But as the tools of genome analysis became more refined, searches for similar genes sometimes turned up sequences that belonged to a species on a different branch of the evolutionary tree. Clearly, vertical gene transfer was not the only mechanism of genetic transmission. Organisms, it turns out, can acquire genes from non-ancestral species through a mechanism called horizontal gene transfer (HGT).
Such genetic exchanges, most common among bacteria and other microbes, are not represented in the tree of life—no single branch connects the two unrelated species. Initial studies suggested that HGT events were extremely common, prompting some to say it was time to replace the tree with a netlike diagram. Other studies have since suggested that methods used to calculate HGT overestimated its frequency: researchers detect HGT events by finding inconsistencies between gene trees and organism, or whole-genome, trees, but statistical errors can artificially increase the number of HGT events."
(2005) Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3(10): e347