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Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).

Publication ,  Journal Article
Herbeck, JT; Degnan, PH; Wernegreen, JJ
Published in: Molecular biology and evolution
March 2005

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 gamma-Proteobacteria. We focus on AT-rich primary endosymbionts to better understand the origins of obligately intracellular lifestyles. Previous phylogenetic analyses 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 gamma-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 nonhomogeneous and nonstationary 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 nonhomogeneous 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 application of a nonhomogeneous model offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and nonstationary base composition.

Duke Scholars

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

March 2005

Volume

22

Issue

3

Start / End Page

520 / 532

Related Subject Headings

  • Symbiosis
  • RNA, Ribosomal, 16S
  • Plants
  • Models, Genetic
  • Genes, Bacterial
  • Evolutionary Biology
  • Evolution, Molecular
  • Enterobacteriaceae
  • Chaperonin 60
  • Base Sequence
 

Citation

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Herbeck, J. T., Degnan, P. H., & Wernegreen, J. J. (2005). Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). Molecular Biology and Evolution, 22(3), 520–532. https://doi.org/10.1093/molbev/msi036
Herbeck, Joshua T., Patrick H. Degnan, and Jennifer J. Wernegreen. “Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).Molecular Biology and Evolution 22, no. 3 (March 2005): 520–32. https://doi.org/10.1093/molbev/msi036.
Herbeck, Joshua T., et al. “Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).Molecular Biology and Evolution, vol. 22, no. 3, Mar. 2005, pp. 520–32. Epmc, doi:10.1093/molbev/msi036.
Journal cover image

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

March 2005

Volume

22

Issue

3

Start / End Page

520 / 532

Related Subject Headings

  • Symbiosis
  • RNA, Ribosomal, 16S
  • Plants
  • Models, Genetic
  • Genes, Bacterial
  • Evolutionary Biology
  • Evolution, Molecular
  • Enterobacteriaceae
  • Chaperonin 60
  • Base Sequence