Inference and characterization of horizontally transferred gene families using stochastic mapping.

ABSTRACT: Macrogenomic events, in which genes are gained and lost, play a pivotal evolutionary role in microbial evolution. Nevertheless, probabilistic-evolutionary models describing such events and methods for their robust inference are considerably less developed than existing methodologies for analyzing site-specific sequence evolution. Here, we present a novel method for the inference of gains and losses of gene families. First, we develop probabilistic-evolutionary models describing the dynamics of gene-family content, which are more biologically realistic than previously suggested models. In our likelihood-based models, gains and losses are represented by transitions between presence and absence, given an underlying phylogeny. We employ a mixture-model approach in which we allow both the gain

SUBMITTER: Cohen O 

PROVIDER: S-EPMC2822287 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature