Subsampling Gene Alignments.
Alignments for each gene were subsampled for sequence and phylogenetic analyses. Each gene alignment was randomly subsampled 100 times per collection date at 5%, 10%, 20%, 30%, and 40%. When fewer than 10 sequences were available for a collection date, all sequences were taken. Median Hamming distances were computed for each set of subsampled alignments. These were bootstrapped 100,000 times, and 95% CIs were estimated and compared to the median Hamming distance for the fully sampled alignment.