Fig. 2

Gene-gene coevolution network for the top 77 significant gene pairs in the full dataset, with nodes colored by gene function, edge color indicating the strength of the inferred interaction, and edge type indicating the polarity of the interaction. A small handful of kinds of genes that are all frequently horizontally transferred—primarily relating to resistance, virulence, or gene transfer itself—tend to dominate the interaction network. The cluster involving bbp, clf, and sdr genes likely is a result of a limitation of automated annotation software, which appears in this case to have given different names to different versions of the same gene families. Thus, these interactions are negative because they represent alternate annotations