A biological domain is a high-level rank used to classify organisms in the three-domain system. Distinguish a taxonomic rank from a primary branch in an inferred phylogenetic tree: retaining familiar names does not settle the branching relationships.
The three-domain system recognizes bacteria, archaea and eukaryotes as three domains. In 1990, Woese, Kandler and Wheelis proposed the domain rank and the names Bacteria, Archaea and Eucarya, using molecular comparisons to argue that the older prokaryote/eukaryote division hid important differences. See Woese, Kandler and Wheelis, 1990: Towards a natural system of organisms.
The associated three-domain ancestry model places the nuclear lineage of eukaryotes alongside archaea, rather than within them. This historically influential interpretation should be distinguished from the two-domain system; listing three familiar groups does not establish three independent primary branches.
The two-domain system recognizes bacteria and archaea as the two primary lineages, placing the nuclear ancestry of eukaryotes within archaea. In this model, archaea as a complete clade includes that eukaryotic lineage; restricting the name to prokaryotic members describes a different grouping. Williams and colleagues' study, published online in 2019 and in a 2020 journal issue, found support for this model and a close relationship to Asgard archaea. See Williams et al., 2020: Phylogenomics provides robust support for a two-domains tree of life.
This updates the interpretation of the 1977 and 1990 classifications rather than undoing their discovery of deep differences between bacteria and archaea. Deep phylogenetic trees depend on the sampled genes, organisms and inference model; the precise closest archaeal relatives and early sequence of events require further evidence. Bacterial ancestry of mitochondria through endosymbiosis is a separate part of eukaryotic history.
