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Scaling properties of protein family phylogenies

DOI: 10.1186/1471-2148-11-155

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Abstract:

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.During the last century, an important effort has been devoted to the understanding of diversification patterns and processes in terms of branching evolutionary trees [1-7]. Tempo and mode of genetic change, and their connections with tempo and mode of speciation is an important issue in this context. In that sense, we address the question of whether similar forces act across the gene level and species-level evolution [8-10], through a comparative analysis of the topological behavior of protein and species phylogenies.Previous analyses of the topological properties of phylogenies have revealed universal patterns of phylogenetic differentiation [3,6,7,11,12]. This means that the impact of evolutionary forces shaping the diversity of life on Earth on the shape of phylogenetic trees is, at least to the level of detail captured by the descriptors used, similar across a broad range of scales, from macro-evolution to speciation and population differentiation, and across diverse organisms such as eukaryotes, eubacteria, archaea or viruses, thereby. This together with the fact that evolutionary forces work at molecular lev

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