Protists evolved to develop what prokaryotes donít have: a membrane enclosed nucleus, mitochondria, chloroplasts, endomembrane system, cytoskeleton, 9+2 flagella, and multiple chromosomes with linear DNA, diploid stage in life cycles, mitosis, meiosis and sex.
Multicellular prokaryotes began being favored by natural selection:
Compartments and organelles in eukaryotes may have evolved from infoldings in prokaryotes and endosymbiosis is responsible for the rest of the organelles developing (especially mitochondria and chloroplasts.)
Endosymbiotic theory says that the origin of eukaryotes is from certain species of prokaryotes (notably photosynthetic and aerobic organisms) living within larger prokaryotes (this especially applies to chloroplasts and mitochondria once again).
Eukaryotes also could have originated from archezoa---single celled prokaryotes (diplomonads) which may have developed a single haploid nucleus in a membrane envelope (without mitochondria and plastids) with simple cytoskeletons.
- filaments began to develop in cyanobacteria
- complex bacterial communities, in which each species benefited from the metabolic specialties of another, began to evolve.
- Compartmentalization of different functions within single cells occurred.