Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
BMC Evol Biol
2006 Dec 06;6:105. doi: 10.1186/1471-2148-6-105.
Show Gene links
Show Anatomy links
Topology testing of phylogenies using least squares methods.
Czarna A
,
Sanjuán R
,
González-Candelas F
,
Wróbel B
.
???displayArticle.abstract???
BACKGROUND: The least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) to the observed distances between taxa is the criterion used for selecting the best topology. The generalized LS (GLS) method for topology testing is often frustrated by the computational difficulties in calculating the covariance matrix and its inverse, which in practice requires approximations. The weighted LS (WLS) allows for a more efficient albeit approximate calculation of the test statistic by ignoring the covariances between the distances.
RESULTS: The goal of this paper is to assess the applicability of the LS approach for constructing confidence sets of trees. We show that the approximations inherent to the WLS method did not affect negatively the accuracy and reliability of the test both in the analysis of biological sequences and DNA-DNA hybridization data (for which character-based testing methods cannot be used). On the other hand, we report several problems for the GLS method, at least for the available implementation. For many data sets of biological sequences, the GLS statistic could not be calculated. For some data sets for which it could, the GLS method included all the possible trees in the confidence set despite a strong phylogenetic signal in the data. Finally, contrary to WLS, for simulated sequences GLS showed undercoverage (frequent non-inclusion of the true tree in the confidence set).
CONCLUSION: The WLS method provides a computationally efficient approximation to the GLS useful especially in exploratory analyses of confidence sets of trees, when assessing the phylogenetic signal in the data, and when other methods are not available.
Adachi,
Model of amino acid substitution in proteins encoded by mitochondrial DNA.
1996, Pubmed
Adachi,
Model of amino acid substitution in proteins encoded by mitochondrial DNA.
1996,
Pubmed
Bracho,
Molecular epidemiology of a hepatitis C virus outbreak in a hemodialysis unit.
2005,
Pubmed
Castresana,
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
2000,
Pubmed
Cavalli-Sforza,
Phylogenetic analysis. Models and estimation procedures.
1967,
Pubmed
Czarna,
Topology testing of phylogenies using least squares methods.
2006,
Pubmed
Desper,
Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.
2004,
Pubmed
Felsenstein,
An alternating least squares approach to inferring phylogenies from pairwise distances.
1997,
Pubmed
Felsenstein,
DISTANCE METHODS FOR INFERRING PHYLOGENIES: A JUSTIFICATION.
1984,
Pubmed
Felsenstein,
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
1985,
Pubmed
Fitch,
Construction of phylogenetic trees.
1967,
Pubmed
Goldman,
Likelihood-based tests of topologies in phylogenetics.
2000,
Pubmed
González-Candelas,
Molecular epidemiology and forensic genetics: application to a hepatitis C virus transmission event at a hemodialysis unit.
2003,
Pubmed
Huelsenbeck,
Accommodating phylogenetic uncertainty in evolutionary studies.
2000,
Pubmed
Kishino,
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea.
1989,
Pubmed
Kuhner,
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
1994,
Pubmed
Lapointe,
Jackknifing of weighted trees: validation of phylogenies reconstructed from distance matrices.
1994,
Pubmed
Marshall,
DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values.
1992,
Pubmed
,
Echinobase
Marshall,
Statistical tests and bootstrapping: assessing the reliability of phylogenies based on distance data.
1991,
Pubmed
Murphy,
Molecular phylogenetics and the origins of placental mammals.
2001,
Pubmed
Posada,
MODELTEST: testing the model of DNA substitution.
1998,
Pubmed
Sanjuán,
Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures.
2005,
Pubmed
Schmidt,
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
2002,
Pubmed
Shi,
The comparison of the confidence regions in phylogeny.
2005,
Pubmed
Shimodaira,
An approximately unbiased test of phylogenetic tree selection.
2002,
Pubmed
Strimmer,
Inferring confidence sets of possibly misspecified gene trees.
2002,
Pubmed
Susko,
Confidence regions and hypothesis tests for topologies using generalized least squares.
2003,
Pubmed
Swofford,
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods.
2001,
Pubmed
Takahata,
A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes.
1981,
Pubmed
,
Echinobase
Waddell,
A phylogenetic foundation for comparative mammalian genomics.
2001,
Pubmed
Yang,
PAML: a program package for phylogenetic analysis by maximum likelihood.
1997,
Pubmed