Population structure analysis.

Mean internal diversity for each time point and DNA source is shown for each patient. Genetic diversity (π), defined as the average number of nucleotide differences per site between any two sequences chosen randomly from the sample population, is calculated with the best evolutionary model found in the jmodeltest Tamura and Nei model [45]. The fixation index, FST, from the AMOVA analysis is a measure of the diversity of randomly chosen sequences within the same sub-population relative to that found in the entire population. A zero value implies that the two populations mix freely, while a value of one implies that the two subpopulations are completely separate. The Slatkin Maddison test uses an estimate of the number of ‘migrations’ between subpopulations to assess population structure, with smaller numbers of migrations (for a given number of sequences) indicating more structure. Both AMOVA and the Slatkin-Maddison test calculate a p value for the null hypothesis of no population structure by randomly permuting sequences between subpopulations; they differ as the AMOVA takes into account the frequency of each unique sequence or haplotype, whereas the Slatkin Maddison test does not.*Probability that a migration event is random after 10,000 resampling replicates.NA, indicates that the test or the data is not applicable or available.