Sampling Properties of the Bootstrap Support in Molecular Phylogeny: Influence of Nonindependence Among Sites

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Abstract
The influence of nonindependence among sites on phylogenetic reconstructions and bootstrap scores was investigated 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.