Lake James A, Rivera Maria C
Molecular Biology Institute, University of California. Los Angeles, USA.
Mol Biol Evol. 2004 Apr;21(4):681-90. doi: 10.1093/molbev/msh061. Epub 2004 Jan 22.
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.
在原核生物基因组中推断出的水平基因转移（HGT）似乎规模巨大，以至于许多科学家认为它可能有效地掩盖了记录在DNA中的大部分生命历史。在这里，我们证明，即使存在广泛的HGT，只要对基因组进化过程进行适当建模，生命之树仍可重建。我们表明，基因组进化过程中发生的基因动态缺失和插入，包括由HGT引入的那些，可以使用类似于用于对序列进化过程中发生的核苷酸替换进行建模的技术来建模。特别是，我们表明适当设计的通用马尔可夫模型是重建基因组进化的合理工具。这些研究表明，只要基因组包含足够多的基因并且满足马尔可夫假设，就有可能重建生命之树。我们还考虑了基因组融合，这是基因序列进化中未遇到的一个过程，并推导了一种识别和重建基因组融合事件的方法。对一个定义明确的经典四基因组问题——多细胞动物的根源——的基因组重建表明，该方法与副线性/对数行列式距离结合使用时，表现非常出色，并且相对不受最近发现的大基因组假象的影响。
