A Rooted Net of Life
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1745-6150-6-45.pdf
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Author(s)
Williams, David
Fournier, Gregory P.
Lapierre, Pascal
Swithers, Kristen S.
Green, Anna G.
Andam, Cheryl P.
Gogarten, J. Peter
Date Issued
September 2011
Journal
Biology Direct
Publisher
BioMed Central Ltd
Citation
Biology Direct. 2011 Sep 21;6(1):45
Version
Final published version
Abstract
Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages. Reviewers W. Ford Doolittle, Eric Bapteste and Robert Beiko.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/1745-6150-6-45
