A monophyletic taxon or clade includes only and all descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.
The Cyanobacteria and Archaea belong to separate lineages, having diverged from an unknown last universal common ancestor (LUCA, "?").
The Cyanobacteria are associated with the first fossils. Formerly called the "blue-green algae", they are not directly related to eukaryotic algae, though it is widely accepted that an endosymbiosis transfer involving Cyanobacteria generated the chloroplasts of photosynthetic eukaryotes.
The Cyanobacteria comprise a familiar bacterial clade, found in freshwater and aquatic environments, soils, hot-springs, Antarctica, and modern stromatolites, to name a few. Cyanobacteria are characterised by oxygenic photosynthesis with chlorophyll a.
A single genus, Gloeobacter, is recognisably basal to all others in that it lacks thylakoids. All other Cyanobacteria are placed in the clade Phycobacteria, which is characterized by chlorophyll a contained in thylakoids. Phycobacteria have traditionally been divided into five orders on the basis of morphological colony characters (below). Chloroplasts are derived from Phycobacteria, though from which subclade is still unknown.
The phylogenetics of early branching within the Life on Earth is not yet elucidated. Two alternative trees are currently considered possible alternatives (left). It is likely that the earliest cell was a heterotroph, employing environmental molecules to meet its energy requirements.
Modern extremophiles are included within the Archaea grouping.
Evolutionary relationships within the prokaryotes are blurred by the phenomenon of horizontal gene transfer, the phenomenon of cross-species genetic transfer peculiar to prokaryotes. Analyses of the tufA gene provide a broad perspective on eubacterial evolution. In conjunction with published rRNA trees, the analyses point to "at least two major radiations within eubacteria and their descendants: one of many eubacterial phyla, a second of cyanobacteria, and possibly a third radiation early in plastid evolution." Diagram
"Cyanobacterial nomenclature has been traditionally based on morphological and reproductive characteristics. It was proposed that they be separated into five Subsections, with I, II and III comprising the nonheterocystous strains and Subsection IV (12 genera) and V (6 genera), the heterocystous strains. Subsection ii and IV more recently were split into two subgroups each based on morphology, with a total of 56 genera across all sections. Another scheme classifies them into 6 orders, with 7 distinct families and 66 genera." [R]
Links: Phylogenetic Classification and the Universal Tree / Phylogenetics / BioMed Central Full text A genomic timescale for the origin of ... / Palaeos Bacteria: Bacteria / A phylogenomic approach to microbial evolution pdf /