Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes - 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.