Fig. 4. Phylogeography of sublineage SL1.

(A) Time-calibrated phylogeny based on the 1956 SL1 genomes (full view of Lm-CC1 in fig. S10). Pies at the nodes represent the probability of ancestral geographical locations, estimated using PastML using the MPPA method with an F81-like model. (B) Inferred spread of SL1 populations across continents. The first introductions of each phylogroup are represented by arrows from their estimated world region origin. Gray labels and arrows denote clades with uncertain ancestral origin among datasets. (C) Proportion of intercontinental transitions per 10-year bins, normalized by the total number of phylogenetic branches per bin.