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MBE Advance Access published online on May 19, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn117
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Reconstructing Evolutionary Graphs: 3D Parsimony

James A. Lake1,2,3,4

1 Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
2 Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
3 Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
4 UCLA Astrobiology Institute, University of California, Los Angeles, CA 90095, USA

Corresponding Author: James Lake, 232 Boyer Hall, 611 South Young Drive, UCLA, Los Angeles, CA 90095, USA, Tele: (310) 825-2546, Fax: (310) 206-7286, Email: Lake (at) mbi.ucla.edu

Received for publication February 18, 2008. Revision received May 7, 2008. Accepted for publication May 10, 2008.

The increasing recognition that symbioses have greatly altered evolution through genome fusions is creating a need for algorithms that can reliably detect and reconstruct fusions. Here we generalize the bootstrappers gambit algorithm (a quartet method) in order to permit it to analyze both bifurcations and fusions under a single mathematical model, and thereby detect past genomic branchings and endosymbioses. This new method, 3D parsimony, can be applied to aligned sequences, such as gene-, indel-, or other genomic presence/absence sequences. It also provides a statistical measure of support for each possible graph. The usefulness of this method is demonstrated by applying it to the Ring of Life.

Key Words: 3D parsimony • ring of life • eukaryotes • fusion digraphs • evolutionary graphs


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Home page
 Phil Trans R Soc BHome page
J. A. Lake, R. G. Skophammer, C. W. Herbold, and J. A. Servin
Genome beginnings: rooting the tree of life
Phil Trans R Soc B, August 12, 2009; 364(1527): 2177 - 2185.
[Abstract] [Full Text] [PDF]


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