MBE Advance Access published online on January 22, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh061
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Molecular Biology Institute, University of California, Los Angeles; MCD Biology, University of California, Los Angeles; Human Genetics, University of California, Los Angeles; Astrobiology Institute, University of California, Los Angeles
* To whom correspondence should be addressed. E-mail: lake{at}mbi.ucla.edu.
The horizontal gene transfer (HGT) being inferred within prokaryotic genomes appears to be sufficiently massive, that many scientists think it may have effectively obscured much of the history of life recorded in DNA. Here we demonstrate that the tree of life can be reconstructed even in the presence of extensive HGT provided the processes of genome evolution are properly modeled. We show that the dynamic deletions and insertions of genes that occur during genome evolution, including those introduced by HGT, may be modeled using techniques similar to those used to model nucleotide substitutions that occur during sequence evolution. In particular, we show that appropriately designed general Markov models are reasonable tools for reconstructing genome evolution. These studies indicate that, provided genomes contain sufficiently many genes and that the Markov assumptions are met, it is possible to reconstruct the tree of life. We also consider the fusion of genomes, a process not encountered in gene sequence evolution, and derive a method for the identification and reconstruction of genome fusion events. Genomic reconstructions of a well defined classical four genome problem, the root of the multicellular animals, show that the method, when used in conjunction with paralinear/logdet distances performs remarkably well and is relatively unaffected by the recently discovered big genome artifact. Key Words:
Horizontal Gene Transfer, Tree of life, Conditioned Reconstruction, Conditioning Genomes, Paralinear/logdet distances, Genome fusions
© 2004 Society for Molecular Biology and Evolution
Original Articles
Deriving the Genomic Tree of Life in the Presence of Horizontal Gene Transfer: Conditioned Reconstruction
2 Molecular Biology Institute, University of California, Los Angeles; IGPP, University of California, Los Angeles; Astrobiology Institute, University of California, Los Angeles
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