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Of Trees and Bushes: Phylogenetic Networks as Tools to Detect, Visualize and Model Reticulate Evolution

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Evolutionary Biology: Exobiology and Evolutionary Mechanisms

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Abstract

Phylogenetic trees have been the main tools for representing evolutionary relationships among biological entities at the level of species and above, and their use has greatly facilitated the discussion and testing of phylogenetic and evolutionary hypotheses. However, they are not well suited to model nor represent well known non-vertical evolutionary events such as recombination, horizontal gene transfer, and polyploid and hybrid speciation. Recent advances in phylogenetic network estimation and implementation to genomic data sets, of which I present a brief summary, can better account for reticulated and complex evolutionary histories.

Molecular phylogeneticists will have failed to find the true tree, not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree

Ford Doolittle

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  1. LATP UMR—CNRS 7353 Evolution Biologique et Modélisation, Aix-Marseille Université, Case 19, 3 Place Victor Hugo, 13331, Marseille CEDEX 3, France

    Antonio Hernandez-Lopez

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Correspondence to Antonio Hernandez-Lopez .

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  1. CNRS UMR 6632, Labo. Evolution Biologique et, Université d'Aix-Marseille, place Victor Hugo 3, Marseille CX 03, 13331, France

    Pierre Pontarotti

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Hernandez-Lopez, A. (2013). Of Trees and Bushes: Phylogenetic Networks as Tools to Detect, Visualize and Model Reticulate Evolution. In: Pontarotti, P. (eds) Evolutionary Biology: Exobiology and Evolutionary Mechanisms. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38212-3_10

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