MBE Advance Access published online on November 3, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi036
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Marine Biological Laboratory Woods Hole, MA 02543
* To whom correspondence should be addressed. Standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. However, this assumption is often violated in biological data sets. In this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction of a bacterial group that spans a wide range of genomic nucleotide contents: obligately endosymbiotic bacteria and free-living or commensal species in the
Research Article
Non-Homogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts within the Enterobacteriales (
-Proteobacteria)
Joshua T. Herbeck, E-mail: herbeck{at}u.washington.edu
Abstract 
-Proteobacteria. We focus on AT-rich primary endosymbionts to better understand the origins of obligately intracellular lifestyles. Previous phylogenetic analysis of this bacterial group point to the importance of accounting for base compositional variation in estimating relationships, particularly between endosymbiotic and free-living taxa. Here, we develop an approach to compare susceptibility of various phylogenetic reconstruction methods to the effects of nucleotide heterogeneity. First, we identify candidate trees of -Proteobacteria groEL and 16S rRNA using approaches that assume homogeneous and stationary base composition, including Bayesian, maximum likelihood, parsimony, and distance methods. We then create permutations of the resulting candidate trees by varying the placement of the AT-rich endosymbiont Buchnera. These permutations are evaluated under the non-homogeneous and non-stationary maximum likelihood model of Galtier and Gouy, which allows equilibrium base content to vary among examined lineages. Our results show that commonly used phylogenetic methods produce incongruent trees of the Enterobacteriales, and that the placement of Buchnera is especially unstable. However, under a non-homogeneous model, various groEL and 16S rRNA phylogenies that separate Buchnera from other AT-rich endosymbionts (Blochmannia and Wigglesworthia) have consistently and significantly higher likelihood scores. Blochmannia and Wigglesworthia appear to have evolved from secondary endosymbionts, and represent an origin of primary endosymbiosis that is independent from Buchnera. This new application of a non-homogeneous model (namely, to evaluate alternative trees developed under homogeneous models) offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and non-stationary base composition.
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