Population genomics meets the taxonomy of cyanobacteria

The emergence of cyanobacterial species (speciation) is driven by mutation, selection, gene flow, and geographical and ecological isolation. Population genomics explores the process of speciation and in turn provides information for our understanding of evolution, diversity, and systematics. However, very little is known about speciation in cyanobacteria, and no framework exists to apply population genomics to taxonomy. Here we review the forces driving the speciation of cyanobacteria and the application of population genomics to taxonomy. We start by discussing species divergence, selection, gene flow, and the phases of speciation. Then we focus on the most frequently used species concepts and their application using population genomics and methods of species delimitation using examples of Prochlorococcus, Microcystis, and Laspinema. Finally, we present guidelines for the methods and techniques of population genomics and their application in the taxonomy of cyanobacteria. Population genomics provides the tools and approaches to bridge species' biology, evolution, and delimitation. Ultimately, this brings taxonomic decisions as close as possible to natural processes.