The evolution of mitochondria in eukaryotic cells is something of a mystery. Many scientists are not completely sure where mitochondria came from, but the best solution out there now is that mitochondria were once separate organisms from cells, something along the lines of a type of bacteria or archaea. Scientists believe that a prokaryote ancestor of mitochondria was consumed by a eukaryotic cell at some point in time, and the prokaryote and eukaryotic cell developed a symbiotic relationship. Through evolution, the prokaryote eventually lost characteristics that it did not need outside of its function in the cell, and became what we now know as the mitochondrion. This being just a theory, it does not guarantee that this is where mitochondria came from, but as of now, it's our best guess that can explain the properties of mitochondria and its behavior in the cell.
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