Recombination Rate and Selection Strength in HIV Intra-patient Evolution
Figure 2
Estimating recombination rates from time resolved data.
Panel A shows the probability of finding a haplotype that is not detected at time in the sample at
as a function of the separation
of the sites. The data labeled ‘recombinant haplotypes’ refers to those combinations, that can be generated by recombination from the alleles detected at time
and displays a pronounced distance dependence. The data labeled ‘other haplotypes’ refers to pairs containing at least one allele not detected at time
, implying an additional mutation or undersampling. The data is averaged over all time points, all patients, and those pairs of polymorphic sites, where both alleles at both sites are seen at least 3 times. Panel B shows the probability of finding the missing haplotype as a function of the product of distance
and time interval
. The fit to the data is shown in black with fit parameters indicated in the legend.