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Egenis · Research

Questioning the Tree of Life (2008-2010)

Maureen O'Malley and John Dupré

Start date



Email Prof. John Dupré, University of Exeter

Email Dr Maureen O'Malley, University of Sydney


http://www.genomicsnetwork.ac.uk/egenis/research/sciencetechnologyandinnovation/Leverhulme trust logo.jpg

Funded by

The Leverhulme Trust


Leverhulme Trust logo The Leverhulme Trust has funded a network of biologists, philosophers and historians to discuss the many issues in constructing the Tree of Life. Several meetings and publications detail these issues and new ways of thinking about them.

The project

The first meeting of the network took place at the Philosophy of Science Association (PSA) meeting, November 6-9 2008 in Pittsburgh (USA). Read the TOL PSA report for an overview of this workshop and a discussion of plans for future activities.

Further dissemination of the project took place in Brisbane, at the ISHPSSB meeting in July, 2009. Session details. Mark Ragan’s presentation has already been published as a paper in Biology Direct, Trees and networks before and after Darwin.

The next group gathering took place in Halifax, Nova Scotia, from July 30 to August 1, 2009. View the Perspectives workshop report.The project culminated with a workshop, Beyond the Tree of Life, held in London in July 2010. Read details of all the talks in the Beyond the Tree of Life London workshop report .

A special issue of Biology and Philosophy (Volume 25, Issue 4, September 2010) on the Tree of Life has now been published. The issue consists of 15 papers, including an introduction.

A special issue in Biology Direct was published in June, 2011 Beyond the Tree of Life containing 9 papers from network members.

The Network members

Eric Bapteste (UPMC, Paris), Yan Boucher (MIT), Richard Burian (Virginia Tech), Ford Doolittle (Dalhousie), Marc Ereshefsky (Calgary University), Laura Franklin-Hall (NYU), Peter Gogarten (University of Connecticut), Jeffrey Lawrence (University of Pittsburgh), Jim Mallet (UCL), Bill Martin (Heinrich-Heine Universität, Düsseldorf), Elliott Sober (University of Wisconsin) and Joel Velasco (Cornell).

Additional participants: John Archibald (Dalhousie), Rob Beiko (Dalhousie), Joe Bielawski (Dalhousie), Frédéric Bouchard (University of Montreal), Lisa Gannett (Saint Mary's University), Eugene Koonin (NCBI), Ulrich Kutschera (Kassel), Nick Lane (UCL), Francois-Joseph Lapointe (Montreal), Christophe Malaterre (IHPST, Paris) James McInerney (NUI Maynooth, Ireland) Gordon McOuat (King’s College University, NS), Greg Morgan (Stevens Institute of Technology, NJ), Staffan Müller-Wille (Exeter), Thomas Pradeu (IHPST, Sorbonne), Olivier Rieppel (The Field Museum, Chicago), Andrew Roger (Dalhousie), Jan Sapp (York University, Toronto), Susan Spath, (independent scholar, California), Peter Stevens (St Louis, Missouri), Davide Vecchi (Universidad de Santiago de Chile) and Rob Wilson (Alberta).


A special issue in Biology Direct was published in June, 2011 Beyond the Tree of Life containing 9 papers from network members.

A special issue of Biology and Philosophy (Volume 25, Issue 4, September 2010) on the Tree of Life has now been published, consisting of the following 15 papers.

O'Malley, M.A., Martin, W., and Dupre, J. The tree of life: Introduction to an evolutionary debate.

Doolittle, W.F. The attempt on the life of the tree of life: Science, philosophy and politics.

Rieppel, O. The series, the network, and the tree: Changing metaphors of order in nature.

Mallet, J. Why was Darwin's view of species rejected by twentieth-century biologists?

O'Malley, M.A. Ernst Mayr, the tree of life, and philosophy of biology.

Ereshefsky, M. Microbiology and the species problem.

Lawrence, J.G., and Retchless, A.C. The myth of bacterial species and speciation.

Andams, C.P., Williams, D., and Gogarten, J.P. Natural taxonomy in light of horizontal gene transfer.

Morgan, G. Evaluating Maclaurin and Sterelny's conception of biodiversity in cases of frequent, promiscous lateral gene transfer.

Bouchard, F. Symbiosis, lateral function transfer, and the (many) saplings of life.

Malaterre, C. Lifeness signatures and the roots of the tree of life.

Beiko, R.G. Gene sharing and genome evolution: Networks in trees and trees in networks.

Velasco, J.D., and Sober, E. Testing for treeness: Lateral gene transfer, phylogenetic inference, and model selection.

Franklin-Hall, L. Trashing life's tree.

Bapteste, E., and Burian, R.M. On the need for integrative phylogenomics, and some steps towards its creation.

For just an overview, read the abstracts of the contributions.

Other publications

Bapteste, E., O'Malley, M.A., Beiko, R.G., et al. (2009). Prokaryotic evolution and the tree of life are two different things. Biology Direct, 4: 34 (This paper is accompanied by three reviews, written by W. Ford Doolittle, Nicolas Galtier and John M. Logsdon).

O'Malley, M.A. (2010). Construction and deconstruction: The influence of lateral gene transfer on the evolution of the Tree of Life. In Oren, A., and Papke, T. (Eds.), Molecular Phylogeny of Microorganisms, Norwich: Horizon pp. 151-166.