Supplementary Files S1-S5

Supplementary File S1: Simulation parameter files and guide trees (ZIP archive) Supplementary File S2: PCA plot based on diversity of bi-allelic SNPs (PDF file). Same projection as in Figure S5, with samples distinguished by different metadata: country of isolation, year of isolation, host immune status, body compartment of isolation ('respiratory' pools BAL and nasal rinse, 'blood' pools whole blood and plasma). Supplementary File S3: Posterior probability and compatibility matrices of bipartitions in gene trees (XLSX spreadsheet) Supplementary File S4: Local LD index values along HCMV whole-genome alignment. (XLSX spreadsheet) Supplementary File S5: Trees of hyper-variable loci with episodes of positive selection highlighted (PDF file)