(A) Table with VIPs. Interactions are described in the third column. For example, 19386720-EBV-dsDNA means that the article with PUBMED ID 19386720 describes an interaction between a mammalian host protein and an Epstein-Barr Virus EBV protein. The dsDNA label is for the fact that EBV is a double-stranded DNA virus (we use ssRNA for single–stranded RNA viruses, ssRNART for single-stranded RNA retroviruses, dsDNA for double-stranded viruses, dsDNART for double-stranded DNA retroviruses and ssDNA for single-stranded DNA viruses). If the interaction in the example was with EBV’s RNA, we would have 19386720-rna-EBV-dsDNA instead of 19386720-EBV-dsDNA. If the interaction was with EBV’s DNA, we would have 19386720-dna-EBV-dsDNA. (B) Table with the mammalian orthologous CDS information. The table contains the synteny information as well as the mammals-wide rates dN and dS for each of the 9,861 orthologs included in the analysis. (C) Table with GO categories with more than 50 VIPs. The table includes the information about the 162 GO biological processes with 50 or more VIPs. (D) Table with the 241 VIPs annotated as immune based on GO annotations. (E) Table with the human polymorphism and divergence information for the McDonald-Kreitman test. (F) Table with pN and pS in great apes. (G) Table with results of the forward simulations for the asymptotic MK test. The brackets give the 95% confidence intervals for the predicted α. Advantageous s is the selection coefficient of advantageous mutations. Deleterious s is the selection coefficient of deleterious mutations. (H) Excess of adaptation in human in highly expressed VIPs and non-VIPs at the RNA or protein levels, VIPs and non-VIPs with a high number of protein-protein interactions. (I) Table with mammalian orthologs and evidence of adaptation. The table provides all the 9,861 orthologs with best reciprocal hits (Material and methods), The first column is Ensembl Gene ID, the second column is BUSTED P-value, and the other columns are BS-REL estimated proportions of selected codons in all the 44 branches tested. Note that the proportions of selected codons are set to zero for those branches where there is no good synteny information (Materials and methods). (J) Table with Genbank identifiers for the 84 mammals ANPEP alignment.