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About the Authors:
Nicholas J. Matzke
Contributed equally to this work with: Nicholas J. Matzke, Patrick M. Shih
Current address: National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee, United States of America
Affiliation: Department of Integrative Biology, University of California, Berkeley, California, United States of America
Patrick M. Shih
Contributed equally to this work with: Nicholas J. Matzke, Patrick M. Shih
Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
Cheryl A. Kerfeld
* E-mail: [email protected]
Affiliations Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America, US Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America
Introduction
The study of bacterial phylogenetics is complicated by the pervasive phenomenon of horizontal gene transfer (HGT), in which gene trees no longer reflect the vertical evolutionary history of cell division due to the incorporation of non-endogenous genes [1]. There is still contention regarding how frequently HGT occurs in nature. In cyanobacteria, per-gene rates of HGT have been estimated to be as low as 16% and as high as 50% [2], [3]. Marine cyanobacteria provide an intriguing case study of HGT, as it is thought that they have undergone a large amount of HGT [4]. The discovery that cyanophages contain laterally-acquired genes associated with the photosynthetic machinery of cyanobacteria provides an attractive mechanism for HGT mediated by phage transduction in marine environments [5].
With such discoveries, the question has arisen: is “tree-thinking” a bankrupt model for understanding evolutionary history, at least in unicellular organisms like cyanobacteria? Doolittle et al. [6] have suggested that tree-thinking may be an inherently flawed way of understanding species relationships due to a bias in assuming relationships in a bifurcating manner rather than in a network [7]. Doolittle has even suggested that “tree thinking is surely a form of typological thinking writ large” [6]. Is it time to abandon the “tree of life” as a metaphor for evolutionary history? Or can the tree of organismal relationships, the tree derived from vertical inheritance of genes through standard cellular replication, still be estimated reliably, despite the horizontal transfer of some genes? However, it is generally accepted that vertical inheritance is vastly more frequent than horizontal transfer, at...