Probabilistic inference of lateral gene transfer events.

Background: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge.

Gene-pseudogene evolution: a probabilistic approach.

Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g.

Genome-wide probabilistic reconciliation analysis across vertebrates.

Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation--a mapping of gene tree vertices to the edges or vertices of a species tree--explains where gene duplications have occurred on the species tree. In this study, we sample reconciliations from a posterior over reconciliations, gene trees, edge lengths and other parameters, given a species tree and gene sequences.