The most recent common ancestor of all currently living organisms is the last universal ancestor, which lived about 3.9 billion years ago. ... 6,331 groups of genes common to all living animals have been identified; these may have arisen from a single common ancestor that lived 650 million years ago in the Precambrian.
If a HYPOTHESIS is wrong scientists come up with a conclusion, the hypothesis doesn't matter for the result. It is just an educated guess based on the results they expect our hope the achieve.