Abstract
Cyanobacteria are among the most important primary producers on the E arth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro‐organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a S ynechococcus ‐like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16 S rRNA sequences and genomes of S ynechococcus ‐like cyanobacteria. Chronograms showed extremely polyphyletic relationships in S ynechococcus , which has not been observed in any other cyanobacteria. Moreover, most S ynechococcus lineages bifurcated after the G reat O xidation E vent, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.