Evolutionary Relationships Among Purple Photosynthetic Bacteria and the Origin of Proteobacterial Photosynthetic Systems

Abstract

The purple bacteria occupy a unique position among photosynthetic bacteria. Nested within the various proteo- bacterial lineages, the origin and evolution of purple bacterial photosynthesis has been the topic of innumer- able debates. Attempts to reconstruct the evolutionary history of individual photosynthetic protein families have further fueled debate over lateral vs. vertical transfer of genetic elements. In this era of high-throughput sequencing we can begin to distance ourselves from this dependency on single-gene and single-protein phy- logenies. Here we present automated comparative genomics-based methods useful for reconstructing the genomic history of not only the purple bacterial lineage, but the proteobacterial lineage as a whole. These reconstructions integrate phylogenetic data inferred from 200 to more than 1000 protein families common to all or part of the proteobacterial lineage. This framework allows us to reconstruct the evolutionary history of each proteobacterial class and parse out the fi ner relationships among photosynthetic species. By telescoping inward on protein families of interest, we can delve deeper than ever before into the convoluted evolutionary origin of the primary photosynthetic traits, phototrophy and autotrophy. While these full-genome comparisons clarify the nature of many poorly understood phylogenetic relationships, they do not yet serve to resolve the entire mystery surrounding the history of proteobacterial phototrophy.