Global Phylogeny and Evolution.
The global phylogeny was reconstructed in FastTree v2.10.1 compiled with double precision under the GTR model with gamma heterogeneity (51), and rooted at the reference sequence. The tree was visualized using ggtree in R (54). Lineages were defined using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages), with lineages with >200 taxa as of the May 19 summary being highlighted in the tree (22) (https://github.com/cov-lineages/lineages). The number of polymorphic sites was calculated as the number of sites which had at least one mutation relative to the reference sequence, Wuhan-Hu-1, ignoring gaps and ambiguities.