Extended Data Fig. 8: Estimates of selection coefficients in a simple example of clonal interference.
From: MPL resolves genetic linkage in fitness inference from complex evolutionary histories
a, Two escape mutations arise in the TW10 epitope targeted by individual CH58 and compete for dominance. b, MPL infers that both TW10 escape variants are positively selected. Estimates based on trajectories of individual variants only infer substantial positive selection for the 1514A variant that fixes. The magnitude of selection inferred with the independent model is also smaller than that inferred by MPL. c, Inferred selection in the HIV-1 5′ half-genome sequence for CH58. Inferred selection coefficients are plotted in tracks. Coefficients of transmitted/founder nucleotides are normalized to zero. Tick marks denote polymorphic sites. Inner links, shown for sites connected to the TW10 epitope, have widths proportional to matrix elements of the inverse of the integrated covariance. Linked sites affect selection estimates within the epitope.
