# An approximately unbiased test of phylogenetic tree selection.

@article{Shimodaira2002AnAU,
title={An approximately unbiased test of phylogenetic tree selection.},
author={Hidetoshi Shimodaira},
journal={Systematic biology},
year={2002},
volume={51 3},
pages={
492-508
}
}
An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira…
2,292 Citations

## Figures and Tables from this paper

The comparison of the confidence regions in phylogeny.
• Mathematics
Molecular biology and evolution
• 2005
This paper evaluated several different procedures for constructing confidence regions for the true evolutionary tree in terms of coverage and size without considering model misspecification, finding the SH, SSOWH, AU, and LW tests led to regions with higher coverage than the nominal level at the price of including large numbers of trees.
Alignment errors strongly impact likelihood-based tests for comparing topologies.
• Biology
Molecular biology and evolution
• 2014
This work shows that the Kishino-Hasegawa (KH) test is biased in the presence of alignment error and can lead to erroneous conclusions, and develops a parametric test that entirely abolishes the biases without data filtering.
Selective Inference for Testing Trees and Edges in Phylogenetics
• Biology
Front. Ecol. Evol.
• 2019
The newly proposed selective inference p-value is useful for testing selected edges to claim that they are significantly supported if $p>1-\alpha$, whereas the non-selective $p- value is still useful forTesting candidate trees to claim to have been rejected if$ p<\alpha\$.
How Bayes tests of molecular phylogenies compare with frequentist approaches
The BHT and BST are shown to construct similar confidence sets to the bootstrap and the Shimodaira Hasegawa test, respectively, which suggests that the known difference among previous tests is mainly due to the null hypothesis considered.
Test a clade in phylogenetic trees.
• Biology
Molecular biology and evolution
• 2006
A new method for testing a portion of a tree based on multiple tests of many 4-taxon trees, which shows that the combination of the approximately unbiased (AU) test and the FDR-controlling procedure provides strong power along with reasonable type I error rate and less heavy computation.
Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics
• Biology
Royal Society Open Science
• 2015
This work investigated new implementations of maximum likelihood and Bayesian SMs and compared these with some currently available alternative approaches, demonstrating that the Bayesian method is a viable alternative to MRP and other non-parametric methods.
Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.
• Computer Science
Genome informatics. International Conference on Genome Informatics
• 2002
Here it is shown that the extremely fast "resampling of estimated log likelihoods" or RELL method behaves well under more general circumstances than previously examined and approximates the bootstrap (BP) proportions of trees better that some bootstrap methods that rely on fast heuristics to search the tree space.
Topology testing of phylogenies using least squares methods
• Biology
BMC Evolutionary Biology
• 2006
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.
• Biology
Systematic biology
• 2012
This work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes.

## References

SHOWING 1-10 OF 50 REFERENCES
CONSEL: for assessing the confidence of phylogenetic tree selection
• Computer Science
Bioinform.
• 2001
UNLABELLED CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees using the multi-scale bootstrap technique, which is less biased than the other conventional p- values.
Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique.
• Mathematics, Economics
Molecular phylogenetics and evolution
• 1995
The complete-and-partial bootstrap technique is proposed as a method for obtaining an unbiased estimate of the confidence level of the monophyly of a particular group of taxa or of an inferred tree topology with the maximum parsimony or neighbor-joining tree reconstruction method.
Likelihood-based tests of topologies in phylogenetics.
• Mathematics
Systematic biology
• 2000
The theory of the Kishino-Hasegawa test is reviewed and it is argued that for the majority of popular applications this test should not be used, and future applications should use appropriate alternative tests instead.
An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
• Biology
• 1993
This work uses computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, and indicates that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one.
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
• Biology
• 1999
A modiﬁcation of the KH test to take into account a multiplicity of testings is presented, which shows how the test was designed for comparing two topologies but is often used for comparing many topologies.
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
• J. Felsenstein
• Economics
Evolution; international journal of organic evolution
• 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
MULTIPLE COMPARISONS OF LOG-LIKELIHOODS AND COMBINING NONNESTED MODELS WITH APPLICATIONS TO PHYLOGENETIC TREE SELECTION
We consider multiple comparisons of log-likelihood's to take account of the multiplicity of testings in selection of nonnested models. A resampling version of the Gupta procedure for the selection
Bootstrap confidence levels for phylogenetic trees.
• Biology
Proceedings of the National Academy of Sciences of the United States of America
• 1996
It is shown that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing, and can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.
PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES
• Biology
Evolution; international journal of organic evolution
• 1967
This paper shows how suitable evolutionary models can be constructed and applied objectively and how the type of data will affect both the method of treatment and the validity of the results.
Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae).
• Biology
Systematic biology
• 2000
The bootstrap proportion, as currently used in phylogenetic analysis, does not accurately capture the classical notion of confidence assessments on the null hypothesis of nonmonophyly, especially in large data sets, and more accurate assessments of confidence as type I error levels remove most of the monotonic decline in confidence with increasing numbers of taxa.