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Endosymbiosis is an ecological association in which one organism, the endosymbiont, lives inside another. The definition specifies location, not that both partners benefit, nor that the internal partner has become an organelle. An intracellular association can remain an association between distinct organisms. Endosymbiotic theory addresses a different question: how particular ancestral bacteria became inherited, functionally integrated organelles during evolution.

The striking consequence is that a eukaryotic biological cell can combine histories: its nuclear lineage and its mitochondria need not have the same ancestry. Mitochondria have bacterial ancestry related to Alphaproteobacteria; the plastids of plants and many algae, including chloroplasts, have ancestry within cyanobacteria. These are ancestral lineages, not a claim that a named living bacterial species is the literal ancestor. Present-day bacteria and organelles have both evolved since their shared ancestors. ^[ref]

Endosymbiotic gene transfer moves genetic material from an endosymbiont or its descendant organelle into the host genome, notably the nuclear genome. A transferred DNA segment can remain silent. For a transferred gene to replace an organelle-encoded function, nuclear gene expression must work and its protein must reach the right compartment through organelle protein import. Transfer of DNA and transport of proteins are distinct processes in opposite directions. ^[ref]

Gene loss and endosymbiotic gene transfer are different: absence from an organelle genome does not by itself show that a functional nuclear copy exists. Conversely, an imported protein may derive from a host gene rather than a transferred gene. The surviving organelle genome is therefore a partial record, not a complete inventory of either ancestral bacteria or the modern organelle's machinery. ^[ref]

Endosymbiotic theory explains the bacterial origins of mitochondria and plastids through enduring internal associations and subsequent integration. Survival inside a biological cell is only part of the problem: exchange through membrane transport, inherited division, gene expression and delivery of required proteins must work together. The elegance is evolutionary reuse of an existing cellular capability, followed by changes that make the partners operate as one system. ^[ref]

The historical On the origin of mitosing cells by Lynn Sagan (1967, abstract and Introduction, pp. 225–226) synthesized a symbiotic account of eukaryotic origins and proposed tests using molecular evidence. Its Introduction explicitly acknowledged earlier proposals. It also hypothesized origins for other structures; the modern evidence for mitochondria and plastids should be assessed separately from the rest of that historical scheme.

Resemblance is a clue, not sufficient evidence of common descent. A small size, two surrounding membranes, division, retained DNA or bacterial-looking ribosomes does not uniquely identify an ancestor. Internal membranes exist outside these organelles, and a similar function can favor similar structures. The stronger question is whether independently examined molecular characters support the same historical relationship.

A concrete genomic observation is the mitochondrial sequence reported in 1997 for Reclinomonas americana: $69,034$ base pairs containing 97 identified genes, including four for a bacterial-type multisubunit RNA polymerase. This is a reported genome inventory, not a calculation from the pictured shape of a mitochondrion. Retention of such bacterial features strengthens the ancestry argument; a living Reclinomonas americana is not itself an ancestral eukaryote. The inspected abstract supplies these observations but not the detailed sequencing protocol or contamination controls, so those details are not attributed to this report here. ^[ref]

A sequence-based investigation obtains nucleotide sequences by DNA sequencing, identifies comparable genes, makes a sequence alignment and uses phylogenetics to infer relationships. The readout is a proposed relationship with support and uncertainty, not a photograph of an ancient encounter. Comparisons of plastid sequences with bacterial sequences support cyanobacterial ancestry, while the exact closest sampled cyanobacterial group has depended on the chosen data and inference. A bacterial affinity in one gene is weaker than coherent evidence across several genes and cellular systems. ^[ref]

For such an analysis, useful checks include distinguishing organelle DNA from bacterial contamination, verifying sequence quality, comparing corresponding rather than unrelated genes, sampling several bacterial groups and testing sensitivity to the sequence alignment and evolutionary mathematical model. These are methodological requirements, not a claim that this article has rerun a particular published analysis. Horizontal gene transfer, gene loss and unequal evolutionary change can make an individual gene's history differ from a whole organism's history. A supported bacterial origin therefore need not identify an extant donor species, an exact date or the original mode of entry. ^[ref]

Organelle protein import brings externally synthesized proteins into an organelle. Many plastid proteins made from nuclear genes carry targeting information recognized by machinery that transports them across the envelope membranes. This delivery enables nuclear genes to supply functions inside a plastid, but the presence of targeting information is not itself evidence that a gene was acquired through endosymbiotic gene transfer. ^[ref]