Scaling properties of protein family phylogenies

Background: One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with those of a set of species phylogenies. Results: The comparative analysis between protein and species phylogenies shows that both sets of phylogenies share a remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/ robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Conclusions: The invariance of the scaling properties at levels spanning from genes to species suggests that rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.