Fig. 2

Maximum-likelihood phylogenies and clustering assignments of (A) pre-Delta introduction wave (N = 19,617) and (B) Delta wave (N = 17,297) sequences. Sequences in the largest five clusters found by each method are coloured, with those in the largest cluster in red, followed by green, blue, yellow, and pink. All other clustered sequences are coloured grey, and non-clustered sequences are in white