TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
@inproceedings{Blomberg2003TESTINGFP, title={TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE}, author={Simon Phillip Blomberg and Theodore Garland and Anthony R. Ives}, booktitle={Evolution; international journal of organic evolution}, year={2003} }
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…
3,700 Citations
A standardized effect size for evaluating and comparing the strength of phylogenetic signal
- BiologyMethods in Ecology and Evolution
- 2021
A non‐parametric, permutation test for the log‐likelihood of an evolutionary model, plus a standardized statistic, Z, from this test, which can be considered a phylogenetic signal effect size, can be used in two‐sample tests to compare the strength of phylogenetics signal for multiple traits.
Rapidly evolving traits and the comparative method: how important is testing for phylogenetic signal?
- Biology, Environmental Science
- 2004
It is shown that the bird song parameters investigated are not correlated to their phylogenetic history, indicating that certain aspects of bird song can be subject to rates of evolution that are much more rapid than speciation events.
Evolutionary Models and Phylogenetic Signal Assessment via Mantel Test
- BiologyEvolutionary Biology
- 2016
A new analytical procedure is described, which incorporates explicitly an evolutionary model in the standard Mantel test (EM-Mantel), which is a good alternative for measuring phylogenetic signal in binary and categorical traits and for datasets with multiple traits.
TESTING FOR PHYLOGENETIC SIGNAL IN BIOLOGICAL TRAITS: THE UBIQUITY OF CROSS‐PRODUCT STATISTICS
- BiologyEvolution; international journal of organic evolution
- 2013
This article shows that the Blomberg et al.
A comparison of metrics for estimating phylogenetic signal under alternative evolutionary models
- BiologyGenetics and molecular biology
- 2012
It is shown that statistical approaches provide valid results and may be still particularly useful when detailed phylogenies are unavailable or when trait variation among species is difficult to describe by more standard Brownian or O-U evolutionary models.
Measuring phylogenetic signal between categorical traits and phylogenies
- BiologyBioinform.
- 2019
The application shows that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories, and shows that it can successfully detect molecular signatures of phenotypic evolution.
Testing and quantifying phylogenetic signals and homoplasy in morphometric data.
- BiologySystematic biology
- 2010
A test for the presence of a phylogenetic signal in morphometric data is proposed, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation of the shape data among the terminal taxa.
Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities.
- BiologyTheoretical population biology
- 2008
Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait-environment relationships.
- Environmental ScienceEcology
- 2018
This work demonstrates how the presence of spatial and phylogenetic autocorrelations can, in some circumstances, lead to inflated type I error rates, suggesting that significant associations can be misidentified and proposes a new randomization approach designed to avoid this issue.
Inference of Adaptive Shifts for Multivariate Correlated Traits
- BiologybioRxiv
- 2017
This work introduces here a simplification of the full multivariate Ornstein-Uhlenbeck model, named scalar OU (scOU), which allows for noncausal correlations and is still computationally tractable, and describes an Expectation Maximization algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion.
References
SHOWING 1-10 OF 158 REFERENCES
Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts
- Biology
- 1992
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.
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
- BiologyThe American Naturalist
- 2002
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.
An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values
- Biology
- 1999
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.
A Generalized Permutation Model for the Analysis of Cross-Species Data
- BiologyJ. Classif.
- 2001
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.
TESTING HYPOTHESES OF CORRELATED EVOLUTION USING PHYLOGENETICALLY INDEPENDENT CONTRASTS: SENSITIVITY TO DEVIATIONS FROM BROWNIAN MOTION
- Biology
- 1996
The results constitute another demonstration of the general superi- ority of phylogenetically based statistical methods over nonphylogenetic ones, even under extreme deviations from a Brownian motion model.
Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects
- Biology
- 1990
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.
METHODS FOR THE ANALYSIS OF COMPARATIVE DATA IN EVOLUTIONARY BIOLOGY
- BiologyEvolution; international journal of organic evolution
- 1991
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.
Truth or Consequences: Effects of Phylogenetic Accuracy on Two Comparative Methods
- Biology
- 1994
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.
PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY
- BiologyEvolution; international journal of organic evolution
- 1991
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
- BiologyThe American Naturalist
- 1985
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.