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Scaling properties of protein family phylogenies

Alejandro Herrada1*, Víctor M Eguíluz1, Emilio Hernández-García1 and Carlos M Duarte23

Author Affiliations

1 Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain

2 Instituto Mediterráneo de Estudios Avanzados, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, E-07190 Esporles, Spain

3 Oceans Institute, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia

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BMC Evolutionary Biology 2011, 11:155  doi:10.1186/1471-2148-11-155

Published: 6 June 2011



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.


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.


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.