A widely accepted theory is that eukaryotic mitochondria "started out" as prokaryotic cells, namely bacteria (or archaea). Mitochondrial DNA in fact is separate from nuclear DNA, and appears to be descended in the maternal line. This convenient uniting of pros and eus makes sense. The question is, though, "why" (the real question is, "HOW?") are prokaryotes (specifically Monera) still the dominant life form on Earth? The answer is not difficult--we are simply part of the frond of life, not its apex.
As Stephen Jay Gould points out in THE BEST BOOK EVER on evolution, Full House, the process of natural selection is not about "progress" but about adaptability, diversity and excellence. In those areas no organism has yet surpassed the prokaryotes, and thus they remain the most populous, most widely distributed, and most successful life form on Earth. Mammals in general and humans in particular, despite our many desirable characteristics, are genetic also-rans. Prokaryotes will be around to re-populate the Earth once homo sapiens has destroyed the rest of the frond.
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