FIG. 1.

Phylogenetic trees of the various genes in the analysis, with host and lineage indicated by branch colors: avian (black), human (red), classical swine (blue), and Eurasian swine (cyan). For PA and PB2, we additionally include triple-reassortant swine sequences (green). The location of the host shift used in the calculations is indicated by an orange dot. Shifting the location of the host-shift event did not appreciably change the results. 1918 and pandemic H1N1 2009 sequences are labeled. Horizontal line represents a branch length corresponding to 0.1 nucleotide substitutions per site. Only the avian and human sequences were used in determining the significant locations, the equilibrium amino acid frequencies, and the ancestral reconstructions as explained in the text.