BibTeX
@MISC{Galtier_influenceof,
author = {Nicolas Galtier},
title = {Influence of Nonindependence Among Sites},
year = {}
}
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Abstract
Abstract.—The influence of nonindependence among sites on phylogenetic reconstructions and bootstrap scores was inves-tigated both analytically and empirically. First, the sampling properties of the bootstrap support in the four-species case was derived for the maximum-parsimony method, assuming either independently or nonindependently evolving sites. The influence of various models of departure from the independence assumption was quantified. Second, trees and bootstrap scores estimated from subsets of consecutive (potentially coevolving) versus dispersed (presumably independent) sites of a ribosomal RNA data set were contrasted. The two approaches consistently suggest that a departure from the assumption of independent sites tends to reduce the amount of phylogenetic information contained in the data, but to increase the apparent statistical support for reconstructed trees, as measured by the bootstrap. In particular, nonindependence can lead to strongly supported wrong internal branches. [Bootstrap; coevolution; molecular phylogeny; ribosomal RNA; site independence.] Independence among sites is a fundamental assump-tion of virtually all methods used to access molecular phylogeny, including model-based methods for recon-structing trees and methods for assessing the level of confidence in reconstructions, among which the boot-strap (Felsenstein, 1985) is by far the most widely used.
Keyphrases
bootstrap score maximum-parsimony method site independence four-species case wrong internal branch fundamental assump-tion model-based method independence assumption phylogenetic information bootstrap support ribosomal rna molecular phylogeny ribosomal rna data set phylogenetic reconstruction independent site various model access molecular phylogeny recon-structing tree apparent statistical support
