Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

To determine whether host jumping occurred more often toward the root or tips of the trees, we calculated the relative node depth for incongruent nodes between virus-host pairs of trees (see Fig 1C and 1D ). This metric counts the number of nodes contained within each clade in the host tree that are not present in the virus tree. Because this number can depend on the size of the tree, we divide each of the node depths by the largest value in the tree. Accordingly, this metric is decreased if incongruent clades correspond to shallow nodes ( Fig 1C) compared to deep nodes (Fig 1D) . For example, the maximum node depth is 1 if a pair of trees differs in the deepest node and approaches 0 if they differ only in very shallow nodes.