MBE Advance Access originally published online on May 19, 2008
Molecular Biology and Evolution 2008 25(8):1677-1682; doi:10.1093/molbev/msn117
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Research Articles |
Reconstructing Evolutionary Graphs: 3D Parsimony
Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles; Molecular Biology Institute, University of California, Los Angeles; Department of Human Genetics, University of California, Los Angeles; and UCLA Astrobiology Institute, University of California, Los Angeles
E-mail: lake{at}mbi.ucla.edu.
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, 3-dimensional 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
1 Present address: 232 Boyer Hall, 611 South Young Drive, University of California, Los Angeles