Consolidation of slow or fast but not moderately evolving genes at the level of pathways and processes

• Three-phase distribution is observed for consolidated pathways/processes.
• Genes within a pathway/process can be consolidated by selection but not by drift.
• The left and right phases correspond to negative and positive selection, respectively.
• Positive selection seems to occur in nature more often than it is supposed to.
• This is important because positive selection is associated with functional change.

Conservatism versus innovation is probably the most important dichotomy of all evolving systems. In molecular evolution the distinction between conservative (negative) selection, innovative (positive) selection and unconstrained evolution (drift) is usually ambiguous at the gene level. Only rare cases with the ratio of nonsynonymous to synonymous nucleotide substitutions above unity (dN/dS > 1) are thought to be due to positive selection, whereas the lower dN/dS ratio may indicate negative selection in combination with drift. The density of the dN/dS ratio for orthologous genes forms a unimodal distribution where no particular regions can be discerned. Here it is shown that at the level of overrepresented pathways and processes the picture is strikingly different. The distribution is strongly polarized with a wide completely depressed middle part. This three-phase distribution is very robust. It is observed with various substitution models and remains at very low significance of overrepresentation (up to p < 0.99). This fact suggests consolidation of either negative or positive selection but not of unconstrained evolution at the level of pathways/processes. The effect is demonstrated for different phylogenetic distances: from human to other primates, mammals and vertebrates. This approach suggests estimating the boundaries for conservative and innovative selection using the pathway/process level. Emphasizing the role of a critical mass of negatively or positively selected genes in a pathway/process, it can elucidate how the bridge between ‘tinkering’ at the gene level and ‘design’ at the higher levels is forming.