Molecular Biology and Evolution, Vol 12, 319-333, Copyright © 1995 by Society for Molecular Biology and Evolution
T Sitnikova, A Rzhetsky and M Nei
We have compared statistical properties of the interior-branch and
bootstrap tests of phylogenetic trees when the neighbor-joining tree-
building method is used. For each interior branch of a predetermined
topology, the interior-branch and bootstrap tests provide the confidence
values, PC and PB, respectively, that indicate the extent of statistical
support of the sequence cluster generated by the branch. In phylogenetic
analysis these two values are often interpreted in the same way, and if PC
and PB are high (say, > or = 0.95), the sequence cluster is regarded as
reliable. We have shown that PC is in fact the complement of the P-value
used in the standard statistical test, but PB is not. Actually, the
bootstrap test usually underestimates the extent of statistical support of
species clusters. The relationship between the confidence values obtained
by the two tests varies with both the topology and expected branch lengths
of the true (model) tree. The most conspicuous difference between PC and PB
is observed when the true tree is starlike, and there is a tendency for the
difference to increase as the number of sequences in the tree increases.
The reason for this is that the bootstrap test tends to become
progressively more conservative as the number of sequences in the tree
increases. Unlike the bootstrap, the interior-branch test has the same
statistical properties irrespective of the number of sequences used when a
predetermined tree is considered. Therefore, the interior-branch test
appears to be preferable to the bootstrap test as long as unbiased
estimators of evolutionary distances are used. However, when the
interior-branch is applied to a tree estimated from a given data set, PC
may give an overestimate of statistical confidence. For this case, we
developed a method for computing a modified version (P'C) of the PC value
and showed that this P'C tends to give a conservative estimate of
statistical confidence, though it is not as conservative as PB. In this
paper we have introduced a model in which evolutionary distances between
sequences follow a multivariate normal distribution. This model allowed us
to study the relationships between the two tests analytically.
ORIGINAL ARTICLE
Interior-branch and bootstrap tests of phylogenetic trees
Institute of Molecular and Evolutionary Genetics, Pennsylvania State University.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. L. Erwin, S. A. Sandstedt, P. J. Bonthuis, J. L. Geelhood, K. L. Nelson, W. C. T. Unrath, M. A. Diggle, M. J. Theodore, C. R. Pleatman, E. A. Mothershed, et al. Analysis of Genetic Relatedness of Haemophilus influenzae Isolates by Multilocus Sequence Typing J. Bacteriol., February 15, 2008; 190(4): 1473 - 1483. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Eirin-Lopez, T. Ishibashi, and J. Ausio H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way FASEB J, January 1, 2008; 22(1): 316 - 326. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. W. Abbott, J. M. Eirin-Lopez, and A. B. Boraston Insight into Ligand Diversity and Novel Biological Roles for Family 32 Carbohydrate-Binding Modules Mol. Biol. Evol., January 1, 2008; 25(1): 155 - 167. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Kolaczkowski and J. W. Thornton Effects of Branch Length Uncertainty on Bayesian Posterior Probabilities for Phylogenetic Hypotheses Mol. Biol. Evol., September 1, 2007; 24(9): 2108 - 2118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Miragaia, J. C. Thomas, I. Couto, M. C. Enright, and H. de Lencastre Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data J. Bacteriol., March 15, 2007; 189(6): 2540 - 2552. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Eirin-Lopez, L. J. Frehlick, and J. Ausio Long-Term Evolution and Functional Diversification in the Members of the Nucleophosmin/Nucleoplasmin Family of Nuclear Chaperones Genetics, August 1, 2006; 173(4): 1835 - 1850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Eirin-Lopez, J. D. Lewis, L. A. Howe, and J. Ausio Common Phylogenetic Origin of Protamine-like (PL) Proteins and Histone H1: Evidence from Bivalve PL Genes Mol. Biol. Evol., June 1, 2006; 23(6): 1304 - 1317. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Dvornyk Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria Microbiology, January 1, 2006; 152(1): 75 - 84. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Hery-Arnaud, G. Bruant, P. Lanotte, S. Brun, A. Rosenau, N. van der Mee-Marquet, R. Quentin, and L. Mereghetti Acquisition of Insertion Sequences and the GBSi1 Intron by Streptococcus agalactiae Isolates Correlates with the Evolution of the Species J. Bacteriol., September 1, 2005; 187(17): 6248 - 6252. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J C R Cardoso, M S Clark, F A Viera, P D Bridge, A Gilles, and D M Power The secretin G-protein-coupled receptor family: teleost receptors J. Mol. Endocrinol., June 1, 2005; 34(3): 753 - 765. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Sanjuan and B. Wrobel Weighted Least-Squares Likelihood Ratio Test for Branch Testing in Phylogenies Reconstructed from Distance Measures Syst Biol, April 1, 2005; 54(2): 218 - 229. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Eirin-Lopez, A. M. Gonzalez-Tizon, A. Martinez, and J. Mendez Birth-and-Death Evolution with Strong Purifying Selection in the Histone H1 Multigene Family and the Origin of orphon H1 Genes Mol. Biol. Evol., October 1, 2004; 21(10): 1992 - 2003. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Denver, S. L. Swenson, and M. Lynch An Evolutionary Analysis of the Helix-Hairpin-Helix Superfamily of DNA Repair Glycosylases Mol. Biol. Evol., October 1, 2003; 20(10): 1603 - 1611. [Abstract] [Full Text]
|
|
|
|
 |
|
 D. Godoy, G. Randle, A. J. Simpson, D. M. Aanensen, T. L. Pitt, R. Kinoshita, and B. G. Spratt Multilocus Sequence Typing and Evolutionary Relationships among the Causative Agents of Melioidosis and Glanders, Burkholderia pseudomallei and Burkholderia mallei J. Clin. Microbiol., May 1, 2003; 41(5): 2068 - 2079. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Meats, E. J. Feil, S. Stringer, A. J. Cody, R. Goldstein, J. S. Kroll, T. Popovic, and B. G. Spratt Characterization of Encapsulated and Noncapsulated Haemophilus influenzae and Determination of Phylogenetic Relationships by Multilocus Sequence Typing J. Clin. Microbiol., April 1, 2003; 41(4): 1623 - 1636. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Piontkivska and M. Nei Birth-and-Death Evolution in Primate MHC Class I Genes: Divergence Time Estimates Mol. Biol. Evol., April 1, 2003; 20(4): 601 - 609. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. K. Davis, R. G. Cook, R. R. Rich, and J. R. Rodgers Hyperconservation of the Putative Antigen Recognition Site of the MHC Class I-b Molecule TL in the Subfamily Murinae: Evidence That Thymus Leukemia Antigen Is an Ancient Mammalian Gene J. Immunol., December 15, 2002; 169(12): 6890 - 6899. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Suzuki, G. V. Glazko, and M. Nei Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics PNAS, December 10, 2002; 99(25): 16138 - 16143. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Gutierrez, D. Sanchez, and A. Marin A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones Mol. Biol. Evol., August 1, 2002; 19(8): 1359 - 1366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Nei, S. Kumar, and K. Takahashi The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small PNAS, October 13, 1998; 95(21): 12390 - 12397. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Stoneking, J. J. Fontius, S. L. Clifford, H. Soodyall, S. S. Arcot, N. Saha, T. Jenkins, M. A. Tahir, P. L. Deininger, and M. A. Batzer Alu Insertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa Genome Res., November 1, 1997; 7(11): 1061 - 1071. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Holland, B Koschorz, L. Holland, and B. Herrmann Conservation of Brachyury (T) genes in amphioxus and vertebrates: developmental and evolutionary implications Development, January 12, 1995; 121(12): 4283 - 4291. [Abstract] [PDF]
|
|