Extended Data Fig. 2: Comparison of the topologies of maximum-likelihood (ML) trees.
From: Redefining the treponemal history through pre-Columbian genomes from Brazil
a) ML tree topology with all genes included in the multiple genome alignment using GTR + G + I as the evolutionary model and 1000 bootstrap repetitions. b) ML tree topology after excluding tp0897, tp0316 and tp0317 and recombinant genes from the multiple genome alignment using GTR + G + I as the evolutionary model and 1000 bootstrap repetitions. The different clades corresponding to TPE and TEN, and the Nichols and SS14 lineages of TPA are colour-coded according to the legend. Bootstrap support values higher than 70% are indicated by pink circles, with circle size proportional to bootstrap support. The subclade SS14-Ω, that includes all SS14-lineage TPA strains except ancient TPA strains, MD06B, MD18Be and MexicoA, is collapsed.
