Eukaryogenesis
Process of forming the first eukaryotic cell
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Eukaryogenesis, the process which created the eukaryotic cell and lineage, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The process is widely agreed to have involved symbiogenesis, in which an archaeon and one or more bacteria contributed to the lineage leading to the last eukaryotic common ancestor (LECA). It appears also to have involved horizontal gene transfers from other groups of bacteria, with some of these transfers mediated by giant viruses. The LECA had a new level of complexity and capability, with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. The sequence of steps involved in the origin of eukaryotes has been disputed, and may not have started with symbiogenesis. In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms.
Context
Life arose on Earth once it had cooled enough for oceans to form. That developed into the last universal common ancestor (LUCA), an organism which had ribosomes and the genetic code, some 3.5-4 billion years ago. It gave rise to two main branches of prokaryotic life, the Bacteria and the Archaea. From among these small-celled, rapidly-dividing ancestors arose the eukaryotes, with a much wider range of cell sizes, nuclei, and cytoskeleton and endomembrane system.[1][2] The eukaryotes form a domain that contains all complex cells and most types of multicellular organism, including the animals, plants, and fungi.[3][4]
Symbiogenesis
According to the theory of symbiogenesis (the endosymbiotic theory) championed by Lynn Margulis, a member of the archaea gained a bacterial cell as a component. The archaeal cell was a member of the Promethearchaeati kingdom. The bacterium was one of the alphaproteobacteria, which had the ability to use oxygen in its respiration. This enabled it – and the archaeal cells that included it – to survive in the presence of oxygen, which was poisonous to other organisms adapted to reducing conditions. The endosymbiotic bacteria became the eukaryotic cell's mitochondria, providing most of the energy of the cell.[1][5][A]
More recently, the archaean has been identified as belonging to the class of Heimdallarchaeia of the phylum Promethearchaeota.[11]
Last eukaryotic common ancestor
The last eukaryotic common ancestor (LECA) is the hypothetical most recent common ancestor of all living eukaryotes, around 2 billion years ago,[3][4] and was most likely a biological population.[12] It is believed to have been a protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin and/or cellulose, and peroxisomes.[13][14]
It had been proposed that the LECA fed by phagocytosis, engulfing other organisms.[13][14] However, in 2022, Nico Bremer and colleagues confirmed that the LECA had mitochondria, and stated that it had multiple nuclei, but disputed that it was phagotrophic. This would mean that the ability found in many eukaryotes to engulf materials developed later, rather than being acquired first and then used to engulf the alphaproteobacteria that became mitochondria.[15]
The LECA has been described as having "spectacular cellular complexity".[16] Its cell was divided into compartments.[16] It appears to have inherited a set of endosomal sorting complex proteins that enable membranes to be remodelled, including pinching off vesicles to form endosomes.[17] Its apparatuses for transcribing DNA into RNA, and then for translating the RNA into proteins, were separated, permitting extensive RNA processing and allowing the expression of genes to become more complex.[18] It had mechanisms for reshuffling its genetic material, and possibly for manipulating its own evolvability. All of these gave the LECA "a compelling cohort of selective advantages".[16]
Eukaryotic sex
Sex in eukaryotes is a composite process, consisting of meiosis and fertilisation, which can be coupled to reproduction.[19] Dacks and Roger[20] proposed on the basis of a phylogenetic analysis that facultative sex was likely present in the common ancestor of all eukaryotes. Early in eukaryotic evolution, about 2 billion years ago, organisms needed a solution to the major problem that oxidative metabolism releases reactive oxygen species that damage the genetic material, DNA.[19] Eukaryotic sex provides a process, homologous recombination during meiosis, for using informational redundancy to repair such DNA damage.[19]
Scenarios
Competing sequences of mitochondria, membranes, and nucleus
Biologists have proposed multiple scenarios for the creation of the eukaryotes. While there is broad agreement that the LECA must have had a nucleus, mitochondria, and internal membranes, the order in which these were acquired has been disputed.[16] In the syntrophic model, the first eukaryotic common ancestor (FECA, around 2.2 gya) gained mitochondria, then membranes, then a nucleus.[16] In the phagotrophic model, it gained a nucleus, then membranes, then mitochondria.[16] In a more complex process, it gained all three in short order, then other capabilities. Other models have been proposed. Whatever happened, many lineages must have been created, but the LECA either out-competed or came together with the other lineages to form a single point of origin for the eukaryotes.[16]
Nick Lane and William Martin have argued that mitochondria came first, on the grounds that energy had been the limiting factor on the size of the prokaryotic cell.[21] Enrique M. Muro et al. have argued, however, that the genetic system needed to reach a critical point that led to a new regulatory system (with introns and the spliceosome), which enabled coordination between genetic networks.[22] The phagotrophic model presupposes the ability to engulf food, enabling the cell to engulf the aerobic bacterium that became the mitochondrion.[16]
Eugene Koonin and others, noting that the archaea share many features with eukaryotes, argue that rudimentary eukaryotic traits such as membrane-lined compartments were acquired before endosymbiosis added mitochondria to the early eukaryotic cell, while the cell wall was lost. In the same way, mitochondrial acquisition must not be regarded as the end of the process, for still new complex families of genes had to be developed after or during the endosymbiotic exchange. In this way, from FECA to LECA, the organisms can be considered as proto-eukaryotes. At the end of the process, LECA was already a complex organism with protein families involved in cellular compartmentalization.[23][24]
Viral eukaryogenesis
Another scenario is viral eukaryogenesis, which proposes that the eukaryotes arose as an emergent superorganism, with the nucleus deriving from a "viral factory" alongside the alphaproteobacterium mitochondrion, hosted by an archaeal cell. In this scenario, eukaryogenesis began when a virus colonised an archaeal cell, making it support the production of viruses. The virus may later have assisted the bacterium's entry into the reprogrammed cell.[25] Eukaryotes share genes for several DNA synthesis and transcription enzymes with DNA viruses (Nucleocytoviricota). Those viruses may thus be older than the LECA and may have exchanged DNA with proto-eukaryotes.[26]
Computational protein crisis
Enrique Muro and colleagues suggested in 2025 that the origin of eukaryotes, an evolutionary transition that occurred only once, may nevertheless have been a highly probable outcome under deep biochemical or informational constraints. It proposes that prokaryotes faced an impending "computational crisis" in their ability to explore new regions of protein sequence space, making the emergence of more complex cellular systems a likely solution rather than a contingent accident.[27]
Associations of microbes
In 2026, Moisès Bernabeu and colleagues stated in Nature on the basis of phylogenomics, across the full range of cellular organisms and viruses, that LECA had derived its proteins from multiple types of bacteria. They suggest that this occurred in repeated horizontal gene transfers, and that some of these most likely took place before the endosymbiosis that created mitochondria.[28] The lead researcher, Toni Gabaldón, commented that the explanation of the origin of eukaryotes as a symbiosis of an archaeon with a bacterium is incomplete, as other bacteria and giant viruses had been involved.[29] The bacteria included Planctomycetota and later the Myxococcota, while the giant viruses belonged to the Nucleocytoviricota. The viruses appear to have served to transfer genes between different microbes and hence to construct the genome of the LECA.[28]
Ancestral lineages: Brown: Alphaproteobacteria; Light brown: Myxococcota; Blue: Asgardarchaeota; Purple: Planctomycetota.
Diversification: crown eukaryotes
In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms with the new capabilities and complexity of the eukaryotic cell.[30][31] Single cells without cell walls are fragile and have a low probability of being fossilised. If fossilised, they have few features to distinguish them clearly from prokaryotes: size, morphological complexity, and (eventually) multicellularity. Early eukaryote fossils, from the late Paleoproterozoic, include acritarch microfossils with relatively robust ornate carbonaceous vesicles of Tappania from 1.63 gya and Shuiyousphaeridium from 1.8 gya.[31]
The position of the LECA (i.e. the root) on the eukaryotic tree of life remains controversial. Some studies believe that the first split after the LECA happened between the Unikonta and the Bikonta (Stechmann and Cavalier-Smith 2003), or between Amorphea and all other eukaryotes (Adl et al. 2012; Derelle and Lang 2012). Some believe that the first split happened within Excavata (al Jewari and Baldauf 2023).[32] Yet others believe in a first split between the Opisthokonta and all others (Cerón-Romero et al. 2024).[33]
Notes
- Margulis and colleagues also suggested that the cell also acquired a Spirochaete bacterium as a symbiont, providing the cell skeleton of microtubules and the ability to move, including the ability to pull chromosomes into two sets during mitosis, cell division[6], however this specific hypothesis never had significant data in its support and has been consistently rejected by the scientific community.[7][8][9][10]