Fig. 4: Phylogenetic relationships among New and Old World L. infantum isolates.

The maximum-likelihood tree was built using a general time-reversible substitution model with branch lengths corrected for ascertainment bias (i.e., the use of only nonvariant sites in sequence alignment). Pairwise genetic distances are haplotype-based, defined as the proportion of non-shared alleles across all SNP sites for which genotypes are called for all individuals (i.e., no missing data in alignment). Outlier isolates NonDel_MS_MAM, NonDel_FR_47, NonDel_PT_151, NonDel_PA_317, and NonDel_PA_85 are excluded. L. donovani strain MHOM/NP/03/BPK282/0 was temporarily included as an outgroup, to identify an L. infantum sample to subsequently root the tree. NonDel_ES_1345 became the outgroup. Circle fill color indicates New vs. Old World origin and read-depth profile on chr31. Font color specifies states sampled in Brazil. Isolates from other countries are labeled in black.