Fig. 3. Phylogeography of ZIKV in the Americas.

Maximum clade credibility phylogeny, estimated from complete and partial Am-ZIKV genomes using a molecular clock phylogeographic approach (Methods). Terminal branches with yellow circles indicate sequences reported in this study. Terminal branches with no circles and reduced opacity are those reported in a companion paper²⁰. Thin vertical grey boxes indicate statistical uncertainty of estimated dates of nodes A, B and C (Extended Data Table 3c). Branch colours indicate the most probable ancestral lineage locations. Diamonds at internal nodes are sized in proportion to clade posterior probabilities. For selected nodes, coloured numbers show the posterior probabilities of ancestral locations and numbers in grey are clade posterior probabilities. Asterisks indicate the three available genomes from microcephaly cases. A black arrow indicates the oldest Brazilian ZIKV sequence. The grey arrow and dotted line denotes when ZIKV was first confirmed in the Americas¹. Nodes A and B are equivalent to the nodes named identically in⁴. Text labels along the bottom of the figure denote clades of sequences from regions outside of NE Brazil. RJ1 to RJ4 are clades from Rio de Janeiro state, TO from Tocantins, and SP1 from São Paulo state. Clades from outside Brazil are denoted CB1 and CB2 (Caribbean), SA1 and SA2 (South America excluding Brazil), and CA1 (Central America). Thin grey horizontal lines along the bottom of the figure denote sequences from Brazil.