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MBE Advance Access published online on October 15, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn219
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© 2008 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Letter

Characterization of Phylogenetic Reticulate Networks based on the Coalescent with Recombination

Miguel Arenas

Dept. of Biochemistry, Genetics and Immunology, University of Vigo, E-36310 Vigo, Spain

Gabriel Valiente

Technical University of Catalonia, E-08034 Barcelona, Spain

David Posada

Dept. of Biochemistry, Genetics and Immunology, University of Vigo, E-36310 Vigo, Spain

Received for publication August 14, 2008. Revision received September 19, 2008. Accepted for publication September 23, 2008.

Phylogenetic networks aim to represent the evolutionary history of taxa. Within these, reticulate networks are explictly able to accommodate evolutionary events like recombination, hybridization or lateral gene transfer. While several metrics exist to compare phylogenetic networks, they make several assumptions regarding the nature of the networks that are not likely to be fulfilled by the evolutionary process. In order to characterize the potential disagreement between the algorithms and the biology, we have used the coalescent with recombination to build the type of networks produced by reticulate evolution, and classified them as regular, tree-sibling, tree-child, or galled-trees. We show that, as expected, the complexity of these reticulate networks is a function of the population recombination rate. At small recombination rates most of the networks produced are already more complex than regular or tree-sibling networks, while with moderate and large recombination rates no network fit into any of the standard classes. We conclude that new metrics still need to be devised in order to properly compare two phylogenetic networks that have arisen from reticulating evolutionary process.


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