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Figure 6 | Retrovirology

Figure 6

From: Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

Figure 6

Selection dynamics of complete genome haplotypes. Dominant haplotypes for each sample are denoted by black circles, and the less abundant haplotypes are denoted by grey squares. The dominant and less abundant haplotypes are connected to those haplotypes from the previous time point having the minimum non-synonymous Hamming distance (mentioned above each edge). The less prevalent haplotypes at day 1543 were closer to the dominant haplotype at the same day compared to any haplotype present at day 476, and thus are shown to have a predecessor at an intermediate time. The rate of replacement by a haplotype genome is represented by dashed lines: in red for dominant haplotypes, and in blue for non-dominant haplotypes. Note that the horizontal axis has no true time scale. Selection coefficients for dominant haplotypes are shown in the inset. Selection coefficients for the dominant haplotype genomes were calculated using the predicted haplotype frequency at time t and its frequency at preceding time point t-1 using the method described in [22]. The mutant was considered to have a prevalence of 3% at the preceding time point (because we cannot reliably detect haplotypes below a 3% frequency).

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