Inferring time-consistent and well-supported horizontal gene transfers

The evolution of gene families is a complicated process that does not always reflect the evolution of the species they come from. These differences between genes and species evolution may be explained using the tree reconciliation model with gene duplication, loss, and horizontal transfer events. However, it is not always clear how to infer credible events from usually incongruent gene and species histories. In this article, we propose a new efficient dynamic programming approach to find evolutionary scenarios in acyclic graphs representing species evolution with horizontal transfers. Next, we formulate a new measure, based on non-parametric bootstrap, called transfer support, to verify the credibility of inferred transfers. Furthermore, we propose a novel iterative method for the inference of well-supported and time-consistent horizontal gene transfers given a multiple sequence alignment, and a species tree. Finally, we show that our method can be used to support known transfer hypotheses from the literature.