How did ribosomal RNA studies change the classification of archaea?

In the 1970s, American microbiologist Carl Woese revolutionized the classification of life by using ribosomal RNA (rRNA) sequence analysis to study evolutionary relationships. Prior to this, prokaryotes were generally considered a single, uniform group of organisms.123

By comparing rRNA sequences, Woese discovered that prokaryotes actually consist of two distinct, ancient lineages: Bacteria and Archaea. This molecular evidence revealed that archaea are as genetically distinct from bacteria as they are from eukaryotes. Consequently, this led to the modern classification of life into three great domains: Archaea, Bacteria, and Eukarya.2341

This shift moved taxonomy away from a sole reliance on phenotypic traits—which can be misleading due to convergent evolution—toward a system based on molecular phylogeny. Subsequent research confirmed that while archaea and bacteria share a prokaryotic cellular structure, they differ significantly in their lipids, cell walls, and RNA polymerase complexity, with the latter often more closely resembling that of eukaryotes.432