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Prokaryotic evolution and the tree of life are two different things

Eric Bapteste*, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher and William Martin

Biology Direct 2009, 4:34 doi:10.1186/1745-6150-4-34

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Proceedings   Open Access

Origin and evolution of gene families in Bacteria and Archaea

R Collins, Hugh Merz, Paul G Higgs BMC Bioinformatics 2011, 12(Suppl 9):S14 (5 October 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)

This article is part of a collection on Beyond the tree of life

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.

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)

This article is part of a collection on Beyond the tree of life

Methodology article   Open Access

Split-based computation of majority-rule supertrees

Anne Kupczok BMC Evolutionary Biology 2011, 11:205 (13 July 2011)

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)

This article is part of a collection on Beyond the tree of life

Opinion   Open Access Highly Accessed

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:33 (29 September 2009)

This article is part of a collection on Evolutionary Biology 150...

A tree is a natural representation of evolution owing to the inherent tree-like character of the replication process but the fundamental units of evolution amenable to tree analysis seem to be individual genetic elements rather than complete genomes.