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. 2010 Mar 24;7(50):1257–1274. doi: 10.1098/rsif.2010.0007

Figure 7.

Figure 7.

Phylogenies of influenza A H3N8's HA in equine hosts, reconstructed from empirical and simulated viral sequences. (a) Phylogeny inferred from equine influenza virus H3N8 sequences isolated in Europe and North America. Split of the American and European lineages occurred between 1986 and 1990. Sequences isolated from North America are shown in blue. Sequences isolated from Europe are shown in red. Three antigenic variants have been well characterized: the original Mia/63 antigenic variant (yellow), the Ky/76 variant (purple) and an unnamed variant (orange) that appears antigenically similar to Mia/63 (Hinshaw et al. 1983). (b) Phylogeny inferred from 200 simulated H3N8 HA sequences. Prior to quarantine, there is linear evolution of EIV's HA until the lineage split in the late 1980s. Viral isolates belonging to the simulated European lineage were only observed in the European patch, whereas viral isolates belonging to the American lineage were isolated in both the North American patch and the European patch. The GTR + I + Γ parameters used in the molecular sequence evolution model were set to those estimated from the influenza A (H3N8) phylogeny shown in (a). These were: (πA, πC, πG, πT) = (0.35, 0.21, 0.22, 0.22), transition rates: AC = 0.97, AG = 5.65, AT = 0.83, CG = 0.35, CT = 7.74, GT = 1, gamma distribution parameter α = 0.91 and proportion of invariant sites f0 = 0.17. Other parameters for the molecular evolution submodel were mnuc = 5.7 × 10−3 mutations per nucleotide site per year and f = 0.01.