There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content (e.g.genome streamlining in Pelagibacter ubique) and the large difference in GC-richness[jargon] between members of several orders. Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes.[jargon] It has been argued[by whom?] that it could be a case of convergent evolution that would result in an artefactual clustering. However, several studies disagree.
Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.
The Class Alphaproteobacteria is divided into three subclassesMagnetococcidae, Rickettsidae and Caulobacteridae. The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales. The Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales.
Comparative analyses of the sequenced genomes have also led to discovery of many conservedinsertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae).
These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups. Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.
^La Scola B, Barrassi L, Raoult D. (2004). "A novel alpha-Proteobacterium, Nordella oligomobilis gen. nov., sp. nov., isolated by using amoebal co-cultures". Research in Microbiology. 155 (1): 47–51. doi:10.1016/j.resmic.2003.09.012.CS1 maint: uses authors parameter (link)
^ abBrenner, Don J.; Krieg, Noel R.; Staley, James T. (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity (ed.). The Proteobacteria. Bergey's Manual of Systematic Bacteriology. 2C (2nd ed.). New York: Springer. p. 1388. ISBN978-0-387-24145-6. British Library no. GBA561951.
^Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–71. doi:10.1016/0092-8674(77)90043-5. PMID890735.
^Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ. (2012) Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int J Syst Evol Microbiol.doi:10.1099/ijs.0.038927-0
^Gupta RS (2005). "Protein signatures distinctive of Alphaproteobacteria and its subgroups and a model for Alpha proteobacterial evolution". Crit Rev Microbiol. 31 (2): 135. doi:10.1080/10408410590922393. PMID15986834.
^Gupta R.S.; Sneath P.H.A. (2007). "Application of the Character compatibility approach to generalized molecular sequence data: Branching order of the Proteobacterial subdivisions". J. Mol. Evol. 64 (1): 90–100. doi:10.1007/s00239-006-0082-2. PMID17160641.