On the need for integrative phylogenomics, and some steps toward its creation Eric Bapteste • Richard M. Burian Published online: 1 May 2010 Ó Springer Science+Business Media B.V. 2010 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 com- plexes. 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 gen- omes. 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 Á Molecular evolution Á Tree of life Á Mobile genetic elements Á Network This paper has its roots in the fertile research fields masterfully sown by Ford Doolittle. E. Bapteste (&) UMR CNRS 7138, UPMC, 7, Quai Saint Bernard, 75005 Paris, France e-mail: eric.bapteste@snv.jussieu.fr R. M. Burian Department of Philosophy – 0126, Virginia Tech, Blacksburg, VA 24061, USA e-mail: rmburian@vt.edu 123 Biol Philos (2010) 25:711–736 DOI 10.1007/s10539-010-9218-2