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it looks like 90% of natural selection was wiped out and the random mutations had to start working with a much smaller base only 250 million years ago.

Actually, it's events like these that often drive evolution.

If an asteroid wipes out 90% of the world's population, the remaining 10% are the organisms that were in some way equipped to survive an asteroid impact.

If a disease wipes out 95% of a species, the remaining 5% are those which were somehow resistant to the disease.

If a vaccine wipes out 99% of a certain virus population, the remaining 1% are of a strain that wasn't affected by the vaccine. Which is really scary, if you think about it.
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