Fig. 2. Probability of phylogenetic structures arising from a single introduction of SARS-CoV-2 in epidemic simulations.

(A) A large polytomy of at least 20 descendent lineages, consistent with the base of both lineages A and B. (B) Topology matching a C/C ancestral haplotype: two clades each one mutation from the ancestor, both with polytomies of at least 20 descendent lineages. (C) Topology matching either a lineage A or lineage B ancestral haplotype: a basal polytomy with at least 20 descendent lineages including a large clade separated by two mutations, also possessing a polytomy of at least 20 descendent lineages. Basal taxa have short branch lengths for clarity. The probability of each phylogenetic structure after a single introduction is reported in the box.