Lateral gene transfer has emerged as an important force in bacterial evolution. A substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. In this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. We have analyzed 50 bacterial complete genomes from nine groups. For each group we use a 16s rRNA phylogeny and a comparison of protein similarity to map gene insertions/deletions onto their species phylogeny. The results reveal that there is poor correlation of genes inserted, deleted, and duplicated with evolutionary branch length. In addition, the numbers of genes inserted, deleted, or duplicated within the same branch are not always correlated with each other. Nor is there any similarity within groups. For example, in the Rhizobiales group, the ratio of insertions to deletions in the evolutionary branch leading to Agrobacterium tumefaciens str. C58 (Cereon) is 0.52, but it is 39.52 for Mesorhizobium loti. Most strikingly, the number of insertions of foreign genes is much larger in the external branches of the trees. These insertions also greatly outnumber the occurrence of deletions, and yet the genome sizes of these bacteria remain roughly constant. This indicates that many of the insertions are specific to each organism and are lost before related species can evolve. Simulations of the process of insertion and deletion, tailored to each phylogeny, support this conclusion.
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