doolittlepatternpluralism2007 - Pattern pluralism and the...

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Pattern pluralism and the Tree of Life hypothesis W. Ford Doolittle, and Eric Bapteste doi:10.1073/pnas.0610699104 published online Jan 29, 2007; PNAS This information is current as of February 2007. This article has been cited by other articles: E-mail Alerts . click here at the top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box Rights & Permissions To reproduce this article in part (figures, tables) or in entirety, see: Reprints To order reprints, see: Notes:
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Pattern pluralism and the Tree of Life hypothesis W. Ford Doolittle* and Eric Bapteste Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 30, 2002. Contributed by W. Ford Doolittle, December 5, 2006 (sent for review November 11, 2006) Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no indepen- dent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolu- tionary models and representations of relationships will be appro- priate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL. lateral gene transfer phylogeny T he meaning, role in biology, and support in evidence of the universal ‘‘Tree of Life’’ (TOL) are currently in dispute (1–15). Some evolutionists believe ( i ) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; ( ii ) that we can with available data and methods reconstruct this tree quite accu- rately; and ( iii ) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second
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