Phylogenies and the Comparative Method

@article{Felsenstein1985PhylogeniesAT,
  title={Phylogenies and the Comparative Method},
  author={Joseph Felsenstein},
  journal={The American Naturalist},
  year={1985},
  volume={125},
  pages={1 - 15}
}
Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause… 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
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: 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
USING PHYLOGENIES TO TEST HYPOTHESES OF ADAPTATION: A CRITIQUE OF SOME CURRENT PROPOSALS
  • P. Frumhoff, H. Reeve
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1994
TLDR
Investigations of the adaptive design of traits and the phylogenetic relationships of taxa have traditionally focused on very different sets of questions, but several authors have begun using reconstructed phylogenies to directly test hypotheses of adaptive character evolution. Expand
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
DETECTING CORRELATION BETWEEN CHARACTERS IN A COMPARATIVE ANALYSIS WITH UNCERTAIN PHYLOGENY
TLDR
A method for performing comparative analyses that is based on an extension of Felsenstein's independent contrasts method, which handles uncertainty in the phylogeny, branch lengths, and other parameters by averaging over all possible trees, weighting each by the probability that the tree is correct. 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
COMPARATIVE METHODS FOR THE ANALYSIS OF CONTINUOUS VARIABLES: GEOMETRIC INTERPRETATIONS
  • F. Rohlf
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 2001
TLDR
It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model, and the PA method is shown to have several problems that limit its usefulness in comparative studies. 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
ADAPTIVE CONSTRAINTS AND THE PHYLOGENETIC COMPARATIVE METHOD: A COMPUTER SIMULATION TEST
TLDR
It was found that correlations estimated without taking phylogeny into account were often quite poor and never substantially better than those produced by the other tested methods, while Felsenstein's independent contrasts (FIC) method gave the best performance in many cases, even when weak constraints had been acting throughout phenotypic evolution. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 22 REFERENCES
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
Felsenstein, J. (Department of Genetics, University of Washington, Seattle, WA 98195) 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool.Expand
Parsimony in Systematics: Biological and Statistical Issues
TLDR
Methods of classification and methods of inferring phylogeny are of course separate issues and only the latter are discussed here. Expand
EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES
  • J. Felsenstein
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1981
TLDR
An iterative REML method is introduced which makes rapid computation of the REML estimate of the evolutionary tree feasible and may also serve as a review of the basic logic of these estimates and tests for those readers unfamiliar with the existing human genetics literature. Expand
The Explanation of Organic Diversity: the Comparative Method and Adaptations for Mating, Mark Ridley. Oxford University Press/Clarendon Press, Oxford (1983), viii, +272. Price £19.00
TLDR
In an extremely hnportant contribution to the comparative literature, Mark Ridley identifies tiffs problem and provides a method for dealing with it. Expand
Outcrossing Versus Ecological Constraints in the Evolution of Dioecy
TLDR
The incidence of dioecy in taxa displaying heterostyly is nearly identical to that seen inTaxa having only homomorphic self-incompatibility, contradicting Thomson and Barrett's (1981) view that style-morph selection may be more important than other ecological factors favoring dioECy in self- incompatible plants. Expand
Size and Scaling in Human Evolution
TLDR
It is thought that the scheme outlined here should be treated as the null hypothesis to be disproved, and the three australopithecines are, in a number of features, scaled variants of the "same" animal. Expand
The phylogeny of parental care in fishes
TLDR
A review of the teleost literature reveals 21 transitions that agree with the hypothesis that in the evolution of parental care, taxa of bony fish should only exhibit certain transitional states. Expand
Relative brain size and basal metabolic rate in terrestrial vertebrates
TLDR
Re-examination of brain–body size relationships for large samples of species from three major vertebrate groups now shows that there is no empirical foundation for the concept of scaling to body surface area, and it seems that brain size may be linked to maternal metabolic turnover. Expand
Insect Chromosome Numbers and Eusociality
TLDR
It is hypothesized that convergence of actual genotypic similarities on the mean reduces likelihood that sterile workers will discriminate among sibs in need of assistance on the basis of their actual relatedness. Expand
Relative brain size and metabolism in mammals.
TLDR
Comparisons of the relation between brain and body weights among extant mammals show that brain sizes have not increased as much as body sizes, but primates also use a larger proportion of their total energy reserves for their brains. Expand
...
1
2
3
...