Editing Evolution of flagella (section)

==Eukaryotic flagellum==
There are two competing groups of models for the evolutionary origin of the [[Eukaryote|eukaryotic]] flagellum (referred to as [[cilium]] below to distinguish it from its bacterial counterpart). Recent studies on the [[microtubule organizing center]] suggest that the most recent ancestor of all eukaryotes already had a complex flagellar apparatus.<ref>{{Cite journal |doi = 10.1111/tpj.12145|pmid = 23398214|title = Evolution of microtubule organizing centers across the tree of eukaryotes|journal = The Plant Journal|volume = 75|issue = 2|pages = 230–244|year = 2013|last1 = Yubuki|first1 = Naoji|last2 = Leander|first2 = Brian S.|doi-access = free}}</ref>

===Endogenous, autogenous and direct filiation models===
These models argue that [[cilia]] developed from pre-existing components of the eukaryotic [[cytoskeleton]] (which has [[tubulin]] and [[dynein]]{{spaced ndash}} also used for other functions) as an extension of the [[mitotic spindle]] apparatus.  The connection can still be seen, first in the various early-branching single-celled eukaryotes that have a [[microtubule]] [[basal body]], where microtubules on one end form a spindle-like cone around the nucleus, while microtubules on the other end point away from the cell and form the cilium.  A further connection is that the [[centriole]], involved in the formation of the mitotic spindle in many (but not all) eukaryotes, is [[Homology (biology)|homologous]] to the cilium, and in many cases ''is'' the basal body from which the cilium grows.

An intermediate stage between spindle and cilium would be a non-swimming appendage made of microtubules with a function subject to [[natural selection]], such as increasing surface area, helping the protozoan remain suspended in water, increasing the chances of bumping into bacteria to eat, or serving as a stalk attaching the cell to a solid substrate.

Regarding the origin of the individual protein components, a paper on the evolution of dyneins<ref>{{Cite journal|author=Gibbons IR |title=Dynein family of motor proteins: present status and future questions |journal=Cell Motility and the Cytoskeleton |volume=32 |issue=2 |pages=136–44 |year=1995 |pmid=8681396 |doi=10.1002/cm.970320214}}</ref><ref>{{Cite journal|vauthors=Asai DJ, Koonce MP |title=The dynein heavy chain: structure, mechanics and evolution |journal=Trends in Cell Biology |volume=11 |issue=5 |pages=196–202 |date=May 2001 |pmid=11316608 |doi=10.1016/S0962-8924(01)01970-5}}</ref> shows that the more complex protein family of ciliary dynein has an apparent ancestor in a simpler cytoplasmic dynein (which itself has evolved from the [[AAA protein]] family that occurs widely in all archea, bacteria and eukaryotes). Long-standing suspicions that tubulin was homologous to FtsZ (based on very weak sequence similarity and some behavioral similarities) were confirmed in 1998 by the independent resolution of the 3-dimensional structures of the two proteins.

===Symbiotic/endosymbiotic/exogenous models===
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]]).

The modern version of the hypothesis was first proposed by [[Lynn Margulis]].<ref>{{Cite journal|author=Sagan L |title=On the origin of mitosing cells |journal=Journal of Theoretical Biology |volume=14 |issue=3 |pages=255–74 |date=March 1967 |pmid=11541392 |doi=10.1016/0022-5193(67)90079-3}}</ref> The hypothesis, though very well publicized, was never widely accepted by the experts, in contrast to Margulis' arguments for the [[Endosymbiotic theory|symbiotic origin of mitochondria and chloroplasts]]. Margulis did strongly promote and publish versions of this hypothesis until the end of her life.<ref>{{Cite book |first=Lynn |last=Margulis |title=Symbiotic planet: a new look at evolution |publisher=Basic Books |location=New York |year=1998 |isbn=978-0-465-07271-2 |oclc=39700477 |url=https://archive.org/details/symbioticplanetn00marg }}{{Page needed|date=September 2010}}</ref>

One primary point in favor of the symbiotic hypothesis was that there are eukaryotes that use symbiotic spirochetes as their [[motility]] [[organelle]]s (some [[parabasalid]]s inside [[termite]] guts, such as ''[[Mixotricha]]'' and ''[[Trichonympha]]'').  
This is an example of co-option and the flexibility of biological systems, and the proposed homologies that have been reported between cilia and spirochetes have stood up to further scrutiny.

Margulis' hypothesis suggests that an archaea acquired [[tubulin]] proteins from a [[eubacter]] ancestor of [[Prosthecobacter]]. However, the homology of [[tubulin]] to the bacterial replication and [[cytoskeleton|cytoskeletal]] protein [[FtsZ]] (see [[Prokaryotic cytoskeleton]]), which was apparently native in [[archaea]], suggesting an endogenous origin of tubulin rather than a symbiotic transfer.