The split genes of Nanoarchaeum equitans are an ancestral character.

The introns early hypothesis predicts that introns were fundamental in assembling the first genes. In Nanoarchaeum equitans some genes are split into two. If these split genes were the ancestral forms, as suggested by the introns early hypothesis, then the end-beginning of the two parts of the split protein in a multiple alignment with the orthologous proteins from the Eukarya and Arachaea domains should make a clear prediction on where the intron in the homologous eukaryotic gene should be positioned. The analysis has shown that the introns are in this position, which is therefore predictable on the basis of the split proteins of N. equitans. This corroborates the hypothesis that the split genes of N. equitans are the plesiomorphic forms of these genes. If true, this would show that the origin of genes was polyphyletic as the monophyletic origin hypothesis would deny the existence, in a real organism, of these ancestral (split) genes, which imply that they were assembled late on and after the domains of life were established. Furthermore, it would seem that hyperthermophily is also an ancestral trait because it is linked to a split gene in N. equitans.