I know this post is old, but…there are other characteristics besides the presence of a nucleus which are used to make this determination. Eukaryotes and Archeae share genes that are not found in true bacteria, for instance. Multiple lines of evidence point to an earlier branching between eukaryotes and archebacteria than between either of them and true bacteria. I agree that it seems counterintuitive.
Whales are a good example of this same phenomenon. Evidence points to a land-dwelling ancestor for whales. So even though they live in the ocean and have fins like fish, they are more closely related to land mammals than any of the phyla of fish. Seems weird on the surface but makes sense once you dive into (HAHAHA GET IT) the evidence. 😉
The Last Universal Ancestor (LUCA) was not one type of organism but 3 early eukaryotes and the first archaea. This has been derived from the application of the Paradigm of Types in Cosmology and Biology.
These organisms were derived from two types of 4 types of chemical combination. Eukaryotes and prokaryotes emerged independently, with eukaryotes preceding prokaryotes and archaea preceding bacteria.
The precipitation of the chemical combinations into biological life involved 232 types of particles which constitute the emission called radiation.
The paradigm also indicates that although the completely sequence genome of life of Earth has 191 types across the three domains, there are 211 types across the three domains in the Universe. The additional 20 exist on one other planet.
The paradigm is presented as the second section of an essay called “Waves and The Cave and the true nature of the Universe”, which is located at home.spin.net.au/paradigm/true.pdf
I am Stephen Mooney and I created the Paradigm of Types in Cosmology and Biology and it constitutes the ultimate paradigm shift revolution in science.