Fig. 3: RIPPLES uncovered evidence that the B.1.355 lineage might have resulted from a recombination event between lineages of B.1.595 and B.1.371.

a, Sub-phylogeny consisting of all 78 B.1.355 samples (purple) and the most closely related 78 samples to nodes 94,353 and 102,299 from lineages B.1.371 and B.1.595, respectively, using the ‘k nearest samples’ function in matUtils²⁰. Nodes 94353 (red) and 102299 (blue) are connected by dotted lines to node 94,354 (purple), the root of lineage B.1.355. Recombination-informative mutations are marked where they occur in the phylogeny, with those occurring in a parent but not shared by the recombinant sequence shown in grey. b, Recombination-informative sites (that is, sites where the recombinant node matches either but not both parent nodes) are shown following the same format as Fig. 2b–d. b was generated using the SNIPIT package (https://github.com/aineniamh/snipit).