Trees and networks based on the control region sequences excluding the R2 repeats.

<p>(a) Phylogenetic tree constructed using Bayesian inference. Numbers on branches are posterior probabilities. Individuals are coded as ID_L or ID_S (the clone number); (b) Statistical parsimony networks for each clade. Each circle represents a single haplotype and circle size is scaled by haplotype frequency. Filled black circles represent missing or unsampled haplotypes. The numbers between haplotypes and sub-networks represent the mutational steps between them. Individuals and haplotypes are coloured by taxon membership as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098035#pone-0098035-g001" target="_blank">Figure 1</a>.