Why the phylogenetic regression appears robust to tree misspecification.

@article{Stone2011WhyTP,
  title={Why the phylogenetic regression appears robust to tree misspecification.},
  author={Eric A. Stone},
  journal={Systematic biology},
  year={2011},
  volume={60 3},
  pages={
          245-60
        }
}
  • E. Stone
  • Published 1 May 2011
  • Mathematics, Medicine
  • Systematic biology
The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confounding similarities due to identity by descent. Because the true phylogeny is unknowable, an estimate must be used, introducing a source of error into phylogenetic comparative analysis… Expand

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References

SHOWING 1-10 OF 48 REFERENCES
METHODS FOR THE ANALYSIS OF COMPARATIVE DATA IN EVOLUTIONARY BIOLOGY
  • M. Lynch
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1991
TLDR
Methods are presented for the estimation of phylogenywide means of characters, the variance‐covariance structure of the components of taxon‐specific means, and the mean phenotypes of ancestral taxa and it is argued that the covarianceructure of phylogenetic effects provides a description of a macroevolutionary pattern. Expand
Phylogeny shape and the phylogenetic comparative method.
TLDR
The impact of phylogeny shape on the results of interspecific statistical analyses incorporating phylogenetic information is explored, and differences in the eigenvectors and eigenvalues of different relationship matrices are used to gauge the impact of possible phylogeny errors. Expand
The phylogenetic regression.
  • A. Grafen
  • Mathematics, Medicine
  • Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1989
TLDR
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. Expand
Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data
TLDR
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. Expand
The uniqueness of the phylogenetic regression
The phylogenetic regression provides the hypothesis testing facilities of general linear models for comparative data with incompletely known phylogenies. It applies Ridley's radiation principle. ItExpand
Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure.
  • M. Pagel
  • Biology, Medicine
  • Journal of theoretical biology
  • 1993
TLDR
Comparative statistical techniques are able to recover the historical trends of evolution, that is, the ways in which evolution has proceeded along the branches of the phylogenetic tree, from analysis of the variation among the contemporary species of a phylogeny. Expand
A COMMENT ON PHYLOGENETIC CORRECTION
TLDR
The effect of taking phylogeny into account is to reduce the variance of the estimated regression or correlation coefficients, and estimates of regression coefficients are unbiased whether or not the correct phylogeny is taken into account. Expand
DETECTING CORRELATION BETWEEN CHARACTERS IN A COMPARATIVE ANALYSIS WITH UNCERTAIN PHYLOGENY
The importance of accommodating the phylogenetic history of a group when performing a comparative analysis is now widely recognized. The typical approaches either assume the tree is known withoutExpand
Truth or Consequences: Effects of Phylogenetic Accuracy on Two Comparative Methods
TLDR
Simulations show independent contrasts to be valid when branch lengths are known, whether or not the topology is known fully, and how the two approaches stand up to incompletely resolved trees and incorrect branch length information—common situations for comparative biologists. Expand
Using the Past to Predict the Present: Confidence Intervals for Regression Equations in Phylogenetic Comparative Methods
TLDR
Passengerines exhibit a lower rate of evolution in both body mass and mass‐corrected BMR; passerines also have significantly smaller body masses than their sister clade, which may justify separate, clade‐specific allometric equations for prediction of avian basal metabolic rates. Expand
...
1
2
3
4
5
...