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We know also almost very little the origin of the nucleus and the cytoskeleton. It is as if all of a sudden, the eukaryotic lineage emerges with a really complex cytoskeleton and a nucleus, and we really dont know where these structures came from.
Many bacteria do contain homologs of eukaryotic actin (MreB) and tubulin (FtsZ) but if you look across all of the cytoskeleton proteins, there are many that dont have bacterial homologs. And similarly many nuclear proteins dont have clear homologs in bacteria or archaea. If we look across all eukaryotes, we can infer that the last common ancestor of all living eukaryotes had a complex cytoskeleton and had a nucleus; there are no intermediates.