Phylogenies and the Comparative Method

@article{Felsenstein1985PhylogeniesAT,
  title={Phylogenies and the Comparative Method},
  author={Joseph Felsenstein},
  journal={The American Naturalist},
  year={1985},
  volume={125},
  pages={1 - 15}
}
Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause… 

PHYLOGENIES, SPATIAL AUTOREGRESSION, AND THE COMPARATIVE METHOD: A COMPUTER SIMULATION TEST

  • E. Martins
  • Biology
    Evolution; international journal of organic evolution
  • 1996
Brownian motion computer simulation was used to test the statistical properties of a spatial autoregressive method in estimating evolutionary correlations between two traits using interspecific comparative data, showing how diagnostic techniques can be useful in detecting and avoiding such situations, but that such techniques should not be used as definitive evidence that phylogenetic correlation is not present in a set of comparative data.

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 define

Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data

A generalized linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character.

Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

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.

USING PHYLOGENIES TO TEST HYPOTHESES OF ADAPTATION: A CRITIQUE OF SOME CURRENT PROPOSALS

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.

DETECTING CORRELATION BETWEEN CHARACTERS IN A COMPARATIVE ANALYSIS WITH UNCERTAIN PHYLOGENY

A method for performing comparative analyses that is based on an extension of Felsenstein's independent contrasts method, which handles uncertainty in the phylogeny, branch lengths, and other parameters by averaging over all possible trees, weighting each by the probability that the tree is correct.

A Generalized Permutation Model for the Analysis of Cross-Species Data

It is shown that the conventional, equally likely (EL) randomization model is a special case of the phylogenetic permutations (PP), and an application of the method is presented to test the correlation between two traits with cross-species data.

COMPARATIVE METHODS FOR THE ANALYSIS OF CONTINUOUS VARIABLES: GEOMETRIC INTERPRETATIONS

  • F. Rohlf
  • Environmental Science
    Evolution; international journal of organic evolution
  • 2001
It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model, and the PA method is shown to have several problems that limit its usefulness in comparative studies.

An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values

Three phylogenetically based statistical methods are presented, including phylogenetically independent contrasts, Monte Carlo computer simulations to obtain null distributions of test statistics, and phylogenetic autocorrelation, which allow traditional topics in comparative and ecological physiology to be addressed with greater rigor.

ADAPTIVE CONSTRAINTS AND THE PHYLOGENETIC COMPARATIVE METHOD: A COMPUTER SIMULATION TEST

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.
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