Determining the evolution of the aminoacyl-trna synthetases by the ratios of evolutionary distance method
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The availability of large numbers of genomic sequences has demonstrated the importance of lateral gene transfer (LGT) in prokaryotic evolution. However, there remains considerable uncertainty concerning the frequency of LGT compared to other evolutionary processes. To examine the frequency of LGT in ancient lineages, a method was developed that utilizes the Ratios of Evolutionary Distances (or RED) to distinguish between alternative evolutionary histories. The advantages of this approach are: the variability inherent in comparing protein sequences is transparent, the direction of LGT and the relative rates of evolution are readily identified, and it is possible to detect other types of evolutionary events. RED-T, an original computer program designed to implement the RED method, was developed during our work. RED-T is a Java application capable of generating scatter plots from given distance matrixes to analyze evolutionary relationships among various levels of taxa. In addition, it is fully capable of importing new gene data for comparison with the control set we developed or allowing the user to develop a new control. The RED method was standardized using 37 genes encoding ribosomal proteins that were believed to share a vertical evolution. Using RED-T, the evolution of the genes encoding the 20 aminoacyl-tRNA synthetases was examined. Although LGTs were common in the evolution of the aminoacyl-tRNA synthetases, they were not sufficient to obscure the organismal phylogeny. Moreover, much of the apparent complexity of the gene tree was consistent with the formation of paralogs in the ancestors to the modern lineages followed by more recent loss of one paralog or the other.