Herpesviruses share a set of 41 core orthologous proteins which are conserved throughout the three subfamilies (Table S5 ) [31] . These core orthologs comprise approximately half of the genome of HSV-1, VZV, EBV and KSHV but less than 25% of mCMV. They can be further subdivided into a group of 31 orthologs with relatively high sequence similarity (approximately 30-60% sequence similarity), and a group of 10 orthologs with little similarity (approximately 16-30% similarity) (Table S6 ). Based on this orthology assignment, we generated an overlay of all protein interactions between the core orthologs detected in any of the five herpesviruses (Core network, Figure 3A ). Of a total of 283 (218 In each rectangle, the value above the lines indicates the observed number of homologous interactions detected in both herpesviruses (in green). The value below the line (in black) gives the total number of interactions detected in the first species (indicated in columns) between proteins which have orthologs in the second species (indicated in rows). On the diagonal, the total number of interactions is shown for each virus. (C) Distribution of the number of conserved interactions between HSV-1 and mCMV for 1000 random orthology assignments (blue line) in comparison to the true number of conserved interactions (red vertical line). For each pairwise comparison, subnetworks were selected between proteins conserved in both viruses and then the orthology assignments between the proteins were randomized. Accordingly, the size and degree distribution of the subnetworks does not change. (D) Comparison of the number of interactions conserved in 2, 3, 4 and 5 species for 1000 random orthology assignments (yellow boxes) to the true number of interactions conserved in that many viruses (red line). Random orthology assignments were created in a similar way as for Figure 2C . non-redundant) core protein interactions detected, 113 (48 nonredundant, 39.9%) were found in more than one species (Table  S7) . For the core network, we did not observe a correlation between sequence similarity and the number of conserved interactions detected ( Figures 3B and 3C ). For example, the interaction between the two tegument proteins UL11 and UL16 in HSV-1 was also detected in mCMV and EBV, although sequence similarity of UL11 and its orthologs across subfamilies is quite low (28%). This interaction was interestingly also observed for HSV-1 in a recent report by Vittone and colleagues [33] . In addition, interactions were not preferentially conserved between closely related species ( Figures 3D and S8) . Accordingly, overlaps between the interaction sets in the core network were not correlated to the true phylogeny of herpesviruses ( Figure 3E ). Indeed, the highest overlap was observed between HSV-1 (a-subfamily) and mCMV (b) which belong to lineages separated early in herpesvirus evolution [7] . However, since our phylogenetic trees are based on relative overlaps between the different species, we cannot exclude that a more complete set of core interactions might have allowed for better separation of the subfamilies. In contrast, when also including subfamily-and species specific interactions (i.e. the complete interaction network of the five herpesviruses with the characteristic sunflower structure, see Figure 4A ), the analysis yielded a phylogeny that was consistent with the known evolutionary relationships ( Figure 4B ). This indicates that the presence of conserved subfamily specific interactions provides sufficient conserved and non-conserved interactions to accurately separate the subfamilies from each other.