With the discovery of the eukaryote nucleus, all living organisms were
neatly divided into prokaryotes, which lacked a nucleus, and eukaryot
es, which possessed it. As data derived directly from the genome becam
e available, it was clear that prokaryotes were comprised of two group
s, Eubacteria and Archaebacteria. These were subsequently renamed at t
he new taxonomic level of Domain as Bacteria and Archaea, with the euk
aryotes named as the Eucarya Domain. The interrelationships of the thr
ee Domains are still subject to discussion and evaluation, as is their
monophyly. Further data, drawn from various protein sequences, sugges
t conflicting schemes, and resolution may not be straightforward Addit
ionally, Bacteria and Archaea as well as Eucarya are largely based on
organisms already in culture. Investigation of the potentially enormou
s quantity of uncultured organisms in nature is likely to have as broa
d-ranging implications as the exploration of new protein sequences.