Abstract
The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representations. When LGT contribution to genome evolution cannot be neglected (e.g., for prokaryotes and mobile genetic elements), the tree becomes misleading. Networks appear as an intuitive way to represent both vertical and horizontal relationships, while overlapping groups within such graphs are more suitable for their classification. Here, we describe a method to represent both vertical and horizontal relationships. We start with a set of genomes whose coded proteins have been grouped into families based on sequence similarity. Next, all pairs of genomes are compared, counting the number of proteins classified into the same family. From this comparison, we derive a weighted graph where genomes with a significant number of similar proteins are linked. Finally, we apply a two-step clustering of this graph to produce a classification where nodes can be assigned to multiple clusters. The procedure can be performed using the Network Analysis Tools (NeAT) website.
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Acknowledgments
I wish to thank Raphael Leplae, Sylvain Brohée and Jacques van Helden for the maintenance of the ACLAME database and NeAT services, respectively, as well as Ariane Toussaint and Denis Thieffry for critical reading of the manuscript and testing the protocol.
Work on the ACLAME project in the BiGRe laboratory was financed by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the EXANAM project (PRODEX agreements No. C90358), the Fonds de la Recherche Scientifique Médicale (FRSM), the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office, project P6/25 (BioMaGNet), and the BioSapiens Network of excellence funded under the sixth Framework program of the European Communities (LSHG-CT-2003-503265).
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Lima-Mendez, G. (2012). Reticulate Classification of Mosaic Microbial Genomes Using NeAT Website. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_5
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DOI: https://doi.org/10.1007/978-1-61779-361-5_5
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