VARIATION
TLDR
A new Bayesian method for fitting evolutionary models to comparative data that incorporates intraspecific variability is described, which differs from an existing likelihood‐based approach in that it requires no a priori inference about species means and variances. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 61 REFERENCES
ADAPTIVE CONSTRAINTS AND THE PHYLOGENETIC COMPARATIVE METHOD: A COMPUTER SIMULATION TEST
TLDR
It was found that correlations estimated without taking phylogeny into account were often quite poor and never substantially better than those produced by the other tested methods, while Felsenstein's independent contrasts (FIC) method gave the best performance in many cases, even when weak constraints had been acting throughout phenotypic evolution. Expand
Comparative analyses for adaptive radiations.
  • P. Harvey, A. Rambaut
  • Biology, Medicine
  • Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 2000
TLDR
It is shown here that under several models of adaptive character evolution and coevolution during an adaptive radiation, which result in closely related species being more similar to each other than to more distantly related species, cross-species analyses are statistically more appropriate than contrast analyses. Expand
PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY
We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and defineExpand
Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts
TLDR
Any (continuous) trait that is inherited from ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic or cultural), according to Felsenstein's method. Expand
Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects
TLDR
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. Expand
Phylogenies and the Comparative Method
TLDR
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. Expand
Historical perspectives in ecology and evolutionary biology: the use of phylogenetic comparative analyses
Hypotheses about the adaptive significance of a trait have long been tested by making comparisons among species. Many recent studies emphasized that conclusions about the origin and maintenance ofExpand
STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION
  • T. F. Hansen
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1997
TLDR
A model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force is presented. Expand
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
TLDR
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. Expand
USING PHYLOGENIES TO TEST HYPOTHESES OF ADAPTATION: A CRITIQUE OF SOME CURRENT PROPOSALS
  • P. Frumhoff, H. Reeve
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1994
TLDR
Investigations of the adaptive design of traits and the phylogenetic relationships of taxa have traditionally focused on very different sets of questions, but several authors have begun using reconstructed phylogenies to directly test hypotheses of adaptive character evolution. Expand
...
1
2
3
4
5
...