Genes with multiple predicted orthologs. (A) Conceptual drawing showing how a gene A1 in A. thaliana can have a neighbourhood that is both conserved when compared to one ortholog P1 in Populus and diverged if compared to another ortholog P5. Lines between genes in different species indicate orthologs. (B) Pairwise comparisons of network neighbourhoods of genes with more than one predicted ortholog at a CLR threshold of two. In each comparison X ─ > Y, the genes in species X is divided into genes where all ortholog-neighbourhoods are conserved in species Y (Uniquely conserved), genes with at least one conserved neighbourhood in species Y (Conserved), genes with at least one conserved and at least one diverged neighbourhood in Y (Conserved and Diverged), genes with at least one diverged neighbourhood in Y (Diverged) and genes with no significant neighbourhoods in Y (None).