Sites identified as undergoing changes in selective pressure during host shifts from birds to humans.

Legend: Position: Sites in H1, H2, and H3 are identified with respect to their H3 positions. (Locations with negative positions represent an N-terminal insertion in H1 relative to H3. Similarly, location H1 271A represents an insertion between locations 271 and 272.) Numbering refer to HA1 unless specified HA2. Sites in N1 and N2 are identified with respect to their own indices. P: P value using LRT for non-homogeneous model (Model 3) compared with homogeneous model (Model 4). δ: Minimum FDR value required for this site to be identified. This should not be equated with the probability that this identification is a false positive. Residues Identities: Residue identity is shown unadorned if its equilibrium frequency is greater than 0.5, in single parentheses if its equilibrium frequency is between 0.1 and 0.5, and in double parentheses if its equilibrium frequency is between 0.01 and 0.1. Residues with equilibrium frequencies below 0.01 are not listed. Selective (Sel.) constraints represent the strength of the selective pressure in the two different hosts as defined in Equation 5. Cal-4: Identity of the amino acid at this location in a sample of the recent Swine flu outbreak (A/California/04/2009(H1N1)).