Fig. 2: Phylodynamics of H5N1 HPAI (2.3.4.4b) viruses in South American marine mammals and birds.

A Time-scale MCC tree inferred for the concatenated genome sequences (~ 13 kb) of 236 H5N1 influenza A viruses (clade 2.3.3.4b) collected in five South American countries (Argentina, Brazil, Chile, Peru, Uruguay) and in South Georgia and the Falkland/Malvinas Islands. Branches are shaded by inferred host species (4 categories). Posterior probabilities are provided for key nodes. The same tree with tip labels and posterior probabilities for all nodes is available in Supplementary Fig. 4. B Direction of virus gene flow between locations and hosts, inferred from “Markov jump” counts across the posterior distribution of trees inferred using a Bayesian approach (values under 0.5 excluded). Different host groups are indicated with different colors: wild birds (orange), marine mammals (red) and terrestrial mammal (blue). The same graphic with 95% HPD (highest posterior density) labels is available in Supplementary Fig. 5. Tree with all location states labeled is available in Supplementary Fig. 6. C Posterior distributions of evolutionary rates (substitutions per site per year) inferred for the complete virus genome (all positions) and for only the third nucleotide position for H5N1 (2.3.4.4b) in South America, partitioned into two host categories: marine mammal clade (excluding any human and avian viruses) and avian (wild bird/poultry) clade (excluding any mammal viruses). Source data for the histogram graph are provided as a Source Data file.