Identifying Changes in Selective Constraints: Host Shifts in Influenza
Illustrative phylogenetic trees showing set of avian and human influenza sequences. A: In the homogeneous models (Models 1 and 2), the same substitution rates are used throughout the tree. B: In the non-homogeneous models (Models 3 and 4) different substitution rates are used for the avian (red) and human (blue) lineages. The root of the tree is assumed to be inside the avian lineage. (Because the model is reversible within the avian clade, the exact location of the root within this clade does not affect the calculation.) The host shift event is assumed to occur at the midpoint of the branch connecting the common ancestor of the human strains with its parent.