Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

ABSTRACT:

Background

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.

Results

We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E

SUBMITTER: Beauregard-Racine J 

PROVIDER: S-EPMC3160433 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature