Figure 2.

Effect of horizontal gene transfers (HGTs) on the observable gene phylogenies. Here we show 4 examples where Eukarya and Bacteria do not share a common ancestor with Archaea – each domain is represented by a color but individual species are not identified. In the left column we have the transfers represented by red arrows defining donor and recipient, while in the right we have the resulting phylogenetic trees. The first scenario (A) is one with no apparent HGT (no change in topology), while B) represents a gene transfer from a Bacteria to an Eukarya, such that for this gene the eukaryotic species will have an homolog resembling a bacterial one (such homologs are called xenologs actually). C) shows a transfer from an archaean ancestor to a bacterial one, and D) describes a transfer from Bacteria to Archaea. Notice that under scenario D the archaean version of the gene is lost and all species share the bacterial one. For scenarios B, C and D we assume that the recipients of the gene transfer lose their original copies, which are replaced by the foreign ones.