A COMMENT ON PHYLOGENETIC CORRECTION

@inproceedings{Rohlf2006ACO,
  title={A COMMENT ON PHYLOGENETIC CORRECTION},
  author={F. James Rohlf},
  year={2006}
}
Abstract Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to phylogeny and there is an expectation that the corrected regression or correlation coefficients will usually be closer to zero. It is shown… Expand
Why the phylogenetic regression appears robust to tree misspecification.
  • E. Stone
  • Mathematics, Medicine
  • Systematic biology
  • 2011
TLDR
This manuscript aims to elucidate how tree misspecification is propagated through a comparative analysis with a focus on the phylogenetic regression under a Brownian motion model of evolution and considers the effect of local phylogenetic perturbations on the regression fit. Expand
Size-Correction and Principal Components for Interspecific Comparative Studies
  • L. Revell
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 2009
TLDR
It is shown that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in the authors' statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. Expand
TESTING FOR PHYLOGENETIC SIGNAL IN BIOLOGICAL TRAITS: THE UBIQUITY OF CROSS‐PRODUCT STATISTICS
To evaluate rates of evolution, to establish tests of correlation between two traits, or to investigate to what degree the phylogeny of a species assemblage is predictive of a trait value so‐calledExpand
An Introduction to Phylogenetic Path Analysis
TLDR
This chapter shows how confirmatory path analysis can be undertaken explicitly controlling for non-independence due to shared ancestry, and presents a step-by-step guide to phylogenetic path analysis using the d-separation method. Expand
Putting phylogeny into the analysis of biological traits: a methodological approach.
TLDR
This paper presents a method for identifying evolutionary strategies from large sets of biological traits, using phylogeny as a source of meaningful historical and ecological information, and extends a multivariate method developed for the analysis of spatial patterns that relies on finding combinations of traits that are phylogenetically autocorrelated. Expand
Multivariate Phylogenetic Comparative Methods: Evaluations, Comparisons, and Recommendations
TLDR
It is concluded that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, whereas algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Expand
Independent contrasts and PGLS regression estimators are equivalent.
We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of theExpand
Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares
Using phylogenetic generalized least squares (PGLS) means to fit a linear regression aiming to investigate the impact of one or several predictor variables on a single response variable whileExpand
Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms.
TLDR
An overview of phylogenetic approaches and their importance for studying the evolution of physiological processes and mechanisms is provided, and the conceptual framework underlying these methods are discussed, and when and how phylogenetic information should be employed are explained. Expand
TESTING THE GENETIC CONSTRAINT HYPOTHESIS IN A PHYLOGENETIC CONTEXT: A SIMULATION STUDY
  • L. Revell
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 2007
TLDR
This is the first study to use individual-based quantitative genetic simulations in a phylogenetic context and shows that, on average, when the process of evolution is genetic drift, the divergence matrix calculated from independent contrasts (DIC) is more highly correlated with G than is the divergence Matrix calculated ignoring phylogenetic nonindependence (D). Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 26 REFERENCES
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
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
An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values
TLDR
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. Expand
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
TLDR
Analysis of variance of log K for all 121 traits indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits, and this work presents new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. 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
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
Rapidly evolving traits and the comparative method: how important is testing for phylogenetic signal?
TLDR
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. Expand
PHYLOGENIES, SPATIAL AUTOREGRESSION, AND THE COMPARATIVE METHOD: A COMPUTER SIMULATION TEST
  • E. Martins
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1996
TLDR
Brownian motion computer simulation was used to test the statistical properties of a spatial autoregressive method in estimating evolutionary correlations between two traits using interspecific comparative data, showing how diagnostic techniques can be useful in detecting and avoiding such situations, but that such techniques should not be used as definitive evidence that phylogenetic correlation is not present in a set of comparative data. Expand
Analysis of comparative data using generalized estimating equations.
TLDR
A new method is introduced, based on the use of generalized estimating equations (GEE), for the analysis of comparative data, to incorporate a correlation matrix that specifies the dependence among observations in the phylogenetic tree of the studied species. Expand
...
1
2
3
...