Fig. 1

Homology, species-level orthology, and synteny conservation. The phylogeny of a gene family that has experienced intra-species HGT (*) and inter-species HGT (**) is superimposed on a species tree (colored ribbons). In the species tree, speciation is followed by diversification into two strains (blue), and a sister species is represented in green. Gene neighborhoods are displayed at the leaves of the gene tree, with the gene of interest in the middle (labeled A–D, larger size, and red border). All sequences (A–D) are homologs. However, only A, B, and C are species-level orthologs, because they descend from the same ancestral sequence at the time of speciation. Of those, A and C were vertically transmitted and share conserved gene neighborhoods (synteny). Sequences B and C are in-paralogs, whereas C and D are out-paralogs