The program ModelFinder (42) as implemented in IQ-TREE was used to infer the optimal substitution model for our genome alignment. A maximum-likelihood phylogenetic tree was then built using the program IQ-TREE v1.4.3 (43), applying the generalized time-reversible (GTR) model with four gamma categories for rate variation, ascertainment bias on, and 1000 ultrafast bootstrap replicates (44). The L3 isolate SRR1188186 (Quebec, Canada) was used as an outgroup.

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