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Beyond the tree of life

The tree of life (TOL), as an organizing metaphor and concept, has been greatly challenged by the discovery of extensive horizontal gene transfer. While various attempts have been made to preserve the traditional TOL, other efforts are now focused on phylogenetic analysis and evolutionary reconstruction beyond the TOL. The articles in this special thematic series ofBiology Direct demonstrate methodologically and conceptually new and constructive ways of working with and thinking about the TOL and its phylogenetic legacy. Whether these approaches modify or ultimately reject the TOL, they show the wealth of insight gained by thinking beyond a central icon of evolutionary biology. Image courtesy of Mandy Budan.

  1. A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in ...

    Authors: Rebecca J Case and Yan Boucher

    Citation: Biology Direct 2011 6:58

    Content type: Review

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  2. Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narra...

    Authors: David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam and J Peter Gogarten

    Citation: Biology Direct 2011 6:45

    Content type: Review

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  3. It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we ...

    Authors: James O McInerney, Davide Pisani, Eric Bapteste and Mary J O'Connell

    Citation: Biology Direct 2011 6:41

    Content type: Hypothesis

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  4. We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additio...

    Authors: Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe and Eric Bapteste

    Citation: Biology Direct 2011 6:39

    Content type: Research

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  5. Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably i...

    Authors: William F Martin

    Citation: Biology Direct 2011 6:36

    Content type: Review

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  6. Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to ...

    Authors: Robert G Beiko

    Citation: Biology Direct 2011 6:34

    Content type: Research

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