Eukaryota, whose members are known as eukaryotes (/juːˈkærioʊts,-əts/), is a diverse domain of organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacteria and Archaea (both prokaryotes) make up the other two domains.
Eukaryotic organisms that cannot be classified under the kingdoms Plantae, Animalia or Fungi are sometimes grouped in the paraphyleticProtista.
The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the Asgard archaea. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among archaea. Eukaryotes represent a small minority of the number of organisms, but, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the Proterozoic eon, likely as flagellatedphagotrophs. Their name comes from the Greek εὖ (eu, "well" or "good") and κάρυον (karyon, "nut" or "kernel").
Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. It is probable that most other membrane-bound organelles are ultimately derived from such vesicles. Alternatively some products produced by the cell can leave in a vesicle through exocytosis.
The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.
Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm.Peroxisomes are used to break down peroxide, which is otherwise toxic. Many protozoans have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. In higher plants, most of a cell's volume is taken up by a central vacuole, which mostly contains water and primarily maintains its osmotic pressure.
The outer mitochondrial membrane is freely permeable and allows almost anything to enter into the intermembrane space while the inner mitochondrial membrane is semi permeable so allows only some required things into the mitochondrial matrix.
Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA. They are now generally held to have developed from endosymbiotic prokaryotes, probably Alphaproteobacteria.
Plants and various groups of algae also have plastids. Plastids also have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion. The capture and sequestering of photosynthetic cells and chloroplasts occurs in many types of modern eukaryotic organisms and is known as kleptoplasty.
Endosymbiotic origins have also been proposed for the nucleus, and for eukaryotic flagella.
Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Flagella and cilia are sometimes referred to as undulipodia, and are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin. These are entirely distinct from prokaryotic flagellae. They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella also may have hairs, or mastigonemes, and scales connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm.
Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups that give rise to various microtubular roots. These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles produce the spindle during nuclear division.
The significance of cytoskeletal structures is underlined in the determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis and chemokinesis. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema.
The cells of plants and algae, fungi and most chromalveolates have a cell wall, a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.
There are many different types of eukaryotic cells, though animals and plants are the most familiar eukaryotes, and thus provide an excellent starting point for understanding eukaryotic structure. Fungi and many protists have some substantial differences, however.
All animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Due to the lack of a cell wall, animal cells can transform into a variety of shapes. A phagocytic cell can even engulf other structures.
Plant cells have a number of features that distinguish them from the cells of the other eukaryotic organisms. These include:
The plasmodesmata, pores in the cell wall that link adjacent cells and allow plant cells to communicate with adjacent cells. Animals have a different but functionally analogous system of gap junctions between adjacent cells.
Less compartmentation between cells; the hyphae of higher fungi have porous partitions called septa, which allow the passage of cytoplasm, organelles, and, sometimes, nuclei; so each organism is essentially a giant multinucleate supercell – these fungi are described as coenocytic. Primitive fungi have few or no septa.
Only the most primitive fungi, chytrids, have flagella.
This diagram illustrates the twofold cost of sex. If each individual were to contribute the same number of offspring (two), (a) the sexual population remains the same size each generation, where the (b) asexual population doubles in size each generation.
Cell division generally takes place asexually by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. Most eukaryotes also have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell and a diploid phase, wherein two copies of each chromosome are present in each cell. The diploid phase is formed by fusion of two haploid gametes to form a zygote, which may divide by mitosis or undergo chromosome reduction by meiosis. There is considerable variation in this pattern. Animals have no multicellular haploid phase, but each plant generation can consist of haploid and diploid multicellular phases.
Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times.
The evolution of sexual reproduction may be a primordial and fundamental characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was present in the common ancestor of all eukaryotes. A core set of genes that function in meiosis is present in both Trichomonas vaginalis and Giardia intestinalis, two organisms previously thought to be asexual. Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, it was inferred that core meiotic genes, and hence sex, were likely present in a common ancestor of all eukaryotes. Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus Leishmania, have been shown to have a sexual cycle. Also, evidence now indicates that amoebae, previously regarded as asexual, are anciently sexual and that the majority of present-day asexual groups likely arose recently and independently.
Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes
One hypothesis of eukaryotic relationships – the Opisthokonta group includes both animals (Metazoa) and fungi, plants (Plantae) are placed in Archaeplastida.
A pie chart of described eukaryote species (except for Excavata), together with a tree showing possible relationships between the groups
In antiquity, the two lineages of animals and plants were recognized. They were given the taxonomic rank of Kingdom by Linnaeus. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980s. The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word protozoa to refer to organisms such as ciliates, and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel in 1866. The eukaryotes thus came to be composed of four kingdoms:
The protists were understood to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really started with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain. At the same time, work on the protist tree intensified, and is still actively going on today. Several alternative classifications have been forwarded, though there is no consensus in the field.
There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the major groups – in particular, Haptophyta, Cryptophyta, Centrohelida, Telonemia, Picozoa,Apusomonadida, Ancyromonadida, Breviatea, and the genus Collodictyon. Overall, it seems that, although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. As Roger & Simpson said in 2009 "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution." Newly identified protists, purported to represent novel, deep-branching lineages, continue to be described well into the 21st century; recent examples including Rhodelphis, putative sister group to Rhodophyta, and Anaeramoeba, anaerobic amoebaflagellates of uncertain placement.
The rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true crown), which was usually divided by the form of the mitochondrial cristae; see crown eukaryotes. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive; but this is now considered an artifact of long-branch attraction, and they are known to have lost them secondarily.
It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists.
The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000–220,050 Mb in the dinoflagellate Prorocentrum micans, showing that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic 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. Later endosymbiosis led to the spread of plastids in some lineages.
Although there is still considerable uncertainty in global eukaryote phylogeny, particularly regarding the position of the root, a rough consensus has started to emerge from the phylogenomic studies of the past two decades. The majority of eukaryotes can be placed in one of two large clades dubbed Amorphea (similar in composition to the unikont hypothesis) and the Diaphoretickes, which includes plants and most algal lineages. A third major grouping, the Excavata, has been abandoned as a formal group in the most recent classification of the International Society of Protistologists due to growing uncertainty as to whether its constituent groups belong together. The proposed phylogeny below includes only one group of excavates (Discoba), and incorporates the recent proposal that picozoans are close relatives of rhodophytes.
The division of the eukaryotes into two primary clades, bikonts (Archaeplastida + SAR + Excavata) and unikonts (Amoebozoa + Opisthokonta), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier. A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.
A highly converged and congruent set of trees appears in Derelle et al. (2015), Ren et al. (2016), Yang et al. (2017) and Cavalier-Smith (2015) including the supplementary information, resulting in a more conservative and consolidated tree. It is combined with some results from Cavalier-Smith for the basal Opimoda. The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the bikonts Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbiotic eukaryote-eukaryote hybrids. Archaeplastida acquired chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, Gloeomargarita lithophora.
The origin of the eukaryotic cell, also known as eukaryogenesis, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. A number of approaches have been used to find the first eukaryote and their closest relatives. The last eukaryotic common ancestor (LECA) is the hypothetical last common ancestor of all living eukaryotes, and was most likely a biological population.
Eukaryotes have a number of features that differentiate them from prokaryotes, including an endomembrane system, and unique biochemical pathways such as sterane synthesis. A set of proteins called eukaryotic signature proteins (ESPs) was proposed to identify eukaryotic relatives in 2002: They have no homology to proteins known in other domains of life by then, but they appear to be universal among eukaryotes. They include proteins that make up the cytoskeleton, the complex transcription machinery, membrane-sorting systems, the nuclear pore, as well as some enzymes in the biochemical pathways.
The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.1 billion years ago. The Geosiphon-like fossil fungusDiskagma has been found in paleosols 2.2 billion years old.
Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time. Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red algae, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.
The presence of eukaryotic-specific biomarkers (steranes) in Australianshales previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old, which was even 300 million years older than the first geological records of the appreciable amount of molecular oxygen during the Great Oxidation Event. However, these Archaean biomarkers were eventually rebutted as later contaminants. Currently, putatively the oldest biomarker records are only ~800 million years old. In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago, and thus there is a huge gap between molecular data and geological data, which hinders a reasonable inference of the eukaryotic evolution through biomarker records before 800 million years ago. The nature of steranes as eukaryotic biomarkers is further complicated by the production of sterols by some bacteria.
Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments 800 million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes, approximately a billion years after their origin (at the latest).
The nuclear DNA and genetic machinery of eukaryotes is more similar to Archaea than Bacteria, leading to a controversial suggestion that eukaryotes should be grouped with Archaea in the clade Neomura. In other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:
Eukaryotes and Archaea developed separately from a modified bacterium.
Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view implies that the UCA was relatively large and complex.
Alternative proposals include:
The chronocyte hypothesis postulates that a primitive eukaryotic cell was formed by the endosymbiosis of both archaea and bacteria by a third type of cell, termed a chronocyte. This is mainly to account for the fact that eukaryotic signature proteins were not found anywhere else by 2002.
The universal common ancestor (UCA) of the current tree of life was a complex organism that survived a mass extinction event rather than an early stage in the evolution of life. Eukaryotes and in particular akaryotes (Bacteria and Archaea) evolved through reductive loss, so that similarities result from differential retention of original features.
Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea, and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below, with a modification of hypothesis 2 making the 4th column: The eocyte hypothesis, in which the Archaea are paraphyletic. (The table and the names for the hypotheses are based on Harish & Kurland, 2017.)
Alternative hypotheses for the base of the tree of life
In recent years, most researchers have favoured either the three domains (3D) or the eocyte hypothesis. An rRNA analysis supports the eocyte scenario, apparently with the Eukaryote root in Excavata. A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is:
In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which comprises Thermoproteota (formerly named eocytes or Crenarchaeota), Nitrososphaerota (formerly Thaumarchaeota), and others. This group is reported contain many of the eukaryotic signature proteins and produce vesicles.
In 2017, there was significant pushback against this scenario, arguing that the eukaryotes did not emerge within the Archaea. Cunha et al. produced analyses supporting the three domains (3D) or Woese hypothesis (2 in the table above) and rejecting the eocyte hypothesis (4 above). Harish and Kurland found strong support for the earlier two empires (2D) or Mayr hypothesis (1 in the table above), based on analyses of the coding sequences of protein domains. They rejected the eocyte hypothesis as the least likely. A possible interpretation of their analysis is that the universal common ancestor (UCA) of the current tree of life was a complex organism that survived an evolutionary bottleneck, rather than a simpler organism arising early in the history of life. On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples. Since then, the publication of additional Asgard archaeal genomes and the independent reconstruction of phylogenomic trees by multiple independent laboratories have provided additional support for an Asgard archaeal origin of eukaryotes.
The origins of the endomembrane system and mitochondria are also unclear. The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts. The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis is one particular version).
In a study using genomes to construct supertrees, Pisani et al. (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an alphaproteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the alphaproteobacterial endosymbiont. The majority of the genes from the symbiont have been transferred to the nucleus. They make up most of the metabolic and energy-related pathways of the eukaryotic cell, while the information system (DNA polymerase, transcription, translation) is retained from archaea.
Different hypotheses have been proposed as to how eukaryotic cells came into existence. These hypotheses can be classified into two distinct classes – autogenous models and chimeric models.
Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium after a eukaryote with a nucleus has evolved. This theory is less held onto because it requires extra assumptions to explain current conditions. For example, as every known eukaryote has a mitochondrion (or at least show signs of having an ancestor that had), one must assumed that all the eukaryotic lineages that did not acquire mitochondria became extinct. The theory also does not explain why anaerobic variants of mitochondria have evolved.
Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria called the proto-mitochondrion. These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphasize the role of endosymbiotic processes behind the origin of mitochondria.
The inside-out hypothesisEdit
The inside-out hypothesis suggests that the fusion between free-living mitochondria-like bacteria, and an archaeon into a eukaryotic cell happened gradually over a long period of time, instead of in a single phagocytotic event. In this scenario, an archaeon would trap aerobic bacteria with cell protrusions, and then keep them alive to draw energy from them instead of digesting them. During the early stages the bacteria would still be partly in direct contact with the environment, and the archaeon would not have to provide them with all the required nutrients. But eventually the archaeon would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process.
It is assumed the archaean group called halophiles went through a similar procedure, where they acquired as much as a thousand genes from a bacterium, way more than through the conventional horizontal gene transfer that often occurs in the microbial world, but that the two microbes separated again before they had fused into a single eukaryote-like cell.
An expanded version of the inside-out hypothesis proposes that the eukaryotic cell was created by physical interactions between two prokaryotic organisms and that the last common ancestor of eukaryotes got its genome from a whole population or community of microbes participating in cooperative relationships to thrive and survive in their environment. The genome from the various types of microbes would complement each other, and occasional horizontal gene transfer between them would be largely to their own benefit. This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence.
The serial endosymbiotic hypothesisEdit
According to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic crenarchaeon (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism.
From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alphaproteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. For example, Thiodendron has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – Desulfobacter and Spirochaeta.
However, such an association based on motile symbiosis has never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments. In addition, the theory posits that mitochondrion-less eukaryotes have existed, tying back to the problem in the autogenous model.
The hydrogen hypothesisEdit
In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophicmethanogenic archaeon (host) with an alphaproteobacterium (the symbiont) gave rise to the eukaryotes. The host used hydrogen (H2) and carbon dioxide (CO2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and CO2 as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation.
Endosymbiotic gene transfer acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host's methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.
The syntrophy hypothesisEdit
The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this model, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a deltaproteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alphaproteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a deltaproteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus, while the deltaproteobacterium contributed towards the cytoplasmic features.
This theory incorporates two selective forces at the time of nucleus evolution
presence of metabolic partitioning to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and
A complex scenario of 6+ serial endosymbiotic events of archaea and bacteria has been proposed in which mitochondria and an asgard related archaeota were acquired at a late stage of eukaryogenesis, possibly in combination, as a secondary endosymbiont. The findings have been rebuked as an artifact.
^ abcStrassert JF, Irisarri I, Williams TA, Burki F (March 2021). "A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids". Nature Communications. 12 (1): 1879. Bibcode:2021NatCo..12.1879S. doi:10.1038/s41467-021-22044-z. PMC7994803. PMID33767194.
^ abcBrown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, et al. (February 2018). "Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group". Genome Biology and Evolution. 10 (2): 427–433. doi:10.1093/gbe/evy014. PMC5793813. PMID29360967.
^ abTikhonenkov DV, Mikhailov KV, Gawryluk RM, Belyaev AO, Mathur V, Karpov SA, et al. (December 2022). "Microbial predators form a new supergroup of eukaryotes". Nature. 612 (7941): 714–719. doi:10.1038/s41586-022-05511-5. PMID36477531. S2CID 254436650.
^"Definition of EUKARYOTE". www.merriam-webster.com. Retrieved 12 December 2022.
^ abGabaldón T (October 2021). "Origin and Early Evolution of the Eukaryotic Cell". Annual Review of Microbiology. 75 (1): 631–647. doi:10.1146/annurev-micro-090817-062213. PMID34343017. S2CID 236916203.
^ abWoese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC54159. PMID2112744.
^Zimmer C (11 April 2016). "Scientists Unveil New 'Tree of Life'". The New York Times. Archived from the original on 24 March 2019. Retrieved 11 April 2016.
^Gribaldo S, Brochier-Armanet C (January 2020). "Evolutionary relationships between archaea and eukaryotes". Nature Ecology & Evolution. 4 (1): 20–21. doi:10.1038/s41559-019-1073-1. PMID31836857.
^Doolittle WF (February 2020). "Evolution: Two Domains of Life or Three?". Current Biology. 30 (4): R177–R179. doi:10.1016/j.cub.2020.01.010. PMID32097647.
^ abWilliams TA, Cox CJ, Foster PG, Szöllősi GJ, Embley TM (January 2020). "Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution. 4 (1): 138–147. doi:10.1038/s41559-019-1040-x. PMC6942926. PMID31819234.
^ abWhitman WB, Coleman DC, Wiebe WJ (June 1998). "Prokaryotes: the unseen majority" (PDF). Proceedings of the National Academy of Sciences of the United States of America. 95 (12): 6578–6583. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC33863. PMID9618454. Archived (PDF) from the original on 20 August 2008. Retrieved 16 September 2011.
^Murat D, Byrne M, Komeili A (October 2010). "Cell biology of prokaryotic organelles". Cold Spring Harbor Perspectives in Biology. 2 (10): a000422. doi:10.1101/cshperspect.a000422. PMC2944366. PMID20739411.
^Whittaker RH (January 1969). "New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms". Science. 163 (3863): 150–60. Bibcode:1969Sci...163..150W. CiteSeerX10.1.1.403.5430. doi:10.1126/science.163.3863.150. PMID5762760.
^Campbell NA, Cain ML, Minorsky PV, Reece JB, Urry LA (2018). "Chapter 13: Sexual Life Cycles and Meiosis". Biology: A Global Approach (11th ed.). New York: Pearson Education. ISBN 978-1-292-17043-5.
^Yamaguchi M, Worman CO (2014). "Deep-sea microorganisms and the origin of the eukaryotic cell" (PDF). Jpn. J. Protozool. 47 (1, 2): 29–48. Archived from the original (PDF) on 9 August 2017. Retrieved 24 October 2017.
^Linka M, Weber AP (2011). "Evolutionary Integration of Chloroplast Metabolism with the Metabolic Networks of the Cells". In Burnap RL, Vermaas WF (eds.). Functional Genomics and Evolution of Photosynthetic Systems. Springer. p. 215. ISBN 978-94-007-1533-2. Archived from the original on 29 May 2016. Retrieved 27 October 2015.
^Marsh M (2001). Endocytosis. Oxford University Press. p. vii. ISBN 978-0-19-963851-2.
^Hetzer MW (March 2010). "The nuclear envelope". Cold Spring Harbor Perspectives in Biology. 2 (3): a000539. doi:10.1101/cshperspect.a000539. PMC2829960. PMID20300205.
^"Endoplasmic Reticulum (Rough and Smooth)". British Society for Cell Biology. Archived from the original on 24 March 2019. Retrieved 12 November 2017.
^"Golgi Apparatus". British Society for Cell Biology. Archived from the original on 13 November 2017. Retrieved 12 November 2017.
^"Lysosome". British Society for Cell Biology. Archived from the original on 13 November 2017. Retrieved 12 November 2017.
^ abcdKarnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, et al. (May 2016). "A Eukaryote without a Mitochondrial Organelle". Current Biology. 26 (10): 1274–1284. doi:10.1016/j.cub.2016.03.053. PMID27185558.
^Saygin D, Tabib T, Bittar HE, Valenzi E, Sembrat J, Chan SY, et al. (July 1957). "Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension". Pulmonary Circulation. 10 (1): 131–144. Bibcode:1957SciAm.197a.131S. doi:10.1038/scientificamerican0757-131. PMID32166015.
^Mack S (1 May 2006). "Re: Are there eukaryotic cells without mitochondria?". madsci.org. Archived from the original on 24 April 2014. Retrieved 24 April 2014.
^Watson J, Hopkins N, Roberts J, Steitz JA, Weiner A (1988). "28: The Origins of Life". Molecular Biology of the Gene (Fourth ed.). Menlo Park, CA: The Benjamin/Cummings Publishing Company, Inc. p. 1154. ISBN 978-0-8053-9614-0.
^Davis JL (13 May 2016). "Scientists Shocked To Discover Eukaryote With NO Mitochondria". IFL Science. Archived from the original on 17 February 2019. Retrieved 13 May 2016.
^Sato N (2006). "Origin and Evolution of Plastids: Genomic View on the Unification and Diversity of Plastids". In Wise RR, Hoober JK (eds.). The Structure and Function of Plastids. Advances in Photosynthesis and Respiration. Vol. 23. Springer Netherlands. pp. 75–102. doi:10.1007/978-1-4020-4061-0_4. ISBN 978-1-4020-4060-3.
^Margulis L (1998). Symbiotic planet: a new look at evolution. New York: Basic Books. ISBN 978-0-465-07271-2. OCLC 39700477.[page needed]
^Lynn Margulis, Heather I. McKhann & Lorraine Olendzenski (ed.), Illustrated Glossary of Protoctista, Jones and Bartlett Publishers, Boston, 1993, p. xviii. ISBN 0-86720-081-2
^Vorobjev IA, Nadezhdina ES (1987). The centrosome and its role in the organization of microtubules. International Review of Cytology. Vol. 106. pp. 227–293. doi:10.1016/S0074-7696(08)61714-3. ISBN 978-0-12-364506-7. PMID3294718.
^Howland JL (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. pp. 69–71. ISBN 978-0-19-511183-5.
^Fry SC (1989). "The Structure and Functions of Xyloglucan". Journal of Experimental Botany. 40 (1): 1–11. doi:10.1093/jxb/40.1.1.
^Raven JA (July 1987). "The role of vacuoles". New Phytologist. 106 (3): 357–422. doi:10.1111/j.1469-8137.1987.tb00149.x.
^Oparka K (2005). Plasmodesmata. Oxford, UK: Blackwell Publishing.
^Raven PH, Evert RF, Eichorm SE (1999). Biology of Plants. New York: W.H. Freeman.
^Silflow CD, Lefebvre PA (December 2001). "Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii". Plant Physiology. 127 (4): 1500–1507. doi:10.1104/pp.010807. PMC1540183. PMID11743094.
^Deacon J (2005). Fungal Biology. Cambridge, Massachusetts: Blackwell Publishers. pp. 4 and passim. ISBN 978-1-4051-3066-0.
^Keeling PJ (October 2004). "Diversity and evolutionary history of plastids and their hosts". American Journal of Botany. 91 (10): 1481–1493. doi:10.3732/ajb.91.10.1481. PMID21652304.
^Patterson DJ. "Amoebae: Protists Which Move and Feed Using Pseudopodia". Tree of Life Web Project. Archived from the original on 15 June 2010. Retrieved 12 November 2017.
^Gould SB, Tham WH, Cowman AF, McFadden GI, Waller RF (2008). "Alveolins, a new family of cortical proteins that define the protist infrakingdom Alveolata". Molecular Biology and Evolution. 25 (6): 1219–1230. doi:10.1093/molbev/msn070. PMID18359944.
^Lane N (June 2011). "Energetics and genetics across the prokaryote-eukaryote divide". Biology Direct. 6 (1): 35. doi:10.1186/1745-6150-6-35. PMC3152533. PMID21714941.
^Dacks J, Roger AJ (June 1999). "The first sexual lineage and the relevance of facultative sex". Journal of Molecular Evolution. 48 (6): 779–783. Bibcode:1999JMolE..48..779D. doi:10.1007/PL00013156. PMID10229582. S2CID 9441768.
^ abRamesh MA, Malik SB, Logsdon JM (January 2005). "A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis". Current Biology. 15 (2): 185–191. doi:10.1016/j.cub.2005.01.003. PMID15668177. S2CID 17013247.
^ abMalik SB, Pightling AW, Stefaniak LM, Schurko AM, Logsdon JM (August 2007). Hahn MW (ed.). "An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis". PLOS ONE. 3 (8): e2879. Bibcode:2008PLoSO...3.2879M. doi:10.1371/journal.pone.0002879. PMC2488364. PMID18663385.
^Akopyants NS, Kimblin N, Secundino N, Patrick R, Peters N, Lawyer P, Dobson DE, Beverley SM, Sacks DL (April 2009). "Demonstration of genetic exchange during cyclical development of Leishmania in the sand fly vector". Science. 324 (5924): 265–268. Bibcode:2009Sci...324..265A. doi:10.1126/science.1169464. PMC2729066. PMID19359589.
^Lahr DJ, Parfrey LW, Mitchell EA, Katz LA, Lara E (July 2011). "The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms". Proceedings: Biological Sciences. 278 (1715): 2081–2090. doi:10.1098/rspb.2011.0289. PMC3107637. PMID21429931.
^Moore RT (1980). "Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts". Botanica Marina. 23: 361–373.
^Goldfuß (1818). "Ueber die Classification der Zoophyten" [On the classification of zoophytes]. Isis, Oder, Encyclopädische Zeitung von Oken (in German). 2 (6): 1008–1019. Archived from the original on 24 March 2019. Retrieved 15 March 2019. From p. 1008: "Erste Klasse. Urthiere. Protozoa." (First class. Primordial animals. Protozoa.) [Note: each column of each page of this journal is numbered; there are two columns per page.]
^Scamardella JM (1999). "Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista" (PDF). International Microbiology. 2 (4): 207–221. PMID10943416. Archived from the original (PDF) on 14 June 2011.
^ abRothschild LJ (1989). "Protozoa, Protista, Protoctista: what's in a name?". Journal of the History of Biology. 22 (2): 277–305. doi:10.1007/BF00139515. PMID11542176. S2CID 32462158. Archived from the original on 4 February 2020. Retrieved 4 February 2020.
^ abSpang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ (May 2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521 (7551): 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC4444528. PMID25945739.
^ abZaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ (January 2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity". Nature. 541 (7637): 353–358. Bibcode:2017Natur.541..353Z. doi:10.1038/nature21031. OSTI 1580084. PMID28077874. S2CID 4458094. Archived from the original on 5 December 2019. Retrieved 28 June 2019.
^ abLiu Y, Zhou Z, Pan J, Baker BJ, Gu JD, Li M (April 2018). "Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota". The ISME Journal. 12 (4): 1021–1031. doi:10.1038/s41396-018-0060-x. PMC5864231. PMID29445130.
^Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. (2005). "The new higher level classification of eukaryotes with emphasis on the taxonomy of protists". The Journal of Eukaryotic Microbiology. 52 (5): 399–451. doi:10.1111/j.1550-7408.2005.00053.x. PMID16248873. S2CID 8060916.
^Harper JT, Waanders E, Keeling PJ (January 2005). "On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes" (PDF). International Journal of Systematic and Evolutionary Microbiology. 55 (Pt 1): 487–496. doi:10.1099/ijs.0.63216-0. PMID15653923. Archived from the original (PDF) on 17 December 2008.
^Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA (December 2006). "Evaluating support for the current classification of eukaryotic diversity". PLOS Genetics. 2 (12): e220. doi:10.1371/journal.pgen.0020220. PMC1713255. PMID17194223.
^Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, et al. (September 2012). "The revised classification of eukaryotes" (PDF). The Journal of Eukaryotic Microbiology. 59 (5): 429–93. doi:10.1111/j.1550-7408.2012.00644.x. PMC3483872. PMID23020233. Archived from the original (PDF) on 16 June 2016.
^ abBurki F (May 2014). "The eukaryotic tree of life from a global phylogenomic perspective". Cold Spring Harbor Perspectives in Biology. 6 (5): a016147. doi:10.1101/cshperspect.a016147. PMC3996474. PMID24789819.
^ abZhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K (June 2012). "Collodictyon – an ancient lineage in the tree of eukaryotes". Molecular Biology and Evolution. 29 (6): 1557–1568. doi:10.1093/molbev/mss001. PMC3351787. PMID22319147.
^Romari K, Vaulot D (2004). "Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences". Limnol Oceanogr. 49 (3): 784–798. Bibcode:2004LimOc..49..784R. doi:10.4319/lo.2004.49.3.0784. S2CID 86718111.
^Roger AJ, Simpson AG (February 2009). "Evolution: revisiting the root of the eukaryote tree". Current Biology. 19 (4): R165–67. doi:10.1016/j.cub.2008.12.032. PMID19243692. S2CID 13172971.
^ abBurki F, Roger AJ, Brown MW, Simpson AG (January 2020). "The New Tree of Eukaryotes". Trends in Ecology & Evolution. 35 (1): 43–55. doi:10.1016/j.tree.2019.08.008. PMID31606140.
^Tovar J, Fischer A, Clark CG (June 1999). "The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica". Molecular Microbiology. 32 (5): 1013–1021. doi:10.1046/j.1365-2958.1999.01414.x. PMID10361303. S2CID 22805284.
^Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, Gabaldón T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, Tielens AG, Friedrich T, Veenhuis M, Huynen MA, Hackstein JH (March 2005). "An anaerobic mitochondrion that produces hydrogen" (PDF). Nature. 434 (7029): 74–79. Bibcode:2005Natur.434...74B. doi:10.1038/nature03343. PMID15744302. S2CID 4401178. Archived (PDF) from the original on 24 January 2019. Retrieved 24 January 2019.
^ abcJagus R, Bachvaroff TR, Joshi B, Place AR (2012). "Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists". Comparative and Functional Genomics. 2012: 1–21. doi:10.1155/2012/134839. PMC3388326. PMID22778692.
^Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ (January 2016). "Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista". Proceedings: Biological Sciences. 283 (1823): 20152802. doi:10.1098/rspb.2015.2802. PMC4795036. PMID26817772.
^Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Rohwer FL, Mylnikov AP, Keeling PJ (December 2017). "A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction" (PDF). Current Biology. 27 (23): 3717–24.e5. doi:10.1016/j.cub.2017.10.051. PMID29174886. S2CID 37933928. Archived (PDF) from the original on 27 April 2019. Retrieved 2 September 2019.
^Bodył A (February 2018). "Did some red alga-derived plastids evolve via kleptoplastidy? A hypothesis". Biological Reviews of the Cambridge Philosophical Society. 93 (1): 201–222. doi:10.1111/brv.12340. PMID28544184. S2CID 24613863.
^Lax G, Eglit Y, Eme L, Bertrand EM, Roger AJ, Simpson AG (November 2018). "Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes". Nature. 564 (7736): 410–414. Bibcode:2018Natur.564..410L. doi:10.1038/s41586-018-0708-8. PMID30429611. S2CID 205570993.
^Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, et al. (January 2019). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". The Journal of Eukaryotic Microbiology. 66 (1): 4–119. doi:10.1111/jeu.12691. PMC6492006. PMID30257078.
^Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J (August 2007). Butler G (ed.). "Phylogenomics reshuffles the eukaryotic supergroups". PLOS ONE. 2 (8): e790. Bibcode:2007PLoSO...2..790B. doi:10.1371/journal.pone.0000790. PMC1949142. PMID17726520.
^ abKim E, Graham LE (July 2008). Redfield RJ (ed.). "EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata". PLOS ONE. 3 (7): e2621. Bibcode:2008PLoSO...3.2621K. doi:10.1371/journal.pone.0002621. PMC2440802. PMID18612431.
^Baurain D, Brinkmann H, Petersen J, Rodríguez-Ezpeleta N, Stechmann A, Demoulin V, Roger AJ, Burger G, Lang BF, Philippe H (July 2010). "Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles". Molecular Biology and Evolution. 27 (7): 1698–1709. doi:10.1093/molbev/msq059. PMID20194427.
^Burki F, Okamoto N, Pombert JF, Keeling PJ (June 2012). "The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins". Proceedings: Biological Sciences. 279 (1736): 2246–2254. doi:10.1098/rspb.2011.2301. PMC3321700. PMID22298847.
^Cavalier-Smith T (2003). "Protist phylogeny and the high-level classification of Protozoa". European Journal of Protistology. 39 (4): 338–348. doi:10.1078/0932-4739-00002. S2CID 84403388.
^Burki F, Pawlowski J (October 2006). "Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts". Molecular Biology and Evolution. 23 (10): 1922–1930. doi:10.1093/molbev/msl055. PMID16829542.
^Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X (September 2016). "Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes". Genome Biology and Evolution. 8 (9): 2683–2701. doi:10.1093/gbe/evw196. PMC5631032. PMID27604879.
^ abcCavalier-Smith T (January 2018). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255 (1): 297–357. doi:10.1007/s00709-017-1147-3. PMC5756292. PMID28875267.
^Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M (February 2015). "Bacterial proteins pinpoint a single eukaryotic root". Proceedings of the National Academy of Sciences of the United States of America. 112 (7): E693–699. Bibcode:2015PNAS..112E.693D. doi:10.1073/pnas.1420657112. PMC4343179. PMID25646484.
^Yang J, Harding T, Kamikawa R, Simpson AG, Roger AJ (May 2017). "Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids". Genome Biology and Evolution. 9 (5): 1161–1174. doi:10.1093/gbe/evx086. PMC5421314. PMID28453770.
^Cavalier-Smith T, Fiore-Donno AM, Chao E, Kudryavtsev A, Berney C, Snell EA, Lewis R (February 2015). "Multigene phylogeny resolves deep branching of Amoebozoa". Molecular Phylogenetics and Evolution. 83: 293–304. doi:10.1016/j.ympev.2014.08.011. PMID25150787.
^Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I (September 2015). "Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi". Current Biology. 25 (18): 2404–2410. doi:10.1016/j.cub.2015.07.053. PMID26365255.
^ abLópez-García P, Eme L, Moreira D (December 2017). "Symbiosis in eukaryotic evolution". Journal of Theoretical Biology. 434: 20–33. Bibcode:2017JThBi.434...20L. doi:10.1016/j.jtbi.2017.02.031. PMC5638015. PMID28254477.
^Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D (February 2017). "An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids". Current Biology. 27 (3): 386–391. doi:10.1016/j.cub.2016.11.056. PMC5650054. PMID28132810.
^de Vries J, Archibald JM (February 2017). "Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?". Current Biology. 27 (3): R103–105. doi:10.1016/j.cub.2016.12.006. PMID28171752.
^ abCavalier-Smith T (June 2010). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biology Letters. 6 (3): 342–345. doi:10.1098/rsbl.2009.0948. PMC2880060. PMID20031978.
^ abCavalier-Smith T (May 2013). "Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa". European Journal of Protistology. 49 (2): 115–178. doi:10.1016/j.ejop.2012.06.001. PMID23085100.
^ abCavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM, Lewis R (December 2014). "Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa". Molecular Phylogenetics and Evolution. 81: 71–85. doi:10.1016/j.ympev.2014.08.012. PMID25152275.
^Cavalier-Smith T, Chao EE, Lewis R (April 2018). "Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria". Protoplasma. 255 (5): 1517–1574. doi:10.1007/s00709-018-1241-1. PMC6133090. PMID29666938.
^He D, Fiz-Palacios O, Fu CJ, Fehling J, Tsai CC, Baldauf SL (February 2014). "An alternative root for the eukaryote tree of life". Current Biology. 24 (4): 465–470. doi:10.1016/j.cub.2014.01.036. PMID24508168.
^Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM (December 2008). "The archaebacterial origin of eukaryotes". Proceedings of the National Academy of Sciences of the United States of America. 105 (51): 20356–20361. Bibcode:2008PNAS..10520356C. doi:10.1073/pnas.0810647105. PMC2629343. PMID19073919.
^Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (March 2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C. CiteSeerX10.1.1.381.9514. doi:10.1126/science.1123061. PMID16513982. S2CID 1615592.
^ abHug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF (April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID27572647.
^O'Malley MA, Leger MM, Wideman JG, Ruiz-Trillo I (March 2019). "Concepts of the last eukaryotic common ancestor". Nature Ecology & Evolution. Springer Science and Business Media LLC. 3 (3): 338–344. doi:10.1038/s41559-019-0796-3. hdl:10261/201794. PMID30778187. S2CID 67790751.
^ abBrocks JJ, Logan GA, Buick R, Summons RE (August 1999). "Archean molecular fossils and the early rise of eukaryotes". Science. 285 (5430): 1033–1036. Bibcode:1999Sci...285.1033B. CiteSeerX10.1.1.516.9123. doi:10.1126/science.285.5430.1033. PMID10446042.
^ abHartman H, Fedorov A (February 2002). "The origin of the eukaryotic cell: a genomic investigation". Proceedings of the National Academy of Sciences of the United States of America. 99 (3): 1420–5. Bibcode:2002PNAS...99.1420H. doi:10.1073/pnas.032658599. PMC122206. PMID11805300.
^Knoll AH, Javaux EJ, Hewitt D, Cohen P (June 2006). "Eukaryotic organisms in Proterozoic oceans". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1470): 1023–1038. doi:10.1098/rstb.2006.1843. PMC1578724. PMID16754612.
^Retallack GJ, Krull ES, Thackray GD, Parkinson DH (2013). "Problematic urn-shaped fossils from a Paleoproterozoic (2.2 Ga) paleosol in South Africa". Precambrian Research. 235: 71–87. Bibcode:2013PreR..235...71R. doi:10.1016/j.precamres.2013.05.015.
^El Albani A, Bengtson S, Canfield DE, Bekker A, Macchiarelli R, Mazurier A, Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C, Fürsich FT, Gauthier-Lafaye F, Janvier P, Javaux E, Ossa FO, Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D, Whitehouse M, Meunier A (July 2010). "Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago". Nature. 466 (7302): 100–104. Bibcode:2010Natur.466..100A. doi:10.1038/nature09166. PMID20596019. S2CID 4331375.
^Bengtson S, Belivanova V, Rasmussen B, Whitehouse M (May 2009). "The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older". Proceedings of the National Academy of Sciences of the United States of America. 106 (19): 7729–7734. Bibcode:2009PNAS..106.7729B. doi:10.1073/pnas.0812460106. PMC2683128. PMID19416859.
^Ward P (9 February 2008). "Mass extinctions: the microbes strike back". New Scientist. pp. 40–43. Archived from the original on 8 July 2008. Retrieved 27 August 2017.
^French KL, Hallmann C, Hope JM, Schoon PL, Zumberge JA, Hoshino Y, Peters CA, George SC, Love GD, Brocks JJ, Buick R, Summons RE (May 2015). "Reappraisal of hydrocarbon biomarkers in Archean rocks". Proceedings of the National Academy of Sciences of the United States of America. 112 (19): 5915–5920. Bibcode:2015PNAS..112.5915F. doi:10.1073/pnas.1419563112. PMC4434754. PMID25918387.
^Brocks JJ, Jarrett AJ, Sirantoine E, Hallmann C, Hoshino Y, Liyanage T (August 2017). "The rise of algae in Cryogenian oceans and the emergence of animals". Nature. 548 (7669): 578–581. Bibcode:2017Natur.548..578B. doi:10.1038/nature23457. PMID28813409. S2CID 205258987.
^Gold DA, Caron A, Fournier GP, Summons RE (March 2017). "Paleoproterozoic sterol biosynthesis and the rise of oxygen". Nature. 543 (7645): 420–423. Bibcode:2017Natur.543..420G. doi:10.1038/nature21412. hdl:1721.1/128450. PMID28264195. S2CID 205254122.
^Wei JH, Yin X, Welander PV (24 June 2016). "Sterol Synthesis in Diverse Bacteria". Frontiers in Microbiology. 7: 990. doi:10.3389/fmicb.2016.00990. PMC4919349. PMID27446030.
^Hoshino Y, Gaucher EA (June 2021). "Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis". Proceedings of the National Academy of Sciences of the United States of America. 118 (25): e2101276118. Bibcode:2021PNAS..11801276H. doi:10.1073/pnas.2101276118. PMC8237579. PMID34131078.
^Isson TT, Love GD, Dupont CL, Reinhard CT, Zumberge AJ, Asael D, et al. (June 2018). "Tracking the rise of eukaryotes to ecological dominance with zinc isotopes". Geobiology. 16 (4): 341–352. doi:10.1111/gbi.12289. PMID29869832.
^Yoshikawa G, Blanc-Mathieu R, Song C, Kayama Y, Mochizuki T, Murata K, Ogata H, Takemura M (April 2019). "Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water". Journal of Virology. 93 (8). doi:10.1128/JVI.02130-18. PMC6450098. PMID30728258. Archived from the original on 30 April 2019.
"New giant virus may help scientists better understand the emergence of complex life". EurekAlert! (Press release). 30 April 2019.
^Martin W (December 2005). "Archaebacteria (Archaea) and the origin of the eukaryotic nucleus". Current Opinion in Microbiology. 8 (6): 630–637. doi:10.1016/j.mib.2005.10.004. PMID16242992.
^Takemura M (May 2001). "Poxviruses and the origin of the eukaryotic nucleus". Journal of Molecular Evolution. 52 (5): 419–425. Bibcode:2001JMolE..52..419T. doi:10.1007/s002390010171. PMID11443345. S2CID 21200827.
^Bell PJ (September 2001). "Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?". Journal of Molecular Evolution. 53 (3): 251–256. Bibcode:2001JMolE..53..251L. doi:10.1007/s002390010215. PMID11523012. S2CID 20542871.
^Wächtershäuser G (January 2003). "From pre-cells to Eukarya – a tale of two lipids". Molecular Microbiology. 47 (1): 13–22. doi:10.1046/j.1365-2958.2003.03267.x. PMID12492850. S2CID 37944519.
^Wächtershäuser G (October 2006). "From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1474): 1787–1806, discussion 1806–1808. doi:10.1098/rstb.2006.1904. PMC1664677. PMID17008219.
^Egel R (January 2012). "Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life". Life. Vol. 2, no. 1. pp. 170–212. doi:10.3390/life2010170. PMC4187143. PMID25382122.
^ abHarish A, Tunlid A, Kurland CG (August 2013). "Rooted phylogeny of the three superkingdoms". Biochimie. 95 (8): 1593–1604. doi:10.1016/j.biochi.2013.04.016. PMID23669449.
^ abHarish A, Kurland CG (July 2017). "Akaryotes and Eukaryotes are independent descendants of a universal common ancestor". Biochimie. 138: 168–183. doi:10.1016/j.biochi.2017.04.013. PMID28461155.
^ abImachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, et al. (January 2020). "Isolation of an archaeon at the prokaryote-eukaryote interface". Nature. 577 (7791): 519–525. Bibcode:2020Natur.577..519I. doi:10.1038/s41586-019-1916-6. PMC7015854. PMID31942073.
^Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P (June 2017). "Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes". PLOS Genetics. 13 (6): e1006810. doi:10.1371/journal.pgen.1006810. PMC5484517. PMID28604769.
^Harish A, Kurland CG (July 2017). "Empirical genome evolution models root the tree of life". Biochimie. 138: 137–155. doi:10.1016/j.biochi.2017.04.014. PMID28478110.
^Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, et al. (March 2018). "Asgard archaea are the closest prokaryotic relatives of eukaryotes". PLOS Genetics. 14 (3): e1007080. doi:10.1371/journal.pgen.1007080. PMC5875740. PMID29596421.
^MacLeod F, Kindler GS, Wong HL, Chen R, Burns BP (2019). "Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes". AIMS Microbiology. 5 (1): 48–61. doi:10.3934/microbiol.2019.1.48. PMC6646929. PMID31384702.
^Zimmer C (15 January 2020). "This Strange Microbe May Mark One of Life's Great Leaps – A organism living in ocean muck offers clues to the origins of the complex cells of all animals and plants". The New York Times. Archived from the original on 16 January 2020. Retrieved 18 January 2020.
^Jékely G (2007). "Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios". Eukaryotic Membranes and Cytoskeleton. Advances in Experimental Medicine and Biology. Vol. 607. New York, N.Y. : Springer Science+Business Media; Austin, Tex. : Landes Bioscience. pp. 38–51. doi:10.1007/978-0-387-74021-8_3. ISBN 978-0-387-74020-1. PMID17977457.
^Cavalier-Smith T (March 2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 2): 297–354. doi:10.1099/00207713-52-2-297. PMID11931142. Archived from the original on 29 July 2017. Retrieved 10 June 2008.
^ abMartin W, Müller M (March 1998). "The hydrogen hypothesis for the first eukaryote". Nature. 392 (6671): 37–41. Bibcode:1998Natur.392...37M. doi:10.1038/32096. PMID9510246. S2CID 338885.
^Pisani D, Cotton JA, McInerney JO (August 2007). "Supertrees disentangle the chimerical origin of eukaryotic genomes". Molecular Biology and Evolution. 24 (8): 1752–1760. doi:10.1093/molbev/msm095. PMID17504772.
^Brueckner J, Martin WF (April 2020). "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes". Genome Biology and Evolution. 12 (4): 282–292. doi:10.1093/gbe/evaa047. PMC7151554. PMID32142116.
^ abLatorre A, Durban A, Moya A, Pereto J (2011). "The role of symbiosis in eukaryotic evolution". In Gargaud M, López-Garcìa P, Martin H (eds.). Origins and Evolution of Life: An astrobiological perspective. Cambridge: Cambridge University Press. pp. 326–339. ISBN 978-0-521-76131-4. Archived from the original on 24 March 2019. Retrieved 27 August 2017.
^Ayala J (April 1994). "Transport and internal organization of membranes: vesicles, membrane networks and GTP-binding proteins". Journal of Cell Science. 107 (Pt 4): 753–763. doi:10.1242/jcs.107.4.753. PMID8056835. Archived from the original on 29 April 2012. Retrieved 27 March 2013.
^Martin WF. "The Origin of Mitochondria". Scitable. Nature education. Archived from the original on 16 June 2013. Retrieved 27 March 2013. That is, it entails a corollary assumption (an add–on to the theory that brings it into agreement with available observations) that all descendants of the initial host lineage, except the one that acquired mitochondria, went extinct.
^Dacks JB, Field MC (August 2018). "Evolutionary origins and specialisation of membrane transport". Current Opinion in Cell Biology. 53: 70–76. doi:10.1016/j.ceb.2018.06.001. PMC6141808. PMID29929066.
^Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ (May 2018). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. Bibcode:2018Natur.557..101M. doi:10.1038/s41586-018-0059-5. PMID29695865. S2CID 13740626. Archived from the original on 21 April 2019. Retrieved 21 April 2019.
Shawna Williams (25 April 2018). "Mitochondria's Bacterial Origins Upended". The Scientist.
^Baum DA, Baum B (October 2014). "An inside-out origin for the eukaryotic cell". BMC Biology. 12: 76. doi:10.1186/s12915-014-0076-2. PMC4210606. PMID25350791.
Terry Devitt (12 December 2014). "New theory suggests alternate path led to rise of the eukaryotic cell". University of Wisconsin-Madison (Press release). Archived from the original on 21 April 2019.
^Brouwers L (12 April 2013). "How genetic plunder transformed a microbe into a pink, salt-loving scavenger". Scientific American. 109 (50): 20537–20542. Archived from the original on 10 October 2018. Retrieved 21 April 2019.
^Wilcox C (9 April 2019). "Rethinking the ancestry of the eukaryotes". Quanta Magazine. Archived from the original on 9 May 2019. Retrieved 8 May 2019.
^McCutcheon JP (October 2021). "The Genomics and Cell Biology of Host-Beneficial Intracellular Infections". Annual Review of Cell and Developmental Biology. 37 (1): 115–142. doi:10.1146/annurev-cellbio-120219-024122. PMID34242059. S2CID 235786110.
^Saygin D, Tabib T, Bittar HE, Valenzi E, Sembrat J, Chan SY, et al. (8 June 2022). "Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension". Pulmonary Circulation. 10 (1). doi:10.1146/knowable-060822-2. PMID32166015.
^Pittis AA, Gabaldón T (March 2016). "Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry". Nature. 531 (7592): 101–104. Bibcode:2016Natur.531..101P. doi:10.1038/nature16941. PMC4780264. PMID26840490.
^Burton ZF (1 August 2017). Evolution since coding: Cradles, halos, barrels, and wings. Academic Press. ISBN 978-0-12-813034-6. Archived from the original on 24 March 2019. Retrieved 27 November 2018.
^Martin WF, Roettger M, Ku C, Garg SG, Nelson-Sathi S, Landan G (February 2017). "Late mitochondrial origin is an artifact". Genome Biology and Evolution. 9 (2): 373–379. doi:10.1093/gbe/evx027. PMC5516564. PMID28199635.