Pattern pluralism and the Tree of Life hypothesis

By W. Ford Doolittle, Eric Bapteste. Proceedings of the National Academy of Sciences of the United States of America, 2007

485 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46f726aeb218d38ad8b6795dce738a3b014ebe5c

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Citations in the corpus

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales (2015, background): “There is a continuing and still intense debate on whether or not a tree of life (species tree) is an adequate representation of the evolution of archaea and bacteria ([60–68] and references therein).”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “Under this view, a Tree of Life (TOL) does not adequately represent evolution of prokaryotes (213,214), not even in the previously envisaged form of a ‘cobweb’ of life where the main vertical flow of genetic information is complemented by functionally important but quantitatively relatively minor ho”
The Logic of Chance: The Nature and Origin of Biological Evolution (2011, background): “Ford Doolittle and Eric Bapteste have argued and demonstrated in compelling examples that a tree can well describe relationships that have nothing to do with common descent, so “tree thinking” was deemed not to be a priori relevant, or at least not central in biology (Doolittle and Bapteste, 2007).”
Understanding Evolutionary Trees (2008, background): “…the earliest period of life’s history, and has been common enough throughout the more recent past, to create a “Web of Life” lacking any single root, rather than a strictly bifurcating tree in which branches, once split, remain separate forever (e.g., Doolittle 2000; Doolittle and Bapteste 2007).”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, background): “Horizontal gene transfer is a well-known and common cause of discordance in the microbial world—so much so that some microbial phylogeneticists have questioned whether a coherent Tree of Life exists for microbes (e.g., Bapteste et al. 2005; Doolittle and Bapteste 2007).”
Microbiology and the species problem (2010, background): “Doolittle and Bapteste (2007) and Franklin (2007) suggest that these varying genetic approaches are not faulty measures of phylogeny; these approaches simply measure the different phylogenies of different parts of a genome.”