Figure 4

Origin of the observed variation in gene copy number between Ascomycete species as explained by tree reconciliation. Panels A and B describe two hypothetical scenarios of how the size of a gene family increased in the extant species: A: enlarged gene family size due to a specific expansion in an extant species (species 1). B: enlarged gene family size in extant species 1 due to an expansion (duplication) in an ancestral node ('D') before the speciation event between species 1 and 2. Extant species 2 lost one of the copies ('L' in a red circle leading to a gray faded branch) C: Tree representing the phylogenetic relations between the studied species. Branches of the tree corresponding to pathogenic species are shaded in yellow. Pie charts indicate, for each of the extant species at the leave of a branch, how many of its gene families with increased size originated through scenario A and B. For instance, for a pathogen, scenario A means that there was a species-specific expansion in the pathogenic branch, while scenario B indicates the gene family in the studied species enlarged because of an ancestral duplication followed by a loss in the non-pathogen, closest to the studied pathogen (see species tree). The color level used in the pie charts (following the blue-to-red scale in below) is an indication for the fraction of enlarged gene families in the studied species, explained by either scenario A or B versus the total number of families included in the phylogenetic analysis. This shows that scenario B occurs much more frequently in absolute numbers in pathogens than in non pathogens.