Fossil records indicate that the earliest eukaryotes appeared approximately 1.8 billion years ago. Molecular clock analysis suggest that the earliest eukaryotes may have emerged around 2 to 2.5 billion years ago. It took almost a billion years for them to become dominant in the ecosystem.
There is currently no consensus on how eukaryotes evolved from prokaryotes. Mitochondrial DNA sequence analysis indicates a closer genetic affinity between eukaryotes and archaea, with mitochondria being more closely related to Gram-negative bacteria, especially α-proteobacteria. Some scientists proposed the endosymbiotic theory: mitochondria originated from α-proteobacteria engulfed by archaea. Over time, these engulfed bacteria established a symbiotic relationship with the host and eventually evolved into specialized organelles. Depending on whether the cell nucleus formed before mitochondria, the endosymbiotic theory is divided into the mitochondrion late model and mitochondrion early model.
Mitochondria were formed after the nuclear membrane and endoplasmic reticulum
Supporters of the mitochondrion late model believe that the cell nucleus had already formed before archaea engulfed prokaryote. During the Great Oxygenation Event, a surviving anaerobic archaea evolved a nuclear envelope to counteract DNA oxidation. The cell membrane gradually invaginated to form a primitive endomembrane system. They could also control the cytoskeleton to change shape and had taken on phagocytosis. These structural changes allowed archaeas to tolerate low levels of oxygen.
An archaea engulfed an α-proteobacterium but only partially digested it. The α-proteobacterium survived within the host and further oxidized the products of glycolysis by the citric acid cycle and electron transport chain. They produced more energy for the archaea and consumed oxygen to create an anaerobic environment for it. In return, the archaea provided the α-proteobacterium with pyruvate as food. They perfectly formed a endosymbiotic system. Over time, the α-proteobacterium transferred much of its DNA into the archaea DNA (gene horizontal transfer is common in bacteria). The lipids on the outer side of the cell wall became the outer membrane of the mitochondria, while the peptidoglycan on the inner side disappeared. The cell membrane invaginated to form cristae, increasing its surface area by about 10 times. This structure favored maintaining the proton gradient and increasing energy utilization efficiency, as most of the protons were trapped in the cristae and not easily diffused from the outer membrane. The α-proteobacterium transformed into specialized energy-providing mitochondria.
Engulfment required a significant amount of energy to change the entire cell membrane structure, and the functions of the nuclear envelope and endoplasmic reticulum also needed a lot of energy. Without mitochondria to supply energy, archaeas would not have been able to engulf the ancestors of mitochondria. Thus, this hypothesis faced a dilemma.
Mitochondria were formed before the nuclear membrane and endoplasmic reticulum
To address this issue, some scientists proposed that engulfment occurred before the formation of the cell nucleus and endomembrane system. In the poor oxygen deep ocean, facultative anaerobic α-proteobacteria existed. They carried out aerobic respiration in oxygen abundant condition, or ferment organic substances under anaerobic conditions. The by-products of fermentation, hydrogen and carbon dioxide, were raw materials for methanogens to survive. Methanogens approached these bacteria and changed their shape to tightly embrace them. Occasionally, the α-proteobacteria would be completely surrounded by the methanogens and starve to death. Fragments of their genes might integrate into the methanogens' DNA. After countless attempts, a certain methanogen acquired the genes to absorb organic substances from the external environment and undergo fermentation. When it engulfed an α-proteobacterium again, the fermentation products of methanogen happened to be food of α-proteobacterium. They could survive inside the methanogen.
At this point, the methanogen became independent of methane metabolism due to its newly acquired skills. Even without hydrogen and carbon dioxide, it could survive. Why would it still compete with sulfate-reducing bacteria in the dark and oxygen-deprived seabed? So, they left the seabed and swam towards the oxygen-rich sea surface. There, the α-proteobacteria initiated aerobic respiration to provide a large source of energy for the host. Over time, the α-proteobacteria transformed into mitochondria specialized in energy production. The genes used to synthesize lipids also moved to the host's DNA, and made the nuclear envelope and endomembrane system with help of mitochondria.
Before this, all organisms relied on simple and rapid reproduction to win the competition. However, the tremendous energy provided by mitochondria completely changed the course of evolution. Organisms now had another choice and evolved towards larger and more complex forms.