Beyond the tree of life
Biology Direct
Edited by: Dr Maureen O'Malley and Dr Yan Boucher
Collection published: 30 June 2011
Last updated: 10 November 2011
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 of Biology 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.
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Molecular musings in microbial ecology and evolution
Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011)
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Biased gene transfer and its implications for the concept of lineage
Cheryl P Andam, J Peter Gogarten Biology Direct 2011, 6:47 (23 September 2011)
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Editor’s summary
Evolutionary histories of three aminoacyl-tRNA synthetases show that the concept of organismal lineage in the prokaryotic world is defined by vertical inheritance and horizontal gene transfer biased towards close relatives.
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A Rooted Net of Life
David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam, J Peter Gogarten Biology Direct 2011, 6:45 (21 September 2011)
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The public goods hypothesis for the evolution of life on Earth
James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell Biology Direct 2011, 6:41 (23 August 2011)
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Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste Biology Direct 2011, 6:39 (20 July 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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From the scala naturae to the symbiogenetic and dynamic tree of life
Ulrich Kutschera Biology Direct 2011, 6:33 (30 June 2011)
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Telling the whole story in a 10,000-genome world
Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Early evolution without a tree of life
William F Martin Biology Direct 2011, 6:36 (30 June 2011)
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How stands the Tree of Life a century and a half after The Origin?
Maureen A O'Malley, Eugene V Koonin Biology Direct 2011, 6:32 (30 June 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Energetics and genetics across the prokaryote-eukaryote divide
Nick Lane Biology Direct 2011, 6:35 (30 June 2011)
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