The endosymbiotic theory, now generally accepted by biologists, concerns the origins of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells. According to this theory, these organelles originated as separate prokaryotic organisms which were taken inside the cell as endosymbionts. Mitochondria developed from proteobacteria (in particular, Rickettsiales or close relatives) and chloroplasts from cyanobacteria.
The endosymbiotic theory was first proposed by Andreas Schimper in 1883. The idea that plastids were originally endosymbionts was first suggested by Konstantin Mereschkowsky in 1905, and the same idea for mitochondria was suggested by Ivan Wallin in the 1920s. These theories were initially dismissed on the assumption that they did not contain DNA. This was proven false in the 1960s, leading Hans Ris to resurrect the idea.
The endosymbiotic hypothesis was fleshed out and 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 ultrastructural similarities to prokaryotes. See also Evolution of flagella.
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 natural selection is incomplete (see Evolution and natural selection). However, others have argued that endosymbiosis constitutes slavery 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 (Gabaldón et. al. 2006).
Evidence that mitochondria and plastids arose via ancient endosymbiosis of bacteria is as follows:
- Both mitochondria and plastids contain DNA that is fairly different from that of the cell nucleus and that is similar to that of bacteria (in being circular and in its size).
- 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 plastids are formed only through a process similar to binary fission. In some algae, such as Euglena, the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell. In such a case, the plastids will not regenerate.
- Much of the internal structure and biochemistry of plastids, for instance the presence of thylakoids and particular chlorophylls, is very similar to that of cyanobacteria. Phylogenetic estimates constructed with bacteria, plastids, and eukaryotic genomes also suggest that plastids are most closely related to cyanobacteria.
- DNA sequence analysis and phylogenetic estimates suggests that nuclear DNA contains genes that probably came from the plastid.
- Some proteins encoded in the nucleus are transported to the organelle, and both mitochondria and plastids have small genomes compared to bacteria. This is consistent with an increased dependence on the eukaryotic host after forming an endosymbiosis. Most genes on the organellar genomes have been lost or moved to the nucleus. Most genes needed for mitochondrial and plastid function are located in the nucleus. Many originate from the bacterial endosymbiont.
- Plastids are present in very different groups of protists, some of which are closely related to forms lacking plastids. This suggests that if chloroplasts originated de novo, they did so multiple times, in which case their close similarity to each other is difficult to explain. Many of these protists contain "secondary" plastids that have been acquired from other plastid-containing eukaryotes, not from cyanobacteria directly.
- These organelle's ribosomes are like those found in bacteria (70s).
A possible secondary endosymbiosis (i.e. involving eukaryotic plastids) has been observed by Okamoto & Inouye (2005). The heterotrophic protist Hatena behaves like a predator until it ingests a green algae, which looses its flagella and cytoskeleton, while Hatena, now a host, switches to photosynthetic nutrition, gains the ability to move towards light and loses its feeding apparatus.
- Mitochondria and plastids, like nuclear DNA and unlike prokaryotic DNA, contain introns. Some form of transfer between nuclear and mitochondrial/plastid DNA must have taken place (likely organelle → nuclear transfer → organelle) or, alternatively, a mechanism for turning off portions of early proto-mitochondrial/plastid DNA must have been in place in early symbiotes.
- Neither mitochondria nor plastids can survive outside the cell, having lost many essential genes required for survival. This objection is easily accounted for by simply accounting for the large timespan that the mitochondria/plastids have co-existed with their hosts; genes and systems which were no longer necessary were simply deleted, or in many cases, transferred into the host genome instead (In fact these transfers constitute an important way for the host cell to regulate mitochodrial activity)
- Evolution of flagella (Discusses the endosymbiont theory of the evolution of flagella, and has more on Margulis)
- Hydrogen hypothesis
- Transfer of mitochondrial and chloroplast DNA to the nucleus
- Viral Eukaryogenesis (hypothesis that the cell nucleus originated from endosymbiosis).
- 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.) 
- Fiona S.L. Brinkman, Jeffrey L. Blanchard, Artem Cherkasov, Yossef Av-Gay, Robert C. Brunham, Rachel C. Fernandez, B. Brett Finlay, Sarah P. Otto, B.F. Francis Ouellette, Patrick J. Keeling, Ann M. Rose, Robert E.W. Hancock, and Steven J.M. Jones (2002,) Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast Genome Res., 12: pp 1159 - 1167. 
- Okamoto, N. & Inouye, I. (2005), "A Secondary Symbiosis in Progress?", Science, 310, p. 287
- Gabaldón T. et al (2006), "Origin and evolution of the peroxisomal proteome", Biology Direct, 1 (8),. (Provides evidence that contradicts an endosymbiotic origin of peroxisomes. Instead it is suggested that they evolutionarily originate from the Endoplasmic Reticulum)