Parallel change in evolutionary rate leads to rate covariation. Most proteins encoded in a genome evolve over the same species tree and so have evolved for the same amount of chronological time over each branch. Yet individual proteins experience varying rates of sequence evolution over those same branches. Hypothetical protein “A” experienced rapid evolution in one species lineage (red branch) and an exceptionally slow rate of evolution in another (blue branch). Another protein “B” experienced very similar rate variation during the evolution of these species, so that its branch rates are positively correlated with the rates of protein A (upper plot). Their evolutionary rate covariation suggests a relationship between A and B. Another protein, “C,” also experienced acceleration and deceleration, but its evolutionary pattern did not result in ERC with protein B (lower plot). Note that the values in these plots are rates of sequence evolution normalized to the expected rate given the species tree.
