A method for the analysis of comparative data

@article{Pagel1992AMF,
  title={A method for the analysis of comparative data},
  author={Mark Pagel},
  journal={Journal of Theoretical Biology},
  year={1992},
  volume={156},
  pages={431-442}
}
  • M. Pagel
  • Published 21 June 1992
  • Biology
  • Journal of Theoretical Biology

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.

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.

Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty

A computer program is presented, Fels-Rand, that performs random trees from the known phylogeny that are fully-resolved but consistent with the known tree, and the usefulness of Xlisp-Stat as a system for phylogenetic computation is discussed.

CONDUCTING PHYLOGENETIC COMPARATIVE STUDIES WHEN THE PHYLOGENY IS NOT KNOWN

  • E. Martins
  • Biology
    Evolution; international journal of organic evolution
  • 1996
A method is proposed to conduct phylogenetic analyses of comparative or interspecific data when the true phylogeny is not known and the mean of this distribution is proposed as a reasonable estimate of the true evolutionary statistic of interest.

Random Sampling of Constrained Phylogenies : Conducting Phylogenetic Analyses When the Phylogeny Is Partially Known

The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information and proposes a method that overcomes these problems and should prove useful for randomizations involved in a variety of phylogenetic statistical analyses.

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

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.

Polytomies in Comparative Analyses of Continuous Characters

Differences between the two types of phylogeny, where the true phylogeny linking the species in the data set be known in full, including the lengths of the branches in units of expected variance of change for the character(s) being studied, are presented.

The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts.

The results suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data and the use ofrandom phylogenies is not beneficial in the absence of knowledge of the true phylogeny.

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.
...

References

SHOWING 1-10 OF 11 REFERENCES

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.

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.

The phylogenetic regression.

  • A. Grafen
  • Biology
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1989
One conclusion is that the dates of splits between taxa, even supplemented by rates of neutral gene evolution, do not provide the ‘ true ’ covariance structure, and a pragmatic approach is adopted.

Recent Developments in the Analysis of Comparative Data

With current knowledge of phylogenies, there is a trade-off in the choice of a comparative method: those that control phylogenetic effects with greater certainty are either less applicable to real data, or they make restrictive or untestable assumptions.

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

EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES

  • J. Felsenstein
  • Computer Science
    Evolution; international journal of organic evolution
  • 1981
An iterative REML method is introduced which makes rapid computation of the REML estimate of the evolutionary tree feasible and may also serve as a review of the basic logic of these estimates and tests for those readers unfamiliar with the existing human genetics literature.

Carnivore Life History Patterns: Allometric, Phylogenetic, and Ecological Associations

Previous approaches to life history problems are considerably varied, and reviews may be found in Stearns (1976, 1977, 1980), Southwood (1976), Horn (1978), Horn and Rubenstein (1984), Western and

The comparative method in evolutionary biology

The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis

Molecular and Biochemical Evolution of the Carnivora

The fissiped carnivores includes taxa that are entirely carnivorous, insectivorous, and omnivorous and that have cursorial, arboreal, fossorial, and aquatic habits that have confounded the efforts of taxonomists to relate certain taxa.