Deriving the genomic tree of life in the presence of horizontal gene transfer: Conditioned reconstruction

被引:68
作者
Lake, JA [1 ]
Rivera, MC
机构
[1] Univ Calif Los Angeles, Mol Biol Inst, Los Angeles, CA 90024 USA
[2] Univ Calif Los Angeles, Astrobiol Inst, Los Angeles, CA USA
[3] Univ Calif Los Angeles, Inst Geophys & Planetary Sci, Los Angeles, CA USA
关键词
horizontal gene transfer; tree of life; conditioned reconstruction; conditioning genomes; paralinear/logdet distances; genome fusions;
D O I
10.1093/molbev/msh061
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:681 / 690
页数:10
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