The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
Figure 1
An overview of our phylogenetic inference procedure is given. We look only at histidine kinase domains from HPKs, and compare the distribution of these to the species tree. When homologs in distant outgroups are more distantly related, we infer simple vertical descent. Paralogs and distances that contradict species phylogeny result in our inference of gene duplication or horizontal transfer. Only events (such as duplication or transfer) that occurred more recently than the cutoff as described in the Methods are considered. Four hypothetical cases are shown, and each is labeled as present/absent (“1” or “0”) from each outgroup according to the procedure described in the Methods.