[citation needed] There are two competing groups of models for the evolutionary origin of the eukaryotic flagellum (referred to as cilium below to distinguish it from its bacterial counterpart).
[1] These models argue that cilia developed from pre-existing components of the eukaryotic cytoskeleton (which has tubulin and dynein – also used for other functions) as an extension of the mitotic spindle apparatus.
These models argue that the cilium evolved from a symbiotic Gracilicutes (ancestor of spirochete and Prosthecobacter) that attached to a primitive eukaryote or archaebacterium (archaea).
For example, the bubonic plague bacterium Yersinia pestis has an organelle assembly very similar to a complex flagellum, except that it is missing only a few flagellar mechanisms and functions, such as a needle to inject toxins into other cells.
However, the true relationship could be the reverse: recent phylogenetic research strongly suggests the type three secretory system evolved from the flagellum through a series of gene deletions.
[7] Reactive oxygen species (ROS) generated by flagellation can cause oxidative damage to DNA and are mutagenic with researchers asking "Did the innovation of a functional flagellum impact either the short- or long-term rate of bacterial evolution?".
[9] However, the structure of eubacterial flagellae varies based on whether their motor systems run on protons or sodium, and on the complexity of the flagellar whip.
A hypothesis on the evolutionary pathway of the eubacterial flagellum argues that a secretory system evolved first, based around the SMC rod- and pore-forming complex.
In addition to no sequence similarity being detected between the genes of the two systems, the archaeal flagellum appears to grow at the base rather than the tip, and is about 15 nanometers (nm) in diameter rather than 20.