This is a recent discovery about 40 years ago, based entirely on the biochemistry and genetics of the new family of bacteria:-http://blogs.scientificamerican.com/artful-amoeba/2013/01/12/archaea-are-more-wonderful-than-you-know/?WT_mc_id=SA_DD_20130114-"In many ways, archaea look more like us than bacteria — but you have to look closely to see it. "Us" would be the eukaryotes, the life forms that house their DNA in packets called nuclei (among many other traits). The group includes pretty much everything except archaea and bacteria.
 
Archaea possess DNA and RNA polymerases — enzymes that replicate DNA and RNA — that look like simpler versions of the ones found in eukaryotes. And their single circular chromosomes can have more than one origin of replication, like eukaryotes but unlike bacteria.
 
In order to condense their DNA enough to fit inside a cell, bacteria use a protein called gyrase to twist their DNA into coils. Archaea do this too, but they also wrap their DNA around proteins called histones that, again, look like simpler versions of the histones around which eukaryotes wrap their DNA. As far as I know, bacteria do not possess histones.
 
These compelling similarities — of which there are more deeper in the biochemical weeds that I am omitting for space — between archaeal and eukaryotic cells has led some to suggest that in addition to the bacterial engulfment/symbiosis that created mitochondria and chloroplasts, some other more mysterious symbiosis or chimerism may have occurred between an ancient archaeon and bacterium to produce the first proto-eukaryotic cell. Or it may suggest that eukaryotes, in fact, evolved from archaea."