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The simplest of evidence is that the prokaryotes are separated into two distinct groups and it is claimed that Archaea, which look very like conventional bacteria on the outside, are as different from bacteria as we are! The reasoning comes from their ribosomal RNA. Since ribosomes have a role in protein synthesis, they tend to remain unchanged in evolution. This is because any mutation is likely to impair their function. But mutations do accumulate very slowly, in subtle and random ways which don't affect them too much. The Archaea live in all sorts of weird places that bacteria wouldn't be able to survive such as oil deposits deep in the earth, in hot springs and very salty water.

Hope this helps, just did my Biology homework which was this :)

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