Tree of Life Meaning - Tree of Life Article Series

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Tree of Life Meaning


Tree of Life - Article series

Beyond the tree of life

Edited by: Dr Maureen O'Malley and Dr Yan Boucher

Collection published: 30 June 2011  Last updated: 10 November 2011

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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 Tree Of Life, they show the wealth of insight gained by thinking beyond a central icon of evolutionary biology.

                                                        Image courtesy of Mandy Budan




Review   Open Access


Molecular musings in microbial ecology and evolution 

Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011)


Research   Open Access


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)



Review   Open Access Highly Accessed


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)


Hypothesis   Open Access Highly Accessed


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)


Research   Open Access


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)


Review   Open Access Highly Accessed


Early evolution without a tree of life 

William F Martin Biology Direct 2011, 6:36 (30 June 2011)


Research   Open Access Highly Accessed


Energetics and genetics across the prokaryote-eukaryote divide 

Nick Lane Biology Direct 2011, 6:35 (30 June 2011)


Research   Open Access Highly Accessed


Telling the whole story in a 10,000-genome world 

Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011)


Opinion   Open Access Highly Accessed


From the scala naturae to the symbiogenetic and dynamic tree of life 

Ulrich Kutschera Biology Direct 2011, 6:33 (30 June 2011)


Review   Open Access Highly Accessed


Review   Open Access Highly Accessed

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)

How stands the Tree of Life a century and a half after The Origin?

Maureen A O'Malley1 and Eugene V Koonin2*

Author Affiliations

1 Department of Philosophy, Quadrangle A14, University of Sydney, NSW 2006, Australia

2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD20894, USA

The electronic version of this article is the complete one and can be found online at:

Received: 14 March 2011
Accepted: 30 June 2011
Published: 30 June 2011

© 2011 O'Malley and Koonin; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We examine the Tree of Life (TOL) as an evolutionary hypothesis and a heuristic. The original TOL hypothesis has failed but a new "statistical TOL hypothesis" is promising. The TOL heuristic usefully organizes data without positing fundamental evolutionary truth.


This article was reviewed by W. Ford Doolittle, Nicholas Galtier and Christophe Malaterre.


"And after a while you'll hear a deep voice saying, "Neighbor, how stands the Union?" Then you better answer the Union stands as she stood, rock-bottomed and copper sheathed, one and indivisible, or he's liable to rear right out of the ground."

The Devil and Daniel Webster (Stephen Vincent Benet, 1937)

"On a huge hill,

Cragged, and steep, Truth stands, and he that will

Reach her, about must and about must go"

Satire III (John Donne, written 1593-1600)

Looking back to go beyond the Tree of Life

One might think that there is nothing further that could be said about the last decades of debate on the Tree of Life (TOL). There is certainly no need to recapitulate the numerous overviews of these debates as they set out the positions of key participants (e.g.,[1-3]). However, as the pageantry of 2009's "Darwin Year" subsides, it seems to be an appropriate time to reflect on where TOL studies are headed in relation to the legacies on which they draw. We will consider two key issues: the specific effects of these debates on the conceptual frameworks of TOL studies, and how these frameworks are actually used. We will discuss whether they function as hypotheses or heuristics. To put it in a deliberately over-simplified way, it seems useful to examine two basic questions:

• What are reasonable interpretations of the TOL in the postgenomic era?

• What is the utility of the TOL for research in evolutionary biology and perhaps beyond?

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