Ancient horizontal gene transfer can benefit phylogenetic reconstruction.

Although horizontal gene transfer (HGT) is usually considered a disruptive force in recovering organismal phylogeny, it creates important phylogenetic information. In the 'net of life', the recipient of an ancient gene transfer can be the ancestor of a lineage that inherits the transferred gene; thus, the transferred gene marks the recipient and its descendants as a monophyletic group. Ancient gene transfer events can also reveal the order of emergence of donor and recipient lineages. In addition, these ancient events can significantly shape the genetic systems of the recipients and can play a part in their long-term evolution. In this article, we discuss the recent progress in phylogenetic application of ancient HGTs and describe two examples of transfer events to the ancestor of red algae and green plants that support a common origin of these two groups. We also address the potential pitfalls of this application.