ERVW-1 and infection: Fig 1 shows average pairwise distance in the pol separately for each codon position. Most diversity in pol is synonymous and accumulates at 3rd codon positions, while diversity at 1st and 2nd codon positions remained low throughout. This pattern was less pronounced in other genes [24, 37] (see also S1 and S2 Figs). In env, in particular, frequent selective sweeps result in a saturation of diversity later in infection [17, 24].