It’s evolution in action; there are always small variations within a population, and those small variations become larger variations if they are emphasized in a population that’s separate from another, and if they are not disadvantageous to survival. In the case of mitochondrial Eve, we’re talking about hundreds of thousands of years for this to happen.
It’s also worth noting that mitochondrial Eve is simply the most recent common ancestor of all living humans; at the time she lived, there were plenty of other humans who already sported diversity within their population. Their diversity is responsible for our diversity; their lines are still intact as well, just not all of them to all of us.
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