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Biology & Philosophy

, Volume 25, Issue 4, pp 711–736 | Cite as

On the need for integrative phylogenomics, and some steps toward its creation

  • Eric BaptesteEmail author
  • Richard M. Burian
Article

Abstract

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years.

Keywords

Lateral gene transfer Molecular evolution Tree of life Mobile genetic elements Network 

Notes

Acknowledgments

We thank the “Questioning the Tree of Life” project, sponsored by the Leverhulme Trust, for encouraging this contribution. EB thanks J. Leigh, P. Lopez, S. Halary, F.J. ‘Quick’ Lapointe and Y. Boucher for stimulating discussions; RB thanks J. Jelesko, R. Jensen, B. Mukhopadhyay, and J. Sebutal for stimulating discussions.

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© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.UMR CNRS 7138UPMCParisFrance
  2. 2.Department of Philosophy – 0126Virginia TechBlacksburgUSA

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