The Three Domains are the taxonomic groups Archaea, Bacteria (also called Eubacteria), and Eucarya.

This level of taxons was created in light of the research of Carl Woese, who studied prokaryotic rRNA. It was determined that the rRNA sequences suggested that prokayrotes divided into two distinct groups early on.

The Woese et al original paper seems to have been:
Woese CR, Kandler O, Wheelis ML "TOWARDS A NATURAL SYSTEM OF ORGANISMS - PROPOSAL FOR THE DOMAINS ARCHAEA, BACTERIA, AND EUCARYA" Proceedings of Natural Acadamy of Sciences USA 87: (12) 4576-4579 JUN 1990

However, as with all naming problems, there is considerable disagreement. Some (myself included) prefer 'Empire' to Domain, as this seems to be a step above Kingdom. On the other hand the ugly sounding 'Ur-Kingdom' is also a possibility. Most problematic is the Domain called archea or archaea - pronounced ar-key and ar-KAY-a respectively. Even more confusing is the proposal to redefine hyperthermophiles as 'eocyte' (from eos - dawn). Although initially the divisions were based on ribosomal RNA, other features (such as protein sequence or cell structure) also have to be accounted for. Most interesting is the problem of where the first Eukarya came from; a variant of the endosymbiotic hypothesis.

Mostly stolen from: Proc Natl Acad Sci U S A 1995 Mar 28;92(7):2421-3 Of archae and eo: what's in a name?

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