Final answer:
A) Archaea and Eukarya are more closely related to each other based on phylogenetic tree evidence. They share a more recent common ancestor than either does with Bacteria, and have several similar traits that Bacteria do not, supporting their closer evolutionary relationship.
Step-by-step explanation:
Archaea and Eukarya are evolutionarily more closely related to each other than to Bacteria. This is based on the evidence from phylogenetic trees, which show that the Eukarya domain appears to have shared a more recent common ancestor with the Archaea than with the Bacteria. These phylogenetic trees are developed using comparisons of ribosomal RNA base sequences among living organisms, which reflect evolutionary relationships.
In addition to molecular evidence, Archaea have genes, proteins, and metabolic pathways in common with Eukaryotes that are not present in Bacteria, supporting the close evolutionary ties between Archaea and Eukarya. Furthermore, the hypothesis that Eukaryotes may have arisen through a fusion event between an ancestral Archaeal cell and a Bacterial cell aligns with the evidence of their mixed characteristics, such as the presence of a nucleus and cytoplasm, similar to Eukaryan cells.
Understanding the evolutionary relationship between Archaea, Bacteria, and Eukarya is crucial for our comprehension of early life on Earth and the development of the three domains of life. Such knowledge has dramatically changed our understanding of evolution and the history of life forms on our planet.