Results from the selection, distance and midpoint rooting analyses.

N: number of strains (haplotypes) sequenced. bp: number of aligned nucleotides used in the PAML analyses.aThe percent of sites with ω = dN/dS>1. ω estimated from the M8 model implemented in PAML. NA: Non-applicable, non-coding intergenic region.bAverage ω (dN/dS) for sites with dN/dS>1. NA: Non-applicable, since no sites had dN/dS>1.cdN/dS estimated for the two haplotypes of CL Brener using PAML's codeml program with the pairwise distance estimation option (runmode = −2).dEstimate of the % corrected distance for all sites (Kimura 2-parameter) or for synonymous sites only (Ks) between a strain of TcI (SC13) and a strain of TcII (CBB cl3), corresponding to the largest genetic distance within T. cruzi. NA: Non-applicable, non-coding intergenic region.eThe topology obtained with midpoint rooting (See Figure 1 for Topology definitions). ND (Non Described topology): the topology obtained was different from the topologies described in Figure 1.fHSP70 is an intergenic region, thus selection tests were not conducted.gThe midpoint rooting topology was different from the topology reconstructed with an outgroup (Table 2).*Only significant for M8 vs M8a (p ≤ 0.05).**Significant for M8 vs M8a (p ≤ 0.01), M1 vs M2 (p ≤ 0.05), and M7 vs M8 (p ≤ 0.05).***p value ≤0.0001 in all three tests (M1 vs M2, M7 vs M8, M8 vs M8a).