Evolutionary events explaining gene copy number variations between pathogens and non-pathogens. Numbers at each node represent the presence ('1') or absence ('0') of members of a hypothetical gene family in each lineage descending from an ancestral species. A) Pathogen-specific gene family gains (Class 1). This event explains the origin of gene families that are not present in an ancestral species common to both pathogenic and non-pathogenic lineages, but appear in one extant pathogen or in an ancestral node that gives rise to exclusively pathogenic lineages. B) Pathogen-specific gene family expansions (Class 2): gene families that are already present in the last common ancestor of the extant species become expanded in a lineage specific way (denoted by a star (*)). C) Non-pathogen-specific losses (Class 3). This event results in gene families that were either present in the last common ancestor of all species or in an ancestor common to both pathogenic and non-pathogenic lineages to become lost selectively in non-pathogenic lineages. Loss of a gene family refers to selective loss of all its members in the considered species or ancestral node. In our study, non-pathogen-specific gene family loss was only observed in extant species. Note that in the pathogenic lineages where members of the considered families were not lost, sometimes a further expansion of the families was observed as denoted by a star (*). D) Pathogen-specific gene family losses (Class 4): gene families either already present in the last common ancestor of all species or in an ancestral species common to both pathogenic and non-pathogenic lineages got lost selectively in pathogenic lineages. In our study, this pathogen-specific gene family loss was also only observed in extant species.