Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

@article{Garland1992ProceduresFT,
  title={Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts},
  author={Theodore Garland and Paul H. Harvey and Anthony R. Ives},
  journal={Systematic Biology},
  year={1992},
  volume={41},
  pages={18-32}
}
We discuss and clarify several aspects of applying Felsenstein's (1985, Am. Nat. 125: 1n15) procedures to test for correlated evolution of continuous traits. This is one of several available comparative methods that maps data for phenotypic traits onto an existing phylogenetic tree (derived from independent information). Application of Felsenstein's method does not require an entirely dichotomous topology. It also does not require an assumption of gradual, clocklike character evolution, as… Expand

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References

SHOWING 1-10 OF 48 REFERENCES
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
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
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
A method for the analysis of comparative data
Felsenstein (1985) developed a method for analyzing comparative data that calculates a set of mutually independent comparisons among the species. The method was designed to be used with phylogeniesExpand
Phylogenies and quantitative characters
TLDR
Systematists and evolutionary geneticists don't often talk to each other, and they routinely dispaiage each other's work as being of little relevance to evolution, but changes in the methods of collecting and analyzing data are invalidating some of these views. Expand
THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES
TLDR
The separation of phylogenetic from specific effects proposed here also allows phylogenetic factors to be explicitly included in cross‐species comparative analyses of adaptation, which solves a long‐standing problem in evolutionary comparative studies. Expand
Rate Tests for Phenotypic Evolution Using Phylogenetically Independent Contrasts
  • T. Garland
  • Biology, Medicine
  • The American Naturalist
  • 1992
TLDR
It is shown that phylogenetically independent contrasts (Felsenstein 1985) allow simple and statistically valid comparisons of evolutionary rates among monophyletic groups of extant (or extinct) species. Expand
A Comparative Method
  • G. Bell
  • Biology
  • The American Naturalist
  • 1989
TLDR
It is argued that covariance between taxa is attributable to ancestry and covariance within taxa to function, and that adaptive hypotheses should be tested by the within-taxon correlation. Expand
ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL
TLDR
The results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation. Expand
PHYLOGENIES AND THE ANALYSIS OF EVOLUTIONARY SEQUENCES, WITH EXAMPLES FROM SEED PLANTS
  • M. Donoghue
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1989
TLDR
A cladistic test of the hypothesis that the evolution of dioecy is favored in animal‐dispersed plants indicates that dioECy may have originated somewhat more often in such lineages, which must largely account for the observed species‐level correlation between dispersal and breeding system. Expand
...
1
2
3
4
5
...