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- Worms in space |
The tailed phages are a very ancient group of organisms. We don't know exactly how ancient they are, but a good argument can be made that their age as a group is most likely measured in billions of years. One thing is quite clear however: they have not been sitting around on their duffs during that time. Genomic sequencing and analysis from the Pittsburgh Bacteriophage Institute as well as a number of other labs shows that these viruses swap genes with each other in an orgy of horizontal gene exchange not even approached in other groups of organisms. The figure at the bottom of the page compares the genome organizations of a group of five phages that infect the bacterium Escherichia coli, with the different colors identifying homologous modules of genes. The mosaicism is obvious; evidently all of the phages in this group participate in swapping gene modules with other members of the group. This is a shocking result for anyone who knows that phages l and Mu, two of the most intensively studied organisms in the Biosphere, are officially classified into two very different taxonomic groups. In a recent publication from the Lawrence, Hatfull and Hendrix laboratories, it is argued that the extensive mosaicism in the tailed phages means first of all that the evolutionary history of this group cannot be represented by a simple branching phylogeny; rather their actual phylogeny is a web or reticulum. Second, we show that such a reticulated phylogeny cannot be accurately represented by a hierarchical taxonomy, the sort that was introduced 250 years ago by Linneaus and has been used by biologists (including virologists) ever since. The figure on the right shows that a different group of phages, the ssDNA filamentous phages, are also demonstrably mosaic, and so the same reservations about their phylogeny and taxonomy apply. In the paper we propose a new type of taxonomic system for viruses that is congruent with and therefore does not obscure the complex history of the viruses.
You might ask why we give a rat's (Rattus norvegicus) ass about the taxonomy of bacteriophages. After all, isn't taxonomy the most boring of all biological subjects, reserved for old boobies who don't have enough neurons left to think about real scientific questions? Before you make up your mind, consider this: the way the taxonomy is organized strongly influences the way we think about the biological relationships among the organisms it describes. We show in the paper that a hierarchical taxonomy applied to a mosaic population not only obscures much of the available biological information about the relationships among the members of the population, it actively misleads by implying false relationships. So, the blue-footed booby's exuberance may be justified, in that if you want to think about some of the Big Questions, like the evolution, or the population structure, or the population dynamics of the biggest and most important population on Earth, you had better not try to do it armed only with a defective, misleading description of what you're looking at. Research into the effects of bacteriophage on genome evolution is a continued area of research for the Pittsburgh Bacteriophage Institute.
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