Figure 3.

Phylogenetic reconstructions

(A) Maximum Likelihood topology returned by IQTree (Minh et al., 2020) using a TVM + F + R6 substitution model and a total of 21,279 polymorphic sites. Node supports are indicated using SH-aLRT support (Guindon et al., 2010) (left), as well as the ultrafast bootstrap approximation (Hoang et al., 2018) (right) when superior or equal to 80%. Only one value is shown when both supports are equal to 100%.

(B) Consensus maximal clade credibility phylogeny obtained with BEAST v2 (Bouckaert et al., 2019) restricting the sequence alignment to ancient and modern plague genomes phylogenetic clustering with or descending from second pandemic strains.