It is an analytical review of a crucially important evolutionary phenomenon—horizontal gene transfer—the true scope of which has become apparent only after multiple prokaryotic genomes have been sequenced. Many researchers are understandably interested in horizontal gene transfer, and this paper seems to provide a coherent conceptual framework for theoretical and experimental analysis of this phenomenon.

This paper is a review and as such describes neither a specific new discovery nor a method. However, in my assessment, it has two innovative aspects: 1) for the first time, conservative quantitative estimates are given of the number of genes that likely have been acquired via horizontal transfer in a variety of prokaryotic genomes; 2) an evolutionary classification of horizontal gene transfer events is presented.

The extensive, genome-wide horizontal gene transfer became apparent when several bacterial and archaeal genomes had been sequenced in 1997-1998. The first publications arguing for extensive horizontal gene transfer, including those from our group, appeared at that time. By the end of the 20^th century, it was time to try and place these findings within a single conceptual framework.

Ever since the work of Charles Darwin, evolution of life was depicted as a huge tree with several big trunks and numerous branches and twigs. Even when some inconsistencies in evolution of individual genes were detected, this was largely attributed to inaccuracies in the methods used for evolutionary reconstruction. However, the first careful comparisons of the complete genomes of simple organisms, archaea and bacteria, showed beyond reasonable doubt that the tree metaphor of life's evolution was hopelessly flawed because horizontal gene transfer involves a major fraction of genes in each genome. Thus, the notion of a tree as an adequate description of organismal evolution needs to be either abandoned or substantially modified such that a tree will depict evolution of a small core of genes minimally prone to horizontal transfer will be overlaid with connections showing horizontal gene flow.