The endosymbiotic theory concerns the origins of mitochondria and chloroplasts, which are organelles of eukaryotic cells. According to this theory, these originated as prokaryotic endosymbionts, which came to live inside eukaryotic cells. The theory postulates that the mitochondria evolved from aerobic bacteria (probably proteobacteria, related to the rickettsias), and that the chloroplast evolved from endosymbiotic cyanobacteria (autotrophic prokaryotes). The evidence for this theory is compelling as a whole, and it is now generally accepted.
The idea that chloroplasts were originally endosymbionts was first suggested by Konstantin Mereschkowsky in 1905, and the same idea form mitochondria was suggested by Ivan Wallin in the 1920s. These ideas were later resurrected by Henry Ris , based largely on the discovery that they contain DNA.
The endosymbiotic hypothesis was popularized by Lynn Margulis. In her 1981 work Symbiosis in Cell Evolution she argued that eukaryotic cells originated as communities of interacting entities, including endosymbiotic spirochaetes that developed into eukaryotic flagella and cilia. This last idea has not received much acceptance, since flagella lack DNA and do not show ultrastrucural similarities to prokaryotes. According to Margulis and Sagan (1996), "Life did not take over the globe by combat, but by networking" (i.e., by cooperation), and Darwin's notion of evolution driven by competition is incomplete. However, others have argued that endosymbiosis involves helotry rather than mutualism.
The possibility that peroxisomes may have an endosymbiotic origin has also been considered, although they lack DNA. Christian de Duve proposed that they may have been the first endosymbionts, allowing cells to withstand growing amounts of free molecular oxygen in the Earth's atmosphere. However, it now appears that they may be formed de novo, contradicting the idea that they have a symbiotic origin.
Evidence that mitochondria and chloroplasts arose via an ancient endosymbiosis of a bacteria is as follows:
- Both mitochondria and chloroplasts contain DNA, which is fairly different from that of the cell nucleus, and that is similar to that of bacteria (in being circular and in its size).
- Mitochondria utilize a different genetic code than the eukaryotic host cell; this code is very similar to bacteria and Archaea.
- They are surrounded by two or more membranes, and the innermost of these shows differences in composition compared to the other membranes in the cell. The composition is like that of a prokaryotic cell membrane.
- New mitochondria and chloroplasts are formed only through a process similar to binary fission. In some algae, such as Euglena, the chloroplasts can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell. In such a case, the chloroplasts will not regenerate.
- Much of the internal structure and biochemistry of chloroplasts, for instance the presence of thylakoids and particular chlorophylls, is very similar to that of cyanobacteria. Phylogenies built with bacteria, chloroplasts, and eukaryotic genomes also suggest that chloroplasts are most closely related to cyanobacteria.
- DNA sequence analysis and phylogeny suggests that nuclear DNA contains genes that probably came from the chloroplast.
- Some genes encoded in the nucleus are transported to the organelle, and both mitochondria and chloroplasts have unusually small genomes compared to other organisms. This is consistent with an increased dependence on the eukaryotic host after forming an endosymbiosis.
- Chloroplasts appear in very different groups of protists, which are in general more closely related to forms lacking them than to each other. This suggests that if chloroplasts originated as part of the cell, they did so multiple times, in which case their close similarity to each other is difficult to explain.
- The size of both organelles is comparable to bacteria.
- These organelle's ribosomes are like those found in bacteria (70s).
- Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walter, Molecular Biology of the Cell, Garland Science, New York, 2002. ISBN 0-8153-3218-1. (General textbook)
- Jeffrey L. Blanchard and Michael Lynch (2000), "Organellar genes: why do they end up in the nucleus?", Trends in Genetics, 16 (7), pp. 315-320. (Discusses theories on how mitochondria and chloroplast genes are transferred into the nucleus, and also what steps a gene needs to go through in order to complete this process.) 
- Paul Jarvis (2001), "Intracellular signalling: The chloroplast talks!", Current Biology, 11 (8), pp. R307-R310. (Recounts evidence that chloroplast-encoded proteins affect transcription of nuclear genes, as opposed to the more well-documented cases of nuclear-encoded proteins that affect mitochondria or chloroplasts.)