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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]

Horizontal gene transfer moves genetic material between lineages through routes other than ordinary inheritance from parent to offspring. Endosymbiotic gene transfer is a specialized case involving an internal partner or its descendant organelle.