Supplementary Tables S1-S5

Supplementary Table S1: Matrix of genotypes defined within each of the genes Supplementary Table S2: Lineages in gene trees under significant positive selection. The table is a summary of branches across all HCMV gene trees that evolved under significant (corrected p-value < 0.05) positive selection according to the aBSREL test (Smith et al. 2015), i.e. with a non-null proportion of sites evolving under a dN/dS rate higher than 1 (proportion and rate of positively selected sites are indicated by columns “WtOmegaOver1” and “OmegaOver1”, respectively). The table is a collated output of HyPhy program, complemented with the list of strains contained in one clade defined by each branch. Genes that are both high-LD and hypervariable (Table 2, Supplementary Table S2) are highlighted in orange. Supplementary Table S3: Summary of positive selection, LD and diversity scans Supplementary Table S4: List of genes with the strongest hotspots of nucleotidic diversity (hyper-variable genes). Supplementary Table S5: Summary statistics of local LD detection in simulated genomes.