Tangled Branches in the Phylogenetic Tree hile 16S rDNA sequencing has given remarkable new insight into the evolutionary relatedness of organisms, total genome sequencing promises to reveal myriad additional information. In some cases this will serve to clarify the evolutionary picture, providing solid evidence that two organisms are, in fact, closely related. Genomic sequencing, however, can also give information that conflicts with that of rDNA data, creating an uncomfortable confusion. Already, examples exist that challenge the current rDNA phylogenetic tree. For example, sequences of some genes for highly conserved proteins show a closer relationship between some members of the Archaea and Bacteria than their rDNA sequences suggest. This conflicting data might be accounted for by evidence suggesting that horizontal DNA transfer has occurred even between distantly related
organisms. Due to gene transfer, an organism from one domain may contain genes acquired from an organism in a different domain. As a result, some suggest that the phylogenetic tree may be closer to a shrub, with lateral gene transfer giving rise to intertwining branches.
The vast amount of genetic knowledge being obtained is affecting bacterial nomenclature. As more genomes are sequenced, the evolutionary relatedness among organisms will become apparent. Nomenclature is bound to change because present-day classification is based on shared properties and not evolutionary relationships. Already, some species of what were formerly included in the genus Streptococcus have been removed to create two relatively new genera, Enterococcus and Lactococcus. The genera Pseudomonas and Bacillus will likely be similarly subdivided. Meanwhile, other bacteria will be moved from one existing genus to another. All of these changes will create a potential source of confusion for the scientist and layperson alike.
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