MBE Advance Access originally published online on January 22, 2004
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mol. Biol. Evol. 21(4):681-690. 2004
DOI: 10.1093/molbev/msh061
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Deriving the Genomic Tree of Life in the Presence of Horizontal Gene Transfer: Conditioned Reconstruction
,
,
,||
* Molecular Biology Institute
Molecular, Cell, and Developmental Biology
Human Genetics
Astrobiology Institute
|| Institute of Geophysics and Planetary Physics, University of California, Los Angeles
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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. A. Lake Reconstructing Evolutionary Graphs: 3D Parsimony Mol. Biol. Evol., August 1, 2008; 25(8): 1677 - 1682. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Hao and G. B. Golding The fate of laterally transferred genes: Life in the fast lane to adaptation or death. Genome Res., May 1, 2006; 16(5): 636 - 643. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Susko, J. Leigh, W. F. Doolittle, and E. Bapteste Visualizing and Assessing Phylogenetic Congruence of Core Gene Sets: A Case Study of the {gamma}-Proteobacteria Mol. Biol. Evol., May 1, 2006; 23(5): 1019 - 1030. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. B. Simonson, J. A. Servin, R. G. Skophammer, C. W. Herbold, M. C. Rivera, and J. A. Lake Decoding the genomic tree of life PNAS, May 3, 2005; 102(suppl_1): 6608 - 6613. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Esser, N. Ahmadinejad, C. Wiegand, C. Rotte, F. Sebastiani, G. Gelius-Dietrich, K. Henze, E. Kretschmann, E. Richly, D. Leister, et al. A Genome Phylogeny for Mitochondria Among {alpha}-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes Mol. Biol. Evol., September 1, 2004; 21(9): 1643 - 1660. [Abstract] [Full Text] [PDF]
|
|