Extended Data Fig. 1: Comparison of phylogenetic trees of RNA-directed RNA polymerase domain (NS5/NS5B) produced by different tree-building methods.

Phylogenetic trees constructed by likelihood (a, b) and distance-based (c) methods using flavivirus and ‘flavi-like’ RNA-directed RNA polymerase (RdRP) domain amino-acid sequences. Clades (I–IV) and lineages (a–w) labelled in each tree are based on those in Fig. 1b. Tentative threshold levels of divergence separating clades and lineages are shown as red dotted lines in BEAST and UPGMA trees. An alternative threshold corresponding to the assignment of lineages Ia-Id to a common lineage is shown in a blue dotted line. Abbreviations: BP, before present; BEAST, Bayesian evolutionary analysis by sampling trees cross-platform program; JTT, Jones-Taylor-Thornton matrix; ML, maximum likelihood; UPGMA, unweighted pair group method with arithmetic mean.