One theory describing the origin of eukaryotic cells is that they arose through endosymbiosis. Specifically, chloroplasts and mitochondria are decendants of free-living prokaryotes that were engulfed by larger cells billions of years ago (Caprette 2005). Gradually, the host cell formed a mutually-dependent relationship with the engulfed cells, which eventually became chloroplasts and mitochondria (Caprette 2005). There is much evidence supporting this theory. Chloroplasts and mitochondria have a double-layered membrane (other organelles such as the golgi complex and endoplastic reticulum have one), supporting the notion of prokaryotic cells being engulfed via endocytosis (Bio-Medicine 2009). Also, chloroplasts and mitochondria have their own distinct set of DNA, RNA, and ribosomes. In fact, chloroplasts and mitochondria do not follow the replication rules of the main cell and replicate independently by using a method similar to binary fission (Bio-Medicine 2009).
An interesting application of the presence of a distinct set of DNA is mitochondrial dating. Because mitochondria are mostly uniclonal and do not undergo genetic recombination like eukaryotic cells, mitochondrian DNA is utilized as a highly effective means to trace human ancestry back thousands of years (Delghandi 1998).

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Caprette, D. 2009. Evolutionary Origin of Mitochondria. Accessed 15 January 2010.