Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution
Figure 1
Phylogenetic tree of human and swine NP homologs.
The human and swine NP lineages in this tree are descended from a virus closely related to the 1918 virus. Swine viruses are highlighted in yellow; all other viruses are human. In red are the lines of descent to the human H3N2 strains Aichi/1968 and Texas/2012 from their most-recent common ancestor. In green are the lines of descent to the swine H1N1 strains swine/Wisconsin/1957 and swine/Indiana/2012 from their most-recent common ancestor. Overall, this tree shows NPs from the following lineages: human seasonal H1N1, human H2N2, human H3N2, and North American swine viruses. The tree is a maximum clade credibility summary of a posterior distribution sampled from date-stamped protein sequences using BEAST [51] with a JTT [66] substitution model. See http://jbloom.github.io/mutpath/example_influenza_NP_1918_Descended.html for code, input data, and detailed documentation.