Six months ago, Alastair Simpson and Andrew Roger published in these pages a primer on "The real 'kingdoms' of eukaryotes". This Primer should be seen as a companion to theirs, addressing not only the currently accepted classification of prokaryotes, but also the inferred evolutionary relationships among prokaryotes - Bacteria and Archaea - and between them and eukaryotes. It may seem surprising in this postgenomic era that these are still areas of active research and vigorous controversy. The relationships are not simple ones, however, and there is legitimate disagreement, at the philosophical level, about how the complexities should be dealt with to produce the best 'natural classification'
Walsh, D. A., & Doolittle, W. F. (2005). The real ‘domains’ of life. Current Biology, 15(7), R237–R240. https://doi.org/10.1016/j.cub.2005.03.034