What is the best evidence for a three-domain system?

The best evidence for the three domain system is

Sensitivity to Antibiotics

Explanation:

The three domains of life includes:

Archaea - oldest known domain, ancient forms of bacteria.

Bacteria - all other bacteria that are not included in the Archaea domain.

Eukarya - all the organisms that are eukaryotic or contain membrane-bound organelles and nuclei.

Types of evidences for the three domain system are:

1) differences in the sequences of nucleotides in the cell's robosomal RNAs (rRNA)

2) the cells's membrane lipid structure.

3) its sensitivity to antibiotics.