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Eukaryote
Eukaryotes (/juːˈkærioʊts, -əts/) are organisms whose cells have a nucleus.[1][2][3] All animals, plants, fungi,
and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukaryota

Eukarya, which is one of the three domains of life. Bacteria and Archaea (both prokaryotes) make up the other Temporal range: Orosirian – Present
two domains.[4][5]

The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the Asgard
archaea.[6][7] This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes
incorporated among archaea.[8][9] Eukaryotes represent a small minority of the number of organisms,[10] but,
due to their generally much larger size, their collective global biomass is estimated to be about equal to that of Red mason bee
prokaryotes.[10] Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the Proterozoic eon, likely
as flagellated phagotrophs.[11][12] Their name comes from the Greek εὖ (eu, "well" or "good") and κάρυον
(karyon, "nut" or "kernel").[13]

Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and Golgi apparatus.
Chloroplasts can be found in plants and algae. Prokaryotic cells may contain primitive organelles.[14] Eukaryotes
Boletus edulis
may be either unicellular or multicellular, and include many cell types forming different kinds of tissue. In
comparison, prokaryotes are typically unicellular. Animals, plants, and fungi are the most familiar eukaryotes.
Other eukaryotes are sometimes called protists.[15]

Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In
mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two
Eudorina elegans
rounds of cell division to produce four haploid daughter cells that act as sex cells or gametes. Each gamete has
just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting
from genetic recombination during meiosis.[16]

Contents Chimpanzee

Cell features
Internal membranes
Mitochondria
Plastids
Cytoskeletal structures Ranunculus
Cell wall asiaticus

Differences among eukaryotic cells

Animal cell
Plant cell
Fungal cell
Other eukaryotic cells Isotricha intestinalis
Reproduction
Classification Scientific classification
Phylogeny Domain: Eukaryota

Evolutionary history (Chatton, 1925) Whittaker &

Origin of eukaryotes Margulis, 1978
See also Supergroups and kingdoms
Notes
References Diphoda
External links Discoba
Hemimastigophora
Cell features Diaphoretickes

Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times Archaeplastida
greater than the prokaryotic cell.[17] They have a variety of internal membrane-bound structures, called
Plantae
organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play
an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear Hacrobia
bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.
SAR
Opimoda
Internal membranes
Loukozoa
Podiata

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Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane CRuMs
system.[18] 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 Amorphea
and then pinches off to form a vesicle.[19] It is probable that most other membrane-bound organelles are Obazoa
ultimately derived from such vesicles. Alternatively some products produced by the cell can leave in a vesicle
through exocytosis. Animalia
The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow Fungi
material to move in and out.[20] 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. Eukaryotic organisms that cannot
Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum.[21] In most be classified under the kingdoms
eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles Plantae, Animalia or Fungi are
(cisternae), the Golgi apparatus.[22] sometimes grouped in the
paraphyly Protista.
Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break
down most biomolecules in the cytoplasm.[23] 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.

Mitochondria Cytology Video, Cell Features

Mitochondria are organelles found in all but one

eukaryote,[note 1] and are commonly referred to as "the
The endomembrane system and its powerhouse of the cell".[25] Mitochondria provide energy to
components the eukaryote cell by oxidising sugars or fats and releasing
energy as ATP.[26] They have two surrounding membranes,
each a phospholipid bi-layer; the inner of which is folded into
invaginations called cristae where aerobic respiration takes place.

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 Simplified structure of a mitochondrion
which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA
than to eukaryote RNA.[27] They are now generally held to have developed from endosymbiotic
prokaryotes, probably Alphaproteobacteria.

Some eukaryotes, such as the metamonads such as Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all
have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes, and thus have lost their mitochondria
secondarily.[24] They obtain energy by enzymatic action on nutrients absorbed from the environment. The metamonad Monocercomonoides has also
acquired, by lateral gene transfer, a cytosolic sulfur mobilisation system which provides the clusters of iron and sulfur required for protein synthesis.
The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily.[24][28]

Plastids

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.[29] 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.[30]

Cytoskeletal structures

Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Flagella and cilia are sometimes
referred to as undulipodia,[31] 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.

Microfilamental structures composed of actin and actin binding proteins, e.g., α-actinin, fimbrin, filamin are present in submembranous 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 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.[32]

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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.

Cell wall

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- Longitudinal section through the
expansion when water enters the cell.[33] flagellum of Chlamydomonas
reinhardtii
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.[34]

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.

Animal cell

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 cell

Plant cells have a number of features that distinguish them from the cells of the other eukaryotic
organisms. These include:

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[35] Structure of a typical animal cell
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, pores in the cell wall that link adjacent cells and allow plant cells to
communicate with adjacent cells.[36] Animals have a different but functionally analogous system of
gap junctions between adjacent cells.
Plastids, especially chloroplasts, organelles that contain chlorophyll, the pigment that gives plants
their green color and allows them to perform photosynthesis
Bryophytes and seedless vascular plants only have flagellae and centrioles in the sperm cells.[37]
Sperm of cycads and Ginkgo are large, complex cells that swim with hundreds to thousands of
flagellae.[38]
Conifers (Pinophyta) and flowering plants (Angiospermae) lack the flagellae and centrioles that are
present in animal cells.
Structure of a typical plant cell

Fungal cell

The cells of fungi are similar to animal cells, with the following exceptions:[39]

A cell wall that contains chitin

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.
Fungal Hyphae cells: 1 – hyphal wall, 2 – septum, 3
– mitochondrion, 4 – vacuole, 5 – ergosterol crystal,
Other eukaryotic cells 6 – ribosome, 7 – nucleus, 8 – endoplasmic
reticulum, 9 – lipid body, 10 – plasma membrane,
Some groups of eukaryotes have unique organelles, such as the cyanelles (unusual plastids) of the 11 – spitzenkörper, 12 – Golgi apparatus
glaucophytes,[40] the haptonema of the haptophytes, or the ejectosomes of the cryptomonads. Other
structures, such as pseudopodia, are found in various eukaryote groups in different forms, such as the
lobose amoebozoans or the reticulose foraminiferans.[41] Structures known as cortical alveoli are vesicles present under the cell membrane of many
protists such as dinoflagellates, ciliates and apicomplexan parasites.[42]

Reproduction

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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.[43] This diagram illustrates the twofold cost of sex. If
each individual were to contribute the same number
The evolution of sexual reproduction may be a primordial and fundamental characteristic of of offspring (two), (a) the sexual population remains
eukaryotes. Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was the same size each generation, where the (b)
present in the common ancestor of all eukaryotes.[44] A core set of genes that function in meiosis is asexual population doubles in size each
present in both Trichomonas vaginalis and Giardia intestinalis, two organisms previously thought to generation.

be asexual.[45][46] 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.[45][46] Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus Leishmania, have
been shown to have a sexual cycle.[47] 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.[48]

Classification
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.[49] 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,[50] and this group was expanded until it
encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel
in 1866.[51][52] The eukaryotes thus came to be composed of four kingdoms:

Kingdom Protista
Kingdom Plantae
Kingdom Fungi
Kingdom Animalia

The protists were understood to be "primitive forms", and thus an evolutionary grade, united by their
primitive unicellular nature.[52] 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 Phylogenetic and symbiogenetic tree of living
being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain.[53] organisms, showing a view of the origins of
At the same time, work on the protist tree intensified, and is still actively going on today. Several eukaryotes and prokaryotes
alternative classifications have been forwarded, though there is no consensus in the field.

Eukaryotes are a clade usually assessed to be sister to Heimdallarchaeota in the Asgard grouping in the
Archaea.[54][55][56] In one proposed system, the basal groupings are the Opimoda, Diphoda, the Discoba, and the
Loukozoa. The Eukaryote root is usually assessed to be near or even in Discoba.

A classification produced in 2005 for the International Society of Protistologists,[57] which reflected the consensus
of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. However, in the same year
(2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the
One hypothesis of eukaryotic
Chromalveolata,[58] and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.[59] relationships – the Opisthokonta
A revised classification in 2012[60] recognizes five supergroups. group includes both animals
(Metazoa) and fungi, plants
Archaeplastida
(Plantae) are placed in
Land plants, green algae, red algae, and glaucophytes
(or Primoplantae)
Archaeplastida.
Stramenopiles (brown algae, diatoms, etc.),

SAR supergroup Alveolata, and Rhizaria (Foraminifera, Radiolaria,

and various other amoeboid protozoa)

Excavata Various flagellate protozoa
Amoebozoa Most lobose amoeboids and slime molds
Opisthokonta Animals, fungi, choanoflagellates, etc.

There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the
major groups[61]  – in particular, Haptophyta, Cryptophyta, Centrohelida, Telonemia, Picozoa,[62]
Apusomonadida, Ancyromonadida, Breviatea, and the genus Collodictyon.[63] Overall, it seems that,
although progress has been made, there are still very significant uncertainties in the evolutionary
A pie chart of described eukaryote species (except
history and classification of eukaryotes. As Roger & Simpson said in 2009 "with the current pace of for Excavata), together with a tree showing possible
change in our understanding of the eukaryote tree of life, we should proceed with caution."[64] Newly relationships between the groups
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.[65]
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Phylogeny

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.[66][67]

It has been estimated that there may be 75 distinct lineages of eukaryotes.[68] 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.[68] 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.[68] 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.[61][69][70][71][72][73][24][74][65] 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.[75] The proposed phylogeny below includes only one
group of excavates (Discoba), and incorporates the recent proposal that picozoans are close relatives of rhodophytes.[76]
Eukaryotes  
     
  Hemimastigophora
Diaphoretickes
   
  Cryptista

  Red algae (Rhodophyta)

 
 
 

 
  Picozoa
 
 
Archaeplastida
 (+ Gloeomargarita lithophora) 
  Glaucophyta
 

 
 

  Green plants (Viridiplantae)

 

   
 

  Haptista
 
Diphoda
 
TSAR  
   
Telonemia

  Stramenopiles
 

  Halvaria
 

SAR  
    Alveolata

  Rhizaria
 

 
  Ancoracysta

  Discoba (Excavata)
 

Amorphea  
 

Amoebozoa

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  Apusomonadida
 

  Holomycota (inc. fungi)

Obazoa  
 

Opisthokonta
 

  Holozoa (inc. animals)

 

In some analyses, the Hacrobia group (Haptophyta + Cryptophyta) is placed next to Archaeplastida,[77] but in others it is nested inside the
Archaeplastida.[78] However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group.[79] The
former could be a sister group to the SAR group, the latter cluster with the Archaeplastida (plants in the broad sense).[80]

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.[78][81][82] A 2012 study
produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.[62]

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.[83][84][85][86][87][72][88] 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.[89] Archaeplastida acquired
chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, Gloeomargarita lithophora.[90][91][89]

 
  Glaucophyta

Archaeplastida  
 (+ Gloeomargarita lithophora)    Rhodophyta
 
 
 
    Viridiplantae
 

 
  Haptista
Hacrobia
Diaphoretickes  
   
  Cryptista
Diphoda
   
  Stramenopiles
Halvaria
 
SAR  
    Alveolata

 
  Rhizaria

Eukaryotes
   
  Hemimastigophora

 
  Discoba

 
  Loukozoa
Podiata
  CRuMs
  Diphyllatea, Rigifilida, Mantamonas
Amorphea
   
  Amoebozoa
Opimoda Obazoa
     
  Breviata
   
   
Apusomonadida

 
  Opisthokonta

Cavalier-Smith's tree

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Thomas Cavalier-Smith 2010,[92] 2013,[93] 2014,[94]
and 2017[84] 2018[95]
places the eukaryotic tree's root between Excavata (with ventral feeding
groove supported by a microtubular root) and the grooveless Euglenozoa, and monophyletic Chromista, correlated to a single endosymbiotic event of
capturing a red-algae. He et al.[96] specifically supports rooting the eukaryotic tree between a monophyletic Discoba (Discicristata + Jakobida) and an
Amorphea-Diaphoretickes clade.

 
  Euglenozoa
 
   
  Percolozoa
 
   
  Tsukubamonas globosa
Eolouka
 
 
  Jakobea
Neokaryota
   
  Glaucophytes

Archaeplastida  
    Rhodophytes
 
 
 
Corticata   Viridiplantae
 

 
  Hacrobia
Chromista
 
 
  SAR

Eukaryotes  
    Malawimonas
 
   
  Metamonada
Podiata
   
  Ancyromonadida
 
   
  Mantamonas plastica
 
 
 
Scotokaryota   Diphyllatea
Opimoda
Amorphea  
    Amoebozoa

 
  Breviatea

Obazoa  
    Apusomonadida
 
 
 
  Opisthokonta

Evolutionary history

Origin of eukaryotes

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,[4] and
was most likely a biological population.[100]

Eukaryotes have a number of features that differentiate them from prokaryotes, including an
endomembrane system, and unique biochemical pathways such as sterane synthesis.[101] 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 The three-domains tree and the Eocyte
universal among eukaryotes. They include proteins that make up the cytoskeleton, the complex hypothesis[97]
transcription machinery, membrane-sorting systems, the nuclear pore, as well as some enzymes in the
biochemical pathways.[102]

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Fossils

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.[103] The Geosiphon-
like fossil fungus Diskagma has been found in paleosols 2.2 billion years old.[104]

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.[105] 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.[106] Phylogenetic tree showing a possible relationship
between the eukaryotes and other forms of life;[98]
The presence of eukaryotic-specific biomarkers (steranes) in Australian shales previously indicated that
eukaryotes are colored red, archaea green and
eukaryotes were present in these rocks dated at 2.7 billion years old,[101][107] which was even 300 bacteria blue
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.[108] Currently, putatively the oldest biomarker records are only ~800 million years
old.[109] In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as
2.3 billion years ago,[110] 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.[111][112]

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).[113] Eocyte tree.[99]

In April 2019, biologists reported that the very large medusavirus, or a relative, may have been
responsible, at least in part, for the evolutionary emergence of complex eukaryotic cells from simpler prokaryotic cells.[114]

Relationship to Archaea

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 resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a bacterium, and the nucleus from an
archaeon,[115] from a virus,[116][117] or from a pre-cell.[118][119]
Eukaryotes developed from Archaea, and acquired their bacterial characteristics through the endosymbiosis of a proto-mitochondrion of bacterial
origin.[120]
Eukaryotes and Archaea developed separately from a modified bacterium.

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.[102]
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.[122] Diagram of the origin of life with the Eukaryotes
appearing early, not derived from Prokaryotes, as
Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea, proposed by Richard Egel in 2012. This view
and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below, with a implies that the UCA was relatively large and
modification of hypothesis 2 making the 4th column: The eocyte hypothesis, in which the Archaea are complex.[121]
paraphyletic. (The table and the names for the hypotheses are based on Harish & Kurland, 2017.[123])

Alternative hypotheses for the base of the tree of life

1 – Two empires 2 – Three domains 3 – Gupta 4 – Eocyte

 
   Eukaryota
       
   Archaea    Eukaryota    Eukaryota  
       Archaea   
           Archaea-Crenarchaeota
     
   Bacteria    Archaea    Bacteria
 UCA   UCA   UCA   
       UCA     Archaea-Euryarchaeota
       
   Eukaryota    Bacteria    Archaea
 
   Bacteria

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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.[99][92][93][94][84] A cladogram supporting the eocyte hypothesis, positioning eukaryotes within
Archaea, based on phylogenomic analyses of the Asgard archaea, is:[54][55][56][9]

 TACK 
   
   "Korarchaeota"
 
   
   Thermoproteota
   
     
   "Aigarchaeota"

 
   "Geoarchaeota"

 
   Nitrososphaerota
 
 
 
   "Bathyarchaeota"
 Archaea 
 
 
   "Lokiarchaeota"

 
   "Odinarchaeota"

 
 "Thorarchaeota"
 Asgard   
 
 
   "Heimdallarchaeota"

 
 
   Eukaryota

   (+Alphaproteobacteria)

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.[124]

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).[125] 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.[126][123] 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.[122] On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples.[127]
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.

Details of the relation of Asgard archaea members and eukaryotes are still under consideration,[128] although, in January 2020, scientists reported that
Candidatus Prometheoarchaeum syntrophicum, a type of cultured Asgard archaea, may be a possible link between simple prokaryotic and complex
eukaryotic microorganisms about two billion years ago.[129][124]

Endomembrane system and mitochondria

The origins of the endomembrane system and mitochondria are also unclear.[130] 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.[131] 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).[132]

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.[133] 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.[134]

Hypotheses

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.

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Autogenous models

Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed

first, and later acquired mitochondria.[135] 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.[136]

Mitochondria are proposed to come from the endosymbiosis of an aerobic

proteobacterium, and it is assumed that all the eukaryotic lineages that did not acquire
mitochondria became extinct.[137] Chloroplasts came about from another endosymbiotic
event involving cyanobacteria. Since all known eukaryotes have mitochondria, but not all
have chloroplasts, the serial endosymbiotic theory proposes that mitochondria came
first.

Chimeric models

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.[138][139]
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 hypothesis

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 An autogenous model for the origin of eukaryotes.
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.[140]

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.[141]

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.[142][143][144]

The serial endosymbiotic hypothesis

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.[135]

The hydrogen hypothesis

In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic 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.

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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.[132]

The syntrophy hypothesis

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
prevention of abnormal protein biosynthesis due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and losing
methanogenesis.

6+ serial endosymbiosis scenario

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.[145][146] The findings have been
rebuked as an artifact.[147]

See also
Eukaryote hybrid genome
Evolution of sexual reproduction
List of sequenced eukaryotic genomes
Parakaryon myojinensis
Prokaryote
Nitrososphaerota
Vault (organelle)

Notes
1. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria.[24]

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 This article incorporates public domain material from Science Primer (https://web.archive.org/web/20091208004309/https://www.ncbi.nlm.nih.g
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External links
"Eukaryotes" (http://www.tolweb.org/Eukaryotes/3) (Tree of Life Web Project)
"Eukaryote" (https://www.eol.org/pages/2908256) at the Encyclopedia of Life
Attraction and sex among our microbial Last Eukaryotic Common Ancestors (https://www.theatlantic.com/science/archive/2020/11/how-do-single-ce
lled-organisms-have-sex/617072/), The Atlantic, November 11, 2020

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