Temporal range: Paleoproterozoic - recent 1.6–2.1 billion years ago (possibly as early as 2.7 billion years ago) – Present
|Eukaryotes and some examples of their diversity|
(Chatton, 1925) Whittaker & Margulis,1978
Prokaryote). There are two types of division processes. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.
The domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things; even in a human body there are 10 times more microbes than human cells. However, due to their much larger size, their collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1.6–2.1 billion years ago.
Cell features 1
- Internal membrane 1.1
- Mitochondria and plastids 1.2
- Cytoskeletal structures 1.3
- Cell wall 1.4
Differences among eukaryotic cells 2
- Animal cell 2.1
- Plant cell 2.2
- Fungal cell 2.3
- Other eukaryotic cells 2.4
- Sexual reproduction 3.1
- Chromalveolata + Rhizaria 4.1.1
- Bikonts and unikonts 4.1.2
- Expanded Chromalveolata 4.1.3
- Alternative views 4.1.4
- Phylogeny 4.1
Origin of eukaryotes 5
- Fossils 5.1
- Relationship to Archaea 5.2
- Endomembrane system and mitochondria 5.3
Hypotheses for the origin of eukaryotes 5.4
- Autogenous models 5.4.1
- Chimeric models 5.4.2
- See also 6
- References 7
- External links 8
Eukaryotic cells are typically much larger than those of DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.
Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles or 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.
The nucleus is surrounded by a double membrane (commonly referred to as a nuclear envelope), with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form what is called the endoplasmic reticulum or ER, which is involved in protein transport and maturation. It includes the rough ER 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 ER. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles, called Golgi bodies or dictyosomes.
Vesicles may be specialized for various purposes. For instance, lysosomes contain enzymes that break down the contents of food vacuoles, and peroxisomes are used to break down peroxide, which is toxic otherwise. Many protozoa 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 primarily maintains its osmotic pressure.
Mitochondria and plastids
hydrogenosomes and mitosomes; and thus probably lost the mitochondria secondarily.
Plants and various groups of glucose) through photosynthesis. Others are involved in storing food. Although plastids likely 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.
Endosymbiotic origins have also been proposed for the nucleus, for which see below, and for eukaryotic flagella, supposed to have developed from spirochaetes. This is not generally accepted, both from a lack of cytological evidence and difficulty in reconciling this with cellular reproduction.
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 basal body, also called a kinetosome or 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.
Microfilamental structures composed of actin and actin binding proteins, e.g., α-actinin, fimbrin, filamin are present in submembraneous cortical layers and bundles, as well. Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the network.
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 of one or two, called kinetids, 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 may also be associated in the formation of a 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 haptonema.
The cells of plants, 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.
The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.
Differences among eukaryotic cells
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.
An animal cell is a form of eukaryotic cell that makes up many tissues in animals. Animal cells are distinct from other eukaryotes, most notably plant cells, as they lack cell walls and chloroplasts. They also have smaller vacuoles. Due to the lack of a cell wall, animal cells can adopt a variety of shapes. A phagocytic cell can even engulf other structures.
Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:
- A large central vacuole (enclosed by a membrane, the tonoplast), which maintains the cell's turgor and controls movement of molecules between the cytosol and sap
- A primary cell wall containing cellulose, hemicellulose and pectin, deposited by the protoplast on the outside of the cell membrane; this contrasts with the cell walls of fungi, which contain chitin, and the cell envelopes of prokaryotes, in which peptidoglycans are the main structural molecules
- The plasmodesmata, linking pores in the cell wall that allow each plant cell to communicate with other adjacent cells; this is different from the functionally analogous system of gap junctions between animal cells.
- Plastids, especially chloroplasts that contain chlorophyll, the pigment that gives plants their green color and allows them to perform photosynthesis
- Bryophytes and seedless vascular plants lack flagellae and centrioles except in the sperm cells. Sperm of cycads and Gingko are large, complex cells that swim with hundreds to thousands of flagellae.
- Conifers (Pinophyta) and flowering plants (Angiospermae) lack the flagellae and centrioles that are present in animal cells.
Fungal cells are most similar to animal cells, with the following exceptions:
- A cell wall that contains chitin
- Less definition between cells; the coenocytic.
- Only the most primitive fungi, chytrids, have flagella.
Other eukaryotic cells
Eukaryotes are a very diverse group, and their cell structures are equally diverse. Many have cell walls; many do not. Many have chloroplasts, derived from primary, secondary, or even tertiary endosymbiosis; and many do not. Some groups have unique structures, such as the cyanelles of the glaucophytes, the haptonema of the haptophytes, or the ejectisomes of the cryptomonads. Other structures, such as pseudopods, are found in various eukaryote groups in different forms, such as the lobose amoebozoans or the reticulose foraminiferans.
Nuclear division is often coordinated with cell division. This generally takes place by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. In most eukaryotes, there is also a process of sexual reproduction, typically involving an alternation between haploid generations, wherein only one copy of each chromosome is present, and diploid generations, wherein two are present, occurring through nuclear fusion (syngamy) and meiosis. There is considerable variation in this pattern, however.
Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times. In some multicellular organisms, cells specialized for metabolism will have enlarged surface areas, such as intestinal vili.
Sexual reproduction is widespread among present day eukaryotes, and evidence suggests that it is 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
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Thus, the origin of eukaryotes by endosymbiotic processes has been broadly recognized and accepted so far. Mitochondria and plastids have been known to originate from a bacterial ancestor during parallel adaptation to anaerobiosis. However, there still remains a greater need in assessing the question of how much eukaryotic complexity is being originated via an implementation of these symbiogenetic theories.
The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this theory, eukaryogenesis (i.e. origin of eukaryotic cells) occurred based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a delta-proteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alpha-proteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a delta-proteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus while the delta-proteobacterium contributed towards the cytoplasmic features. This theory incorporates two selective forces that were needed to be considered during the time of nucleus evolution – (a) presence of metabolic partitioning in order to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and (b) prevention of abnormal biosynthesis of proteins that occur due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and the loss of methanogenesis.
In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alpha-proteobacterium (the symbiont) gave rise to the eukaryotes. The host utilized hydrogen (H2) and carbon dioxide (CO
2) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and CO
2 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 (EGT) acted as a catalyst for the host to acquire the symbionts' lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.
According to serial endosymbiotic theory, a union between a motile genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alpha-proteobacteria 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 – Desulphobacter and Spirochaeta. However, such an association based on motile symbiosis have never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments.
Based on the process of mutualistic symbiosis, the hypotheses can be categorized as – the serial endosymbiotic theory (SET), the hydrogen hypothesis (mostly a process of symbiosis where hydrogen transfer takes place among different species), and the syntrophy hypothesis.
Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. 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.
Some models propose that the origins of double layered chloroplasts, in the proto-eukaryotic cell is due to the compartmentalization of DNA vesicles that were formed from the secondary invaginations or more detailed infoldings of cellular membrane.
Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria. According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. As the invaginations differentiated in function, some became separate compartments—giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes. Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it's assumed that all the eukaryotic lineages that did not acquire mitochondria went extinct. Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Since all eukaryotes have mitochondria, but not all have chloroplasts, mitochondria are thought to have come first. This is the serial endosymbiosis theory.
An autogenous model for the origin of eukaryotes.
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.
Hypotheses for the origin of eukaryotes
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 α-proteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont.
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).
Endomembrane system and mitochondria
The chronocyte hypothesis for the origin of the eukaryotic cell 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.
- Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a eubacterium, and the nucleus from an archaeon, from a virus, or from a pre-cell.
- Eukaryotes developed from Archaea, and acquired their eubacterial characteristics from the proto-mitochondrion.
- Eukaryotes and Archaea developed separately from a modified eubacterium.
Eukaryotes are more closely related to Archaea than Bacteria, at least in terms of nuclear DNA and genetic machinery, and one controversial idea is to place them with Archaea in the clade Neomura. However, in other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:
Relationship to Archaea
Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 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 alga, 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 origin of the eukaryotic cell is considered a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. 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.
Origin of eukaryotes
Rhizaria are only moderately supported (65.5% of the studies, i.e., 19 of 29), statistical support for them is inconsistent in multigene genealogies with larger taxon sampling and the group is ambiguously supported in Goloboff et al.
Red algae as basal is also supported by molecular evidence. Cyanidioschyzon, a red alga, is considered basal (sister group to the rest of eukaryotes) by Nagashima et al. and Seckbach. It has the most primitive chloroplast, only 1 mitochondrion, no vacuoles, no trienoic acids, and the smallest eukaryotic genome at 8 Mbp.
There are also the cladistic analyses of Diana Lipscomb based on classical data  which have red algae as basal and Archeoplastida as paraphyletic. In the survey by Parfrey et al. it is recovered in only 42.6% of the molecular analyses that include it, that is, 26 out of 61. It is not recovered in Goloboff et al.'s combined analysis, and is mostly weakly supported in other molecular analyses ). Laura Parfrey et al. point out that Archeoplastida support comes primarily from phylogenomic analyses and these may be picking up misleading endosymbiotic gene transfer signal of genes independently transferred from the plastid to the host nucleus in the 3 archeoplastid clades. And Stiller and Harrell  emphasize that the group can be explained by "short-branch exclusion" and "subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryotic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious 'long-branch attraction' is encountered."
There are also smaller groups of eukaryotes – including the genus Collodictyon, the telonemids and biliphytes – whose position is uncertain or seems to fall outside the major groups. 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."
A paper published in 2009, which re-examined the data used in some of the analyses presented above as well as performing new ones, strongly suggested that the Archaeplastida are polyphyletic. The phylogeny finally proposed in the paper is shown below.
More commonly, the expanded Chromalveolata is shown as more closely related to the Archaeplastida, producing a tree of the form shown below.
Other analyses place the SAR supergroup within an expanded Chromalveolata, although they differ on the placement of the resulting five groups. Rogozin et al. in 2009 produced the tree shown below, where the primary division is between the Archaeplastida and all other eukaryotes.
A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.
The division of the eukaryotes into two primary clades, unikonts and bikonts, derived from an ancestral uniflagellar organism and an ancestral biflagellar organism, respectively, had been suggested earlier.
In another analysis, the Hacrobia are shown nested inside the Archaeplastida, which together form a clade with most of the Excavata, before joining the SAR clade of Stramenopiles, Alveolata and Rhizaria. Together all of these groups make up the bikonts, the Amoebozoa and Opisthokonta forming the unikonts.
Bikonts and unikonts
Some analyses disassemble the Chromalveolata + Rhizaria, showing close relationships with the Archaeplastida. For example, in 2007, Burki et al. produced a tree of the form shown below.
Chromalveolata + Rhizaria
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, suggesting 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.
It has been estimated that there may be 75 distinct lineages of eukaryotes. Most of these lineages are protists.
As of 2011, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizara is not one of the main eukaryote groups; also that the Amoebozoa and Opisthokonta are each monophyletic and form a clade, often called the unikonts. Beyond this, there does not appear to be a consensus.
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.
However, in the same year (2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata, and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.
|Excavata||Various flagellate protozoa|
|Amoebozoa||Most lobose amoeboids and slime moulds|
|Opisthokonta||Animals, fungi, choanoflagellates, etc.|
|Rhizaria||Foraminifera, Radiolaria, and various other amoeboid protozoa|
|Chromalveolata||Stramenopiles (or Heterokonta), Haptophyta, Cryptophyta (or cryptomonads), and Alveolata|
|Archaeplastida (or Primoplantae)||Land plants, green algae, red algae, and glaucophytes|
A classification produced in 2005 for the International Society of Protistologists, which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. Although the published classification deliberately did not use formal taxonomic ranks, other sources have treated each of the six as a separate Kingdom.
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 got going 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.
In 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:
Extant protists usually reproduce asexually under favorable conditions, but tend to reproduce sexually under stressful conditions, such as nutritional limitation and heat shock. An important factor in the induction of sex in some protists appears to be oxidative stress and the production of reactive oxygen species leading to DNA damage.
 Also, evidence now indicates that amoeba, that were previously regarded as asexual, are anciently sexual and that the majority of present day asexual groups likely arose recently and independently. Other studies on eukaryotic species once thought to be asexual have revealed evidence for a sexual cycle. For instance, parasitic protozoa of the genus Leishmania have recently been shown to have a sexual cycle. 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.