TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE

@article{Blomberg2003TESTINGFP,
  title={TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE},
  author={S. Blomberg and T. Garland and A. Ives},
  journal={Evolution},
  year={2003},
  volume={57}
}
Abstract The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous‐valued characters that can be implemented with either phylogenetically… Expand
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References

SHOWING 1-10 OF 127 REFERENCES
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
A Generalized Permutation Model for the Analysis of Cross-Species Data
TLDR
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. Expand
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
TLDR
Simulations show λ to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. Expand
TESTING HYPOTHESES OF CORRELATED EVOLUTION USING PHYLOGENETICALLY INDEPENDENT CONTRASTS: SENSITIVITY TO DEVIATIONS FROM BROWNIAN MOTION
We examined the statistical performance (in terms of type I error rates) of Felsenstein's (1985, Am. Nat. 125:1-15) comparative method of phylogenetically independent contrasts for test- ingExpand
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
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
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
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
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
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
...