View source for Eukaryote

{{Short description|Domain of life having cells with nuclei}}
{{Redirect|Eukaryotic cell|the journal|Eukaryotic Cell (journal)}}
{{pp-move-indef|small=yes}}
{{Use dmy dates|date=October 2020}}
{{Use American English|date=March 2017}}
{{Automatic taxobox
| name=Eukaryota
| fossil_range=[[Orosirian]] – [[Holocene|Present]] {{long fossil range|1850|0 |earliest=2300}}
| image={{Multiple image
| perrow            = 2/2/2
| total_width       = 270
| image1            = Osmia rufa couple (aka).jpg
| caption1          = [[Osmia bicornis|Red mason bee]]
| image2            = Boletus edulis (Tillegem).jpg
| caption2          = ''[[Boletus edulis]]''
| image3            = Eudorina elegans EPA.jpg
| caption3          = ''[[Eudorina elegans]]''
| image4            = Lightmatter chimp.jpg
| caption4          = [[Chimpanzee]]
| image5            = Ranunculus asiaticus4LEST.jpg
| caption5          = ''[[Ranunculus asiaticus]]''
| image6            = Isotricha intestinalis.jpg
| caption6          = ''[[Isotricha intestinalis]]''
| border            = infobox
}}
| taxon=Eukaryota
| authority=([[Édouard Chatton|Chatton]], 1925) [[Robert Whittaker (ecologist)|Whittaker]] & [[Lynn Margulis|Margulis]], 1978
| subdivision_ranks=[[Supergroup (biology)|Supergroups]] and [[Kingdom (biology)|kingdoms]]<ref name="RedAlgalDerivedPlastids"/><ref name="OrphanProtistanLineages"/><ref name="Provora"/>
| subdivision =
*[[Diphoda]]
**?[[Metamonada]]
**[[Discoba]]
**[[Diaphoretickes]]
***[[Hemimastigophora]]
***[[Provora]]
***[[Archaeplastida]]
***[[Cryptista]]
***[[Haptista]]
***[[TSAR]]
****[[Telonemia]]
****[[Harosa|SAR]]
*****[[Rhizaria]]
*****[[Halvaria]]
******[[Stramenopiles]]
******[[Alveolata]]
*[[Opimoda]]
**?[[Ancyromonadida]]
**[[Malawimonadida]]
**[[Podiata]]
***[[CRuMs]]
***[[Amorphea]]
****[[Amoebozoa]]
****[[Obazoa]]
*****[[Breviatea]]
*****[[Apusomonadida]]
*****[[Opisthokonta]]
******[[Holozoa]]
*******[[Ichthyosporea]]
*******[[Pluriformea]]
*******[[Filasterea]]
*******[[Choanoflagellatea]]
*******[[Animalia]]
******[[Holomycota]]
*******[[Nucleariae]]
*******[[Fungi]]
----
Eukaryotic organisms that cannot be classified under the kingdoms Plantae, Animalia or Fungi are sometimes grouped in the [[paraphyletic]] '''[[Protista]]'''.
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}}

'''Eukaryotes''' ({{IPAc-en|j|uː|ˈ|k|ær|i|oʊ|t|s|,_|-|ə|t|s}}) are [[organism]]s whose [[Cell (biology)|cells]] have a [[cell nucleus|nucleus]].<ref name="MW1">{{cite web |title=Definition of EUKARYOTE |url=https://www.merriam-webster.com/dictionary/eukaryote |website=www.merriam-webster.com |access-date=12 December 2022 |language=en}}</ref> 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-domain system|three domains of life]]. [[Bacteria]] and [[Archaea]] (both [[prokaryote]]s) make up the other two domains.<ref name="Gabaldón">{{cite journal | vauthors = Gabaldón T | title = Origin and Early Evolution of the Eukaryotic Cell | journal = Annual Review of Microbiology | volume = 75 | issue = 1 | pages = 631–647 | date = October 2021 | pmid = 34343017 | doi = 10.1146/annurev-micro-090817-062213 | s2cid = 236916203 }}</ref><ref name="w1990">{{cite journal | vauthors = Woese CR, Kandler O, Wheelis ML | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 87 | issue = 12 | pages = 4576–4579 | date = June 1990 | pmid = 2112744 | pmc = 54159 | doi = 10.1073/pnas.87.12.4576 | bibcode = 1990PNAS...87.4576W | doi-access = free }}</ref> 

The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the [[Asgard (archaea)|Asgard]] archaea.<ref name="nyt_2016_apr_11">{{cite news | url=https://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html | title=Scientists Unveil New 'Tree of Life' | newspaper=The New York Times | date=11 April 2016 | access-date=2016-04-11 | vauthors=Zimmer C | archive-date=24 March 2019 | archive-url=https://web.archive.org/web/20190324055739/https://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html | url-status=live }}</ref><ref>{{cite journal | vauthors = Gribaldo S, Brochier-Armanet C | title = Evolutionary relationships between archaea and eukaryotes | journal = Nature Ecology & Evolution | volume = 4 | issue = 1 | pages = 20–21 | date = January 2020 | pmid = 31836857 | doi = 10.1038/s41559-019-1073-1 | doi-access = free }}</ref> This implies that there are only [[Two-domain system|two domains of life]], Bacteria and Archaea, with eukaryotes incorporated among archaea.<ref>{{cite journal |vauthors=Doolittle WF |date=February 2020 |title=Evolution: Two Domains of Life or Three? |journal=Current Biology |volume=30 |issue=4 |pages=R177–R179 |doi=10.1016/j.cub.2020.01.010 |pmid=32097647 |doi-access=free}}</ref><ref name=":1">{{cite journal |vauthors=Williams TA, Cox CJ, Foster PG, Szöllősi GJ, Embley TM |date=January 2020 |title=Phylogenomics provides robust support for a two-domains tree of life |journal=Nature Ecology & Evolution |volume=4 |issue=1 |pages=138–147 |doi=10.1038/s41559-019-1040-x |pmc=6942926 |pmid=31819234}}</ref> Eukaryotes represent a small minority of the number of organisms,<ref name="Whitman etal" /> but, due to their generally much larger size, their collective global [[biomass (ecology)|biomass]] is estimated to be about equal to that of prokaryotes.<ref name="Whitman etal">{{cite journal | vauthors = Whitman WB, Coleman DC, Wiebe WJ | title = Prokaryotes: the unseen majority | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 12 | pages = 6578–6583 | date = June 1998 | pmid = 9618454 | pmc = 33863 | doi = 10.1073/pnas.95.12.6578 | url = http://www.pnas.org/cgi/reprint/95/12/6578.pdf | bibcode = 1998PNAS...95.6578W | access-date = 16 September 2011 | archive-date = 20 August 2008 | archive-url = https://web.archive.org/web/20080820171651/http://www.pnas.org/cgi/reprint/95/12/6578.pdf | url-status = live | doi-access = free }}</ref> Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the [[Proterozoic]] eon, likely as [[Flagellated cell|flagellated]] [[phagotroph]]s.<ref>{{cite journal | vauthors = Leander BS | title = Predatory protists | journal = Current Biology | volume = 30 | issue = 10 | pages = R510–R516 | date = May 2020 | pmid = 32428491 | doi = 10.1016/j.cub.2020.03.052 | s2cid = 218710816 | doi-access = free }}</ref><ref name="RedAlgalDerivedPlastids"/>  Their name comes from the [[Greek language|Greek]] [[wikt:εὖ|εὖ]] (''eu'', "well" or "good") and [[wikt:κάρυον|κάρυον]] (''karyon'', "nut" or "kernel").<ref name="OnlineEtDict">{{OEtymD|eukaryotic}}</ref> 

Eukaryotic cells typically contain other [[organelle|membrane-bound organelles]] such as [[mitochondrion|mitochondria]] and [[Golgi apparatus]]. [[Chloroplast]]s can be found in [[plant]]s and [[algae]]. Prokaryotic cells may contain [[Organelle#Prokaryotic organelles|primitive organelles]].<ref>{{cite journal | vauthors = Murat D, Byrne M, Komeili A | title = Cell biology of prokaryotic organelles | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 10 | pages = a000422 | date = October 2010 | pmid = 20739411 | pmc = 2944366 | doi = 10.1101/cshperspect.a000422 }}</ref> Eukaryotes may be either [[Unicellular organism|unicellular]] or [[Multicellular organism|multicellular]], and include many [[cell type]]s forming different kinds of [[Tissue (biology)|tissue]]. In comparison, prokaryotes are typically unicellular. [[Animal]]s, [[plant]]s, and [[Fungus|fungi]] are the most familiar eukaryotes. Other eukaryotes are sometimes called [[protist]]s.<ref name="Whittaker">{{cite journal | vauthors = Whittaker RH | title = New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms | journal = Science | volume = 163 | issue = 3863 | pages = 150–60 | date = January 1969 | pmid = 5762760 | doi = 10.1126/science.163.3863.150 | citeseerx = 10.1.1.403.5430 | bibcode = 1969Sci...163..150W }}</ref>

Eukaryotes can reproduce both [[asexual reproduction|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 rounds of [[cell division]] to produce four [[Ploidy|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 [[chromosome]]s resulting from [[genetic recombination]] during meiosis.<ref>{{cite book | vauthors = Campbell NA, Cain ML, Minorsky PV, Reece JB, Urry LA |date = 2018|title = Biology: A Global Approach|edition=11th|chapter=Chapter 13: Sexual Life Cycles and Meiosis|publisher = Pearson Education|location = New York|isbn = 978-1-292-17043-5}}</ref>
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==Cell features==
[[File:BC1 Cytology.webm|thumb|Cytology Video, Cell Features]]

[[Cell (biology)#Eukaryotic cells|Eukaryotic cells]] are typically much larger than those of [[prokaryote]]s, having a volume of around 10,000 times greater than the prokaryotic cell.<ref>{{cite journal|title = Deep-sea microorganisms and the origin of the eukaryotic cell|url = http://protistology.jp/journal/jjp47/JJP47YAMAGUCHI.pdf|vauthors = Yamaguchi M, Worman CO|journal = Jpn. J. Protozool.|volume = 47|number = 1,2|date = 2014|pages = 29–48|access-date = 24 October 2017|archive-url = https://web.archive.org/web/20170809103456/http://protistology.jp/journal/jjp47/JJP47YAMAGUCHI.pdf|archive-date = 9 August 2017|url-status = dead}}</ref> They have a variety of internal membrane-bound structures, called [[organelle]]s, and a [[cytoskeleton]] composed of [[microtubule]]s, [[microfilament]]s, and [[intermediate filament]]s, which play an important role in defining the cell's organization and shape. Eukaryotic [[DNA]] is divided into several linear bundles called [[chromosome]]s, which are separated by a [[spindle apparatus|microtubular spindle]] during nuclear division.

===Internal membranes===
[[File:Endomembrane system diagram en (edit).svg|thumb|upright=1.2|left|The endomembrane system and its components]]

Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the [[endomembrane system]].<ref>{{cite book |vauthors=Linka M, Weber AP |chapter=Evolutionary Integration of Chloroplast Metabolism with the Metabolic Networks of the Cells |veditors=Burnap RL, Vermaas WF |title=Functional Genomics and Evolution of Photosynthetic Systems |publisher=Springer |year=2011 |isbn=978-94-007-1533-2 |page=215 |chapter-url=https://books.google.com/books?id=WfzEgaLibuwC&pg=PA215 |access-date=27 October 2015 |archive-date=29 May 2016 |archive-url=https://web.archive.org/web/20160529130011/https://books.google.com/books?id=WfzEgaLibuwC&pg=PA215 |url-status=live }}</ref> Simple compartments, called [[vesicle (biology)|vesicles]] and [[vacuole]]s, can form by budding off other membranes. Many cells ingest food and other materials through a process of [[endocytosis]], where the outer membrane [[Invagination|invaginates]] and then pinches off to form a vesicle.<ref>{{cite book| vauthors = Marsh M | title = Endocytosis| publisher = Oxford University Press| year = 2001| page = vii| isbn = 978-0-19-963851-2}}</ref> It is probable{{citation needed|date=April 2020}} 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 pore]]s that allow material to move in and out.<ref name=TheNuclearEnvelope-NCBI>{{cite journal | vauthors = Hetzer MW | title = The nuclear envelope | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 3 | pages = a000539 | date = March 2010 | pmid = 20300205 | pmc = 2829960 | doi = 10.1101/cshperspect.a000539 }}</ref> 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 [[ribosome]]s 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.<ref>{{cite web |title=Endoplasmic Reticulum (Rough and Smooth) |url=http://bscb.org/learning-resources/softcell-e-learning/endoplasmic-reticulum-rough-and-smooth/ |publisher=British Society for Cell Biology |access-date=12 November 2017 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055727/https://bscb.org/learning-resources/softcell-e-learning/endoplasmic-reticulum-rough-and-smooth/ |url-status=live }}</ref> In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles ([[cisterna]]e), the [[Golgi apparatus]].<ref>{{cite web |title=Golgi Apparatus |url=http://bscb.org/learning-resources/softcell-e-learning/golgi-apparatus/ |publisher=British Society for Cell Biology |access-date=12 November 2017 |archive-url=https://web.archive.org/web/20171113060218/http://bscb.org/learning-resources/softcell-e-learning/golgi-apparatus/ |archive-date=13 November 2017 |url-status=dead }}</ref>

Vesicles may be specialized for various purposes. For instance, [[lysosome]]s contain digestive [[enzyme]]s that break down most [[biomolecule]]s in the cytoplasm.<ref>{{cite web |title=Lysosome |url=http://bscb.org/learning-resources/softcell-e-learning/lysosome/ |publisher=British Society for Cell Biology |access-date=12 November 2017 |archive-url=https://web.archive.org/web/20171113060214/http://bscb.org/learning-resources/softcell-e-learning/lysosome/ |archive-date=13 November 2017 |url-status=dead }}</ref> [[Peroxisome]]s are used to break down [[peroxide]], which is otherwise toxic. Many [[protozoa]]ns have contractile vacuoles, which collect and expel excess water, and [[extrusome]]s, 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===

[[File:Mitochondrion structure.svg|thumb|upright=1.4|Simplified structure of a mitochondrion]] [[Mitochondrion|Mitochondria]] are organelles found in all but one eukaryote,{{refn|group=note|name="Only1"|To date, only one eukaryote, ''[[Monocercomonoides]]'', is known to have completely lost its mitochondria.<ref name="Karn">{{cite journal | vauthors = Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V | display-authors = 6 | title = A Eukaryote without a Mitochondrial Organelle | journal = Current Biology | volume = 26 | issue = 10 | pages = 1274–1284 | date = May 2016 | pmid = 27185558 | doi = 10.1016/j.cub.2016.03.053 | doi-access = free }}</ref>}} and are commonly referred to as "the powerhouse of the cell".<ref>{{cite journal | vauthors = Saygin D, Tabib T, Bittar HE, Valenzi E, Sembrat J, Chan SY, Rojas M, Lafyatis R | display-authors = 6 | title = Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension | journal = Pulmonary Circulation | volume = 10 | issue = 1 | pages = 131–144 | date = July 1957 | pmid = 32166015 | doi = 10.1038/scientificamerican0757-131 | bibcode = 1957SciAm.197a.131S }}</ref> Mitochondria provide energy to the eukaryote cell by oxidising sugars or fats and releasing energy as [[adenosine triphosphate|ATP]].<ref>{{cite web |url=http://www.madsci.org/posts/archives/2006-05/1146679455.Ev.r.html |title=Re: Are there eukaryotic cells without mitochondria? |date=1 May 2006 |work=madsci.org |vauthors=Mack S |access-date=24 April 2014 |archive-date=24 April 2014 |archive-url=https://web.archive.org/web/20140424224700/http://www.madsci.org/posts/archives/2006-05/1146679455.Ev.r.html |url-status=live }}</ref> They have two surrounding [[Mitochondrion#Structure|membranes]], each a [[Lipid bilayer|phospholipid bi-layer]]; the [[Inner mitochondrial membrane|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 [[mitochondrial intermembrane space|intermembrane space]] while the inner mitochondrial membrane is semi permeable so allows only some required things into the mitochondrial matrix.

Mitochondria contain [[Mitochondrial DNA|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.<ref name="MolecGene">{{cite book | vauthors = Watson J, Hopkins N, Roberts J, Steitz JA, Weiner A |title=Molecular Biology of the Gene |date=1988 |publisher=The Benjamin/Cummings Publishing Company, Inc. |location=Menlo Park, CA |isbn=978-0-8053-9614-0 |page=[https://archive.org/details/molecularbiology0004unse/page/1154 1154] |edition=Fourth |chapter=28: The Origins of Life |chapter-url=https://archive.org/details/molecularbiology0004unse/page/1154 }}</ref> They are now generally held to have developed from [[endosymbiosis|endosymbiotic]] prokaryotes, probably [[Alphaproteobacteria]].

Some eukaryotes, such as the [[metamonad]]s 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 [[hydrogenosome]]s and [[mitosome]]s, and thus have lost their mitochondria secondarily.<ref name="Karn"/> 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 [[Iron–sulfur protein|clusters of iron and sulfur]] required for protein synthesis. The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily.<ref name ="Karn"/><ref>{{cite web |url=http://www.iflscience.com/plants-and-animals/first-eukaryote-found-lack-mitochondria |title=Scientists Shocked To Discover Eukaryote With NO Mitochondria |date=13 May 2016 | vauthors = Davis JL |website=IFL Science |access-date=2016-05-13 |archive-url=https://web.archive.org/web/20190217214255/https://www.iflscience.com/plants-and-animals/first-eukaryote-found-lack-mitochondria/ |archive-date=17 February 2019 |url-status=dead }}</ref>

===Plastids===
Plants and various groups of [[algae]] also have [[plastid]]s. Plastids also have [[Chloroplast DNA|their own DNA]] and are developed from [[endosymbionts]], in this case [[cyanobacteria]]. They usually take the form of [[chloroplast]]s 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.<ref>{{cite book| vauthors = Sato N |year=2006|pages= 75–102 |title=The Structure and Function of Plastids|volume=23| veditors = Wise RR, Hoober JK |publisher= Springer Netherlands|chapter=Origin and Evolution of Plastids: Genomic View on the Unification and Diversity of Plastids|isbn=978-1-4020-4060-3|doi=10.1007/978-1-4020-4061-0_4|series=Advances in Photosynthesis and Respiration}}</ref> 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 [[Evolution of flagella|flagella]].<ref name=Margulis>{{cite book |vauthors=Margulis L |title=Symbiotic planet: a new look at evolution |publisher=Basic Books |location=New York |year=1998 |isbn=978-0-465-07271-2 |oclc=39700477 |url=https://archive.org/details/symbioticplanetn00marg }}{{page needed|date=November 2017}}</ref>

===Cytoskeletal structures===
{{Main | Cytoskeleton}}
[[File:Chlamydomonas TEM 09.jpg|thumb|Longitudinal section through the flagellum of ''[[Chlamydomonas reinhardtii]]'']]

Many eukaryotes have long slender motile cytoplasmic projections, called [[flagellum|flagella]], or similar structures called [[cilium|cilia]]. Flagella and cilia are sometimes referred to as [[undulipodia]],<ref>[[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}}</ref> 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 protein]]s 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 [[conifer]]s and [[flowering plant]]s 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.<ref>{{cite book | vauthors = Vorobjev IA, Nadezhdina ES | title = The centrosome and its role in the organization of microtubules | volume = 106 | pages = 227–293 | year = 1987 | pmid = 3294718 | doi = 10.1016/S0074-7696(08)61714-3 | isbn = 978-0-12-364506-7 | series = International Review of Cytology }}</ref>

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 [[Pseudopodia#Morphology|axopodia]] used in flotation or to capture prey, and the [[haptophyte]]s, which have a peculiar flagellum-like organelle called the [[haptonema]].

===Cell wall===
{{Main|Cell wall}}
The cells of plants and algae, fungi and most [[Chromalveolata|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.<ref name="Howland 2000">{{cite book| vauthors = Howland JL | year=2000 | title=The Surprising Archaea: Discovering Another Domain of Life | pages=69–71 | publisher=Oxford University Press | location=Oxford | isbn=978-0-19-511183-5}}</ref>

The major [[polysaccharides]] making up the primary cell wall of [[land plants]] are [[cellulose]], [[hemicellulose]], and [[pectin]]. The cellulose [[microfibril]]s 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]].<ref name="Fry1989">{{cite journal | vauthors = Fry SC |title=The Structure and Functions of Xyloglucan |journal=Journal of Experimental Botany |volume=40 |issue=1 |year=1989 |pages=1–11 |doi=10.1093/jxb/40.1.1}}</ref>

==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===
[[File:Animal cell structure en.svg|thumb|upright=1.4|Structure of a typical animal cell]]
[[File:Plant cell structure-en.svg|thumb|upright=1.4|Structure of a typical [[plant cell]]]]

All animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably [[plant cells|plants]], as they lack [[cell wall]]s and [[chloroplast]]s and have smaller [[vacuole]]s. Due to the lack of a [[cell wall]], animal cells can transform into a variety of shapes. A [[phagocyte|phagocytic]] cell can even engulf other structures.

===Plant cell===
{{Main|Plant cell}}
[[Plant cell]]s 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 [[molecule]]s between the [[cytosol]] and [[plant sap|sap]]<ref name=Raven1987>{{cite journal| vauthors = Raven JA | date=July 1987 | title=The role of vacuoles | journal= New Phytologist | volume=106 | issue=3 | pages=357–422 | doi=10.1111/j.1469-8137.1987.tb00149.x| doi-access=free }}</ref>
* 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 [[fungus|fungi]], which contain [[chitin]], and the [[cell envelope]]s of prokaryotes, in which [[peptidoglycan]]s 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.<ref name=Oparka>{{cite book | vauthors = Oparka K | year=2005 | title=Plasmodesmata | publisher=Blackwell Publishing | location=Oxford, UK}}</ref> Animals have a different but functionally analogous system of [[gap junction]]s between adjacent cells.
* [[Plastid]]s, especially [[chloroplast]]s, [[organelle]]s that contain [[chlorophyll]], the pigment that gives [[plant]]s their green color and allows them to perform [[photosynthesis]]
* [[Bryophyte]]s and [[pteridophyte|seedless vascular plants]] only have flagellae and centrioles in the sperm cells.<ref name="Raven">{{cite book | vauthors = Raven PH, Evert RF, Eichorm SE | year=1999| title= Biology of Plants |  publisher=W.H. Freeman | location=New York }}</ref> Sperm of [[cycad]]s and ''[[Ginkgo]]'' are large, complex cells that swim with hundreds to thousands of flagellae.<ref name="Silflow">{{cite journal | vauthors = Silflow CD, Lefebvre PA | title = Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii | journal = Plant Physiology | volume = 127 | issue = 4 | pages = 1500–1507 | date = December 2001 | pmid = 11743094 | pmc = 1540183 | doi = 10.1104/pp.010807 }}</ref>
* [[Pinophyta|Conifers]] (Pinophyta) and [[flowering plant]]s (Angiospermae) lack the [[flagellum|flagellae]] and [[centriole]]s that are present in animal cells.

===Fungal cell===
[[File:HYPHAE.png|thumb|upright=1.4|Fungal Hyphae cells: 1 – hyphal wall, 2 – septum, 3 – mitochondrion, 4 – vacuole, 5 – [[ergosterol]] crystal, 6 – ribosome, 7 – nucleus, 8 – endoplasmic reticulum, 9 – lipid body, 10 – plasma membrane, 11 – [[spitzenkörper]], 12 – Golgi apparatus]]
The cells of [[fungi]] are similar to animal cells, with the following exceptions:<ref>{{cite book | vauthors = Deacon J |title=Fungal Biology |publisher=Blackwell Publishers |location=Cambridge, Massachusetts |year=2005 |isbn=978-1-4051-3066-0 |pages=4 and passim}}</ref>
* A cell wall that contains [[chitin]]
* Less compartmentation between cells; the [[hypha]]e of higher fungi have porous partitions called [[septum|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, [[chytrid]]s, have flagella.

===Other eukaryotic cells===
Some groups of eukaryotes have unique organelles, such as the cyanelles (unusual plastids) of the [[glaucophyte]]s,<ref name="keeling">{{cite journal | vauthors = Keeling PJ | title = Diversity and evolutionary history of plastids and their hosts | journal = American Journal of Botany | volume = 91 | issue = 10 | pages = 1481–1493 | date = October 2004 | pmid = 21652304 | doi = 10.3732/ajb.91.10.1481 | doi-access = free }}</ref> the haptonema of the [[haptophyte]]s, or the [[ejectosome]]s of the [[cryptomonad]]s. Other structures, such as [[pseudopodia]], are found in various eukaryote groups in different forms, such as the lobose [[amoebozoa]]ns or the reticulose [[foraminiferan]]s.<ref>{{cite web |url=http://tolweb.org/notes/?note_id=51 |vauthors=Patterson DJ |title=Amoebae: Protists Which Move and Feed Using Pseudopodia |publisher=Tree of Life Web Project |access-date=12 November 2017 |archive-date=15 June 2010 |archive-url=https://web.archive.org/web/20100615015212/http://tolweb.org/notes/?note_id=51 |url-status=live }}</ref> Structures known as [[cortical alveoli]] are vesicles present under the cell membrane of many [[protist]]s such as [[dinoflagellate]]s, [[ciliate]]s and [[apicomplexan]] parasites.<ref name="Alveolins">{{cite journal|vauthors=Gould SB, Tham WH, Cowman AF, McFadden GI, Waller RF|date=2008|url=http://mbe.oxfordjournals.org/content/25/6/1219.full|title=Alveolins, a new family of cortical proteins that define the protist infrakingdom Alveolata|journal=Molecular Biology and Evolution|volume=25|issue=6|pages=1219–1230|doi=10.1093/molbev/msn070 |pmid=18359944 }}</ref>

==Reproduction==
[[File:Evolsex-dia1a.png|thumb|upright=1.4|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 [[asexual reproduction|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]], [[alternation of generations|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.<ref name="Lane2011">{{cite journal | vauthors = Lane N | title = Energetics and genetics across the prokaryote-eukaryote divide | journal = Biology Direct | volume = 6 | issue = 1 | page = 35 | date = June 2011 | pmid = 21714941 | pmc = 3152533 | doi = 10.1186/1745-6150-6-35 }}</ref>

The [[evolution of sexual reproduction]] may be a primordial and fundamental characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and [[Andrew J. Roger|Roger]] proposed that facultative sex was present in the common ancestor of all eukaryotes.<ref>{{cite journal | vauthors = Dacks J, Roger AJ | s2cid = 9441768 | title = The first sexual lineage and the relevance of facultative sex | journal = Journal of Molecular Evolution | volume = 48 | issue = 6 | pages = 779–783 | date = June 1999 | pmid = 10229582 | doi = 10.1007/PL00013156 | bibcode = 1999JMolE..48..779D }}</ref> 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.<ref name=Ramesh>{{cite journal | vauthors = Ramesh MA, Malik SB, Logsdon JM | title = A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis | journal = Current Biology | volume = 15 | issue = 2 | pages = 185–191 | date = January 2005 | pmid = 15668177 | doi = 10.1016/j.cub.2005.01.003 | s2cid = 17013247 | doi-access = free }}</ref><ref name=Malik>{{cite journal | vauthors = Malik SB, Pightling AW, Stefaniak LM, Schurko AM, Logsdon JM | title = An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis | journal = PLOS ONE| volume = 3 | issue = 8 | pages = e2879 | date = August 2007 | pmid = 18663385 | pmc = 2488364 | doi = 10.1371/journal.pone.0002879 | veditors = Hahn MW | bibcode = 2008PLoSO...3.2879M | doi-access = free }}</ref> 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.<ref name=Ramesh /><ref name=Malik /> Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus ''[[Leishmania]]'', have been shown to have a sexual cycle.<ref>{{cite journal | vauthors = Akopyants NS, Kimblin N, Secundino N, Patrick R, Peters N, Lawyer P, Dobson DE, Beverley SM, Sacks DL | title = Demonstration of genetic exchange during cyclical development of Leishmania in the sand fly vector | journal = Science | volume = 324 | issue = 5924 | pages = 265–268 | date = April 2009 | pmid = 19359589 | pmc = 2729066 | doi = 10.1126/science.1169464 | bibcode = 2009Sci...324..265A }}</ref> 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.<ref>{{cite journal | vauthors = Lahr DJ, Parfrey LW, Mitchell EA, Katz LA, Lara E | title = The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms | journal = Proceedings: Biological Sciences | volume = 278 | issue = 1715 | pages = 2081–2090 | date = July 2011 | pmid = 21429931 | pmc = 3107637 | doi = 10.1098/rspb.2011.0289 }}</ref>

==Classification==
{{Further|wikispecies:Eukaryota}}
[[File:Tree of Living Organisms 2.png|thumb|upright=1.4|Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes]]
[[File:Eukaryote Phylogeny.png|thumb|One hypothesis of eukaryotic relationships – the [[Opisthokonta]] group includes both animals (Metazoa) and fungi, plants (Plantae) are placed in [[Archaeplastida]].]]
[[File:Eukaryote species pie tree.png|thumb|upright=1.4|A pie chart of described eukaryote species (except for Excavata), together with a tree showing possible relationships between the groups]]
In [[Ancient history|antiquity]], the two lineages of [[animal]]s and [[plant]]s were recognized. They were given the [[taxonomic rank]] of [[Kingdom (biology)|Kingdom]] by [[Carl Linnaeus|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.<ref name="Moore1980">{{cite journal | vauthors = Moore RT |year=1980 |title=Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts |journal=Botanica Marina |volume=23 |pages=361–373}}</ref> 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 [[ciliate]]s,<ref>{{cite journal |author=Goldfuß |title=Ueber die Classification der Zoophyten |journal=Isis, Oder, Encyclopädische Zeitung von Oken |date=1818 |volume=2 |issue=6 |pages=1008–1019 |url=https://www.biodiversitylibrary.org/item/47614#page/530/mode/1up |trans-title=On the classification of zoophytes |language=de |access-date=15 March 2019 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324105702/https://www.biodiversitylibrary.org/item/47614#page/530/mode/1up |url-status=live }} 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.]</ref> and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the [[Protista]], by [[Ernst Haeckel]] in 1866.<ref name=Scamardella1999>{{cite journal| vauthors = Scamardella JM |title=Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista |year=1999 |journal=[[International Microbiology]] |volume=2 |issue=4 |pages=207–221 |pmid=10943416 |url=http://www.im.microbios.org/08december99/03%20Scamardella.pdf |url-status=dead |archive-url=https://web.archive.org/web/20110614000656/http://www.im.microbios.org/08december99/03%20Scamardella.pdf |archive-date=14 June 2011 }}</ref><ref name=Rothschild1989>{{cite journal | vauthors = Rothschild LJ | title = Protozoa, Protista, Protoctista: what's in a name? | journal = Journal of the History of Biology | volume = 22 | issue = 2 | pages = 277–305 | year = 1989 | pmid = 11542176 | doi = 10.1007/BF00139515 | s2cid = 32462158 | author-link = Lynn J. Rothschild | url = https://zenodo.org/record/1232387 | access-date = 4 February 2020 | archive-date = 4 February 2020 | archive-url = https://web.archive.org/web/20200204233203/https://zenodo.org/record/1232387 | url-status = live }}</ref> 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.<ref name=Rothschild1989/> The disentanglement of the deep splits in the [[tree of life (biology)|tree of life]] only really started with [[Nucleic acid sequence|DNA sequencing]], leading to a system of [[domain (biology)|domains]] rather than kingdoms as top level rank being put forward by [[Carl Woese]], uniting all the eukaryote kingdoms under the eukaryote domain.<ref name=":0">{{cite journal | vauthors = Woese CR, Kandler O, Wheelis ML | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 87 | issue = 12 | pages = 4576–4579 | date = June 1990 | pmid = 2112744 | pmc = 54159 | doi = 10.1073/pnas.87.12.4576 | bibcode = 1990PNAS...87.4576W | doi-access = free }}</ref> 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.

Eukaryotes are a clade usually assessed to be sister to [[Heimdallarchaeota]] in the [[Asgard (archaea)|Asgard]] grouping in the [[Archaea]].<ref name="SpangSaw2015" /><ref name="Zaremba-NiedzwiedzkaCaceres2017" /><ref name="Liu_2018" /> In one proposed system{{which|date=August 2022}}, 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{{citation needed|date=August 2022}}.

A [[Kingdom (biology)#International Society of Protistologists Classification 2005|classification produced in 2005 for the International Society of Protistologists]],<ref>{{cite journal | vauthors = Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup O, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MF | display-authors = 6 | title = The new higher level classification of eukaryotes with emphasis on the taxonomy of protists | journal = The Journal of Eukaryotic Microbiology | volume = 52 | issue = 5 | pages = 399–451 | year = 2005 | pmid = 16248873 | doi = 10.1111/j.1550-7408.2005.00053.x | s2cid = 8060916 | doi-access = free }}</ref> which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic '[[Supergroup (biology)|supergroups]]'. However, in the same year (2005), doubts were expressed as to whether some of these supergroups were [[monophyletic]], particularly the [[Chromalveolata]],<ref>{{cite journal | vauthors = Harper JT, Waanders E, Keeling PJ | title = On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 55 | issue = Pt 1 | pages = 487–496 | date = January 2005 | pmid = 15653923 | doi = 10.1099/ijs.0.63216-0 | url = http://www.botany.ubc.ca/keeling/PDF/05chromalvJSEM.pdf | archive-url = https://web.archive.org/web/20081217052013/http://www.botany.ubc.ca/keeling/PDF/05chromalvJSEM.pdf | archive-date = 17 December 2008 | doi-access = free }}</ref> and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.<ref name="parfrey">{{cite journal | vauthors = Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA | title = Evaluating support for the current classification of eukaryotic diversity | journal = PLOS Genetics | volume = 2 | issue = 12 | pages = e220 | date = December 2006 | pmid = 17194223 | pmc = 1713255 | doi = 10.1371/journal.pgen.0020220 }}</ref> A revised classification in 2012<ref name="Adl2012"/> recognizes five supergroups.

{| class="wikitable"
| [[Archaeplastida]]<br />(or Primoplantae) || [[Embryophyte|Land plants]], [[green alga]]e, [[red alga]]e, and [[glaucophyte]]s
|-
| [[SAR supergroup]] || [[Heterokont|Stramenopiles]] ([[brown algae]], [[diatoms]], etc.),<br />[[alveolate|Alveolata]], and [[Rhizaria]] ([[Foraminifera]], [[Radiolaria]],<br />and various other [[amoeboid]] protozoa)
|-
| [[Excavata]] || Various [[flagellate]] protozoa
|-
| [[Amoebozoa]] || Most lobose [[amoeboid]]s and [[slime mold]]s
|-
| [[Opisthokonta]] || [[Animal]]s, [[fungus|fungi]], [[choanoflagellate]]s, etc.
|}

There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the major groups<ref name="burki2014"/>&nbsp;– in particular, [[Haptophyta]], [[Cryptophyta]], [[Centrohelida]], [[Telonemia]], [[Picozoa]],<ref name=ZhaoBurkBratKeel12/> [[Apusomonadida]], [[Ancyromonadida]], [[Breviata|Breviatea]], and the genus ''[[Collodictyon]]''.<ref name=Romari2004>{{cite journal| vauthors = Romari K, Vaulot D | s2cid = 86718111 | name-list-style = vanc | year=2004 | title=Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences | journal=Limnol Oceanogr | volume=49 | issue=3| pages=784–798 | doi=10.4319/lo.2004.49.3.0784| bibcode=2004LimOc..49..784R | doi-access=free }}</ref> Overall, it seems that, although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. As [[Andrew J. Roger|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."<ref>{{cite journal | vauthors = Roger AJ, Simpson AG | title = Evolution: revisiting the root of the eukaryote tree | journal = Current Biology | volume = 19 | issue = 4 | pages = R165–67 | date = February 2009 | pmid = 19243692 | doi = 10.1016/j.cub.2008.12.032 | s2cid = 13172971 | doi-access = free }}</ref> 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.<ref name="BurkiRoger2020">{{cite journal | vauthors = Burki F, Roger AJ, Brown MW, Simpson AG | title = The New Tree of Eukaryotes | journal = Trends in Ecology & Evolution | volume = 35 | issue = 1 | pages = 43–55 | date = January 2020 | pmid = 31606140 | doi = 10.1016/j.tree.2019.08.008 | doi-access = free }}</ref>

===Phylogeny===
<!-- This subsection is linked to (e.g. from "Archaeplastida"). Leave an anchor with the name "Phylogeny" if you change the title -->
The [[rRNA]] trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true [[crown group|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.<ref>{{cite journal | vauthors = Tovar J, Fischer A, Clark CG | title = The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica | journal = Molecular Microbiology | volume = 32 | issue = 5 | pages = 1013–1021 | date = June 1999 | pmid = 10361303 | doi = 10.1046/j.1365-2958.1999.01414.x | s2cid = 22805284 | doi-access = free }}</ref><ref>{{cite journal | vauthors = 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 | title = An anaerobic mitochondrion that produces hydrogen | journal = Nature | volume = 434 | issue = 7029 | pages = 74–79 | date = March 2005 | pmid = 15744302 | doi = 10.1038/nature03343 | bibcode = 2005Natur.434...74B | s2cid = 4401178 | url = https://pure.rug.nl/ws/files/9768620/2005NatureBoxma.pdf | access-date = 24 January 2019 | archive-date = 24 January 2019 | archive-url = https://web.archive.org/web/20190124152230/https://pure.rug.nl/ws/files/9768620/2005NatureBoxma.pdf | url-status = live }}</ref>

It has been estimated that there may be 75 distinct lineages of eukaryotes.<ref name=Jagus2012>{{cite journal | vauthors = Jagus R, Bachvaroff TR, Joshi B, Place AR | title = Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists | journal = Comparative and Functional Genomics | volume = 2012 | pages = 1–21 | year = 2012 | pmid = 22778692 | pmc = 3388326 | doi = 10.1155/2012/134839 | doi-access = free }}</ref> 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.<ref name="Jagus2012"/> 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 [[peroxisome]]s.<ref name="Jagus2012"/> 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.<ref name="burki2014"/><ref name="UntanglingEarlyEukaryotes"/><ref name="EarlyMitoGenomeRed"/><ref name="Kleptoplastidy Hypothesis"/><ref name="OrphanProtistanLineages"/><ref name="Karn" /><ref name="HemiSuperKingdom"/><ref name="RedAlgalDerivedPlastids"/><ref name="BurkiRoger2020"/> 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.<ref name="AdlBass2019"/> The proposed phylogeny below includes only one group of excavates ([[Discoba]]), and incorporates the recent proposal that [[picozoa]]ns are close relatives of rhodophytes.<ref name="SchönZlatogursky2021"/>

{{Clade|{{clade
|label1=[[Diphoda]]
|1={{clade
|1={{clade
|1=[[Hemimastigophora]]
|label2=[[Diaphoretickes]]
|2={{clade
|1={{clade
|1=[[Cryptista]]
|label2=[[Archaeplastida]]
|sublabel2=<small> (+ ''[[Gloeomargarita lithophora]]'') </small>
|2={{clade
|                            1={{clade
|                                1=[[Red algae]] (Rhodophyta) [[File:Bangia.jpg|40 px]]
|                                 2=[[Picozoa]]
}}
  |2={{Clade
  |                                1=[[Glaucophyta]] [[File:Glaucocystis sp.jpg|60 px]]
  |                                2=[[Green plants]] (Viridiplantae) [[File:Pediastrum (cropped).jpg|60 px]]
  }}  
     }}
}}
|                     2={{clade
|                           1={{clade
|1=[[Haptista]] [[File:Raphidiophrys contractilis.jpg|60 px]]
|label2=[[TSAR]]
             |2={{clade
                |1=[[Telonemia]]
|            label2=[[SAR supergroup|SAR]]
|            2={{clade
| label1=[[Halvaria]]
|               1={{clade
|                     1=[[Stramenopiles]] [[File:Ochromonas.png|40 px]]
|                     2=[[Alveolata]] [[File:Ceratium furca.jpg|80 px]]
                  }}
|               2=[[Rhizaria]] [[File:Ammonia tepida.jpg|60 px]]
                }}
              }}
}}
|2=''[[Ancoracysta]]''
            }}
}}
}}

|         2=[[Discoba]] (Excavata) [[File:Euglena mutabilis - 400x - 1 (10388739803) (cropped).jpg|55px]]
}}
|         label2=[[Amorphea]]
|         2={{clade
|             1=[[Amoebozoa]] [[File:Chaos carolinensis Wilson 1900.jpg|60 px]]
|label2=[[Obazoa]]
|             2={{clade
|                 1=[[Apusomonadida]] [[File:Apusomonas.png|60 px]]
|                 label2=[[Opisthokonta]]
|                 2={{clade
|                     1=[[Holomycota]] (inc. fungi) [[File:Asco1013.jpg|60 px]]
|                     2=[[Holozoa]] (inc. animals) [[File:Comb jelly.jpg|45 px]]
                    }}
                }}
}}        }}|label1=Eukaryotes|style1=font-size:80%; line-height:80%}}

In some analyses, the [[Hacrobia]] group ([[Haptophyta]] + [[Cryptophyta]]) is placed next to [[Archaeplastida]],<ref name="Burki2007">{{cite journal | vauthors = Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J | title = Phylogenomics reshuffles the eukaryotic supergroups | journal = PLOS ONE| volume = 2 | issue = 8 | pages = e790 | date = August 2007 | pmid = 17726520 | pmc = 1949142 | doi = 10.1371/journal.pone.0000790 | veditors = Butler G | bibcode = 2007PLoSO...2..790B | doi-access = free }}</ref> but in others it is nested inside the Archaeplastida.<ref name=KimGraham2008>{{cite journal | vauthors = Kim E, Graham LE | title = EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata | journal = PLOS ONE| volume = 3 | issue = 7 | pages = e2621 | date = July 2008 | pmid = 18612431 | pmc = 2440802 | doi = 10.1371/journal.pone.0002621 | veditors = Redfield RJ | bibcode = 2008PLoSO...3.2621K | doi-access = free }}</ref> However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group.<ref name="BaurBrinPeteRodr10">{{cite journal | vauthors = Baurain D, Brinkmann H, Petersen J, Rodríguez-Ezpeleta N, Stechmann A, Demoulin V, Roger AJ, Burger G, Lang BF, Philippe H | title = Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles | journal = Molecular Biology and Evolution | volume = 27 | issue = 7 | pages = 1698–1709 | date = July 2010 | pmid = 20194427 | doi = 10.1093/molbev/msq059 | doi-access = free }}</ref> The former could be a sister group to the [[SAR supergroup|SAR group]], the latter cluster with the [[Archaeplastida]] (plants in the broad sense).<ref name=Burki2012>{{cite journal | vauthors = Burki F, Okamoto N, Pombert JF, Keeling PJ | title = The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins | journal = Proceedings: Biological Sciences | volume = 279 | issue = 1736 | pages = 2246–2254 | date = June 2012 | pmid = 22298847 | pmc = 3321700 | doi = 10.1098/rspb.2011.2301 }}</ref>

The division of the eukaryotes into two primary clades, [[bikonts]] ([[Archaeplastida]] + [[SAR supergroup|SAR]] + [[Excavata]]) and [[unikonts]] ([[Amoebozoa]] + [[Opisthokonta]]), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier.<ref name="KimGraham2008"/><ref name="CavalierSmith2003">{{cite journal | vauthors = Cavalier-Smith T |s2cid=84403388 | name-list-style = vanc |author-link=Thomas Cavalier-Smith |title=Protist phylogeny and the high-level classification of Protozoa |journal=European Journal of Protistology |year=2003 |volume=39 |issue=4 |pages=338–348 |doi=10.1078/0932-4739-00002}}</ref><ref name="pmid16829542">{{cite journal | vauthors = Burki F, Pawlowski J | title = Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts | journal = Molecular Biology and Evolution | volume = 23 | issue = 10 | pages = 1922–1930 | date = October 2006 | pmid = 16829542 | doi = 10.1093/molbev/msl055 | doi-access = free }}</ref> A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.<ref name=ZhaoBurkBratKeel12>{{cite journal | vauthors = Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K | title = Collodictyon – an ancient lineage in the tree of eukaryotes | journal = Molecular Biology and Evolution | volume = 29 | issue = 6 | pages = 1557–1568 | date = June 2012 | pmid = 22319147 | pmc = 3351787 | doi = 10.1093/molbev/mss001 | author-link5 = Dag Klaveness (limnologist) }}</ref>

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.<ref>{{cite journal | vauthors = Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X | title = Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes | journal = Genome Biology and Evolution | volume = 8 | issue = 9 | pages = 2683–2701 | date = September 2016 | pmid = 27604879 | pmc = 5631032 | doi = 10.1093/gbe/evw196 }}</ref><ref name="Cavalier-Smith_2018"/><ref>{{cite journal | vauthors = Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M | title = Bacterial proteins pinpoint a single eukaryotic root | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 7 | pages = E693–699 | date = February 2015 | pmid = 25646484 | pmc = 4343179 | doi = 10.1073/pnas.1420657112 | bibcode = 2015PNAS..112E.693D | doi-access = free }}</ref><ref>{{cite journal | vauthors = Yang J, Harding T, Kamikawa R, Simpson AG, Roger AJ | title = Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids | journal = Genome Biology and Evolution | volume = 9 | issue = 5 | pages = 1161–1174 | date = May 2017 | pmid = 28453770 | pmc = 5421314 | doi = 10.1093/gbe/evx086 }}</ref><ref>{{cite journal | vauthors = Cavalier-Smith T, Fiore-Donno AM, Chao E, Kudryavtsev A, Berney C, Snell EA, Lewis R | title = Multigene phylogeny resolves deep branching of Amoebozoa | journal = Molecular Phylogenetics and Evolution | volume = 83 | pages = 293–304 | date = February 2015 | pmid = 25150787 | doi = 10.1016/j.ympev.2014.08.011 | doi-access = free }}</ref><ref name="OrphanProtistanLineages"/><ref>{{cite journal | vauthors = 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 | title = Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi | journal = Current Biology | volume = 25 | issue = 18 | pages = 2404–2410 | date = September 2015 | pmid = 26365255 | doi = 10.1016/j.cub.2015.07.053 | doi-access = free }}</ref> The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the [[bikont]]s Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbiotic eukaryote-eukaryote hybrids.<ref name="López-García_2017"/> Archaeplastida acquired [[chloroplast]]s probably by endosymbiosis of a prokaryotic ancestor related to a currently extant [[Cyanobacteria|cyanobacterium]], ''[[Gloeomargarita lithophora]]''.<ref>{{cite journal | vauthors = Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D | title = An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids | journal = Current Biology | volume = 27 | issue = 3 | pages = 386–391 | date = February 2017 | pmid = 28132810 | pmc = 5650054 | doi = 10.1016/j.cub.2016.11.056 }}</ref><ref>{{cite journal | vauthors = de Vries J, Archibald JM | title = Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium? | journal = Current Biology | volume = 27 | issue = 3 | pages = R103–105 | date = February 2017 | pmid = 28171752 | doi = 10.1016/j.cub.2016.12.006 | doi-access = free }}</ref><ref name="López-García_2017">{{cite journal | vauthors = López-García P, Eme L, Moreira D | title = Symbiosis in eukaryotic evolution | journal = Journal of Theoretical Biology | volume = 434 | pages = 20–33 | date = December 2017 | pmid = 28254477 | pmc = 5638015 | doi = 10.1016/j.jtbi.2017.02.031 | bibcode = 2017JThBi.434...20L }}</ref>

{{Clade|style=font-size:80%; line-height:80%
|label1=Eukaryotes
  |1={{clade
    |label1=[[Diphoda]]
    |1={{Clade
      |2=[[Hemimastigophora]]
      |3=[[Discoba]]
      |label1=[[Diaphoretickes]]
      |1={{clade
        |1={{clade
          |label1=[[Archaeplastida]] |sublabel1=<small> (+ ''[[Gloeomargarita lithophora]]'') </small>
          |1={{Clade
            |1=[[Glaucophyta]]
            |2={{clade
              |1=[[Rhodophyta]]
              |2=[[Viridiplantae]]
               }}
             }}
          |label2=[[Hacrobia]]
          |2={{clade
            |1=[[Haptista]]
            |2=[[Cryptista]]
             }}
           }}
       |label2=[[SAR supergroup|SAR]]
       |2={{clade
         |label1=[[Halvaria]]
         |1={{clade
           |1=[[Stramenopiles]]
           |2=[[Alveolata]]
             }}
         |2=[[Rhizaria]]
           }}
         }}
       }}
    |label2=[[Opimoda]]
    |2={{clade
      |1=[[Loukozoa]]
      |label2=[[Podiata]]
      |2={{clade
        |label1=[[CRuMs]]
        |1=[[Varisulca|Diphyllatea]], [[Rigifilida]], [[Varisulca|Mantamonas]]
        |label2=[[Amorphea]]
        |2={{clade
          |1=[[Amoebozoa]]
          |label2=[[Obazoa]]
          |2={{clade
            |1=[[Breviata]]
            |2={{clade
              |1=[[Apusomonadida]]
              |2=[[Opisthokonta]]
               }}
             }}
           }}
         }}
       }}
     }}
   }}

==== Cavalier-Smith's tree ====

[[Thomas Cavalier-Smith]] 2010,<ref name="Cavalier-Smith2010b">{{cite journal | vauthors = Cavalier-Smith T | title = Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree | journal = Biology Letters | volume = 6 | issue = 3 | pages = 342–345 | date = June 2010 | pmid = 20031978 | pmc = 2880060 | doi = 10.1098/rsbl.2009.0948 }}</ref> 2013,<ref name="Cavalier-Smith2013">{{cite journal | vauthors = Cavalier-Smith T | title = Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa | journal = European Journal of Protistology | volume = 49 | issue = 2 | pages = 115–178 | date = May 2013 | pmid = 23085100 | doi = 10.1016/j.ejop.2012.06.001}}</ref> 2014,<ref name="cavalier2014">{{cite journal | vauthors = Cavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM, Lewis R | title = Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa | journal = Molecular Phylogenetics and Evolution | volume = 81 | pages = 71–85 | date = December 2014 | pmid = 25152275 | doi = 10.1016/j.ympev.2014.08.012 | doi-access = free }}</ref> 2017<ref name="Cavalier-Smith_2018">{{cite journal | vauthors = Cavalier-Smith T | title = Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences | journal = Protoplasma | volume = 255 | issue = 1 | pages = 297–357 | date = January 2018 | pmid = 28875267 | pmc = 5756292 | doi = 10.1007/s00709-017-1147-3 }}</ref> and 2018<ref>{{cite journal | vauthors = Cavalier-Smith T, Chao EE, Lewis R | title = Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria | journal = Protoplasma | volume = 255 | issue = 5 | pages = 1517–1574 | date = April 2018 | pmid = 29666938 | pmc = 6133090 | doi = 10.1007/s00709-018-1241-1 }}</ref> 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.<ref>{{cite journal | vauthors = He D, Fiz-Palacios O, Fu CJ, Fehling J, Tsai CC, Baldauf SL | title = An alternative root for the eukaryote tree of life | journal = Current Biology | volume = 24 | issue = 4 | pages = 465–470 | date = February 2014 | pmid = 24508168 | doi = 10.1016/j.cub.2014.01.036 | doi-access = free }}</ref> specifically supports rooting the eukaryotic tree between a monophyletic [[Discoba]] ([[Discicristata]] + [[Jakobidae|Jakobida]]) and an [[Amorphea]]-[[Diaphoretickes]] clade.

{{Clade
|style= font-size:80%; line-height:80%
|label1=Eukaryotes
|1={{Clade
  |1=[[Euglenozoa]]
    |2={{Clade
      |1=[[Percolozoa]]
  |2={{Clade
    |label1=[[Eolouka]]
    |1={{Clade
      |1=[[Tsukubea|''Tsukubamonas globosa'']]
      |2=[[Jakobea]]
       }}
      |label2=[[Neokaryotes|Neokaryota]]
      |2={{Clade
        |label1=[[Corticata]]
        |1={{Clade
          |label1=[[Archaeplastida]]
            |1={{clade
             |1=[[Glaucophytes]]
            |2={{Clade
               |1=[[Rhodophytes]]
               |2=[[Viridiplantae]]
            }}
           }}
          |label2=[[Chromista]]
          |2={{clade
              |1=[[Hacrobia]]
              |2=[[SAR supergroup|SAR]]
             }}
           }}
        |label2=[[Scotokaryotes|Scotokaryota]]
        |sublabel2=[[Opimoda]]
        |2={{Clade
          |1=[[Malawimonadea|''Malawimonas'']]
          |2={{Clade
            |1=[[Metamonada]]
            |label2=[[Podiata]]
            |2={{Clade
              |1=[[Ancyromonadida]]
              |2={{Clade
                |1={{Clade
                  |1=[[Mantamonadidae|''Mantamonas plastica'']]
                  |2=[[Varisulca|Diphyllatea]]
                   }}
                |label2=[[Amorphea]]
                |2={{Clade
                  |1=[[Amoebozoa]]
                  |label2=[[Obazoa]]
                  |2={{Clade
                    |1=[[Breviatea]]
                    |2={{Clade
                      |1=[[Apusomonadida]]
                      |2=[[Opisthokonta]]
                       }}
                     }}
                   }}
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
   }}
 }}

==Evolutionary history==
=== Origin of eukaryotes<!-- A link to this section is at History of Earth#Emergence of eukaryotes--> <span class="anchor" id="Eukaryogenesis"></span><span class="anchor" id="Origin_of_eukaryotes"></span><span class="anchor" id="Last_common_ancestor"></span>===
[[File:Eocyte hypothesis.png|thumb|upright=1.4|The three-domains tree and the [[Eocyte hypothesis]]<ref>{{cite journal | vauthors = Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM | title = The archaebacterial origin of eukaryotes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 51 | pages = 20356–20361 | date = December 2008 | pmid = 19073919 | pmc = 2629343 | doi = 10.1073/pnas.0810647105 | bibcode = 2008PNAS..10520356C | doi-access = free }}</ref>]]
[[File:Collapsed tree labels simplified.png|thumb|upright=1.4|[[Phylogenetic tree]] showing a possible relationship between the eukaryotes and other forms of life;<ref>{{cite journal | vauthors = Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P | title = Toward automatic reconstruction of a highly resolved tree of life | journal = Science | volume = 311 | issue = 5765 | pages = 1283–1287 | date = March 2006 | pmid = 16513982 | doi = 10.1126/science.1123061 | bibcode = 2006Sci...311.1283C | citeseerx = 10.1.1.381.9514 | s2cid = 1615592 }}</ref> eukaryotes are colored red, [[archaea]] green and [[bacteria]] blue]]
[[File:Phylogenetic Tree of Life.png|thumb|upright=1.4|Eocyte tree.<ref name="tree_life_2016">{{cite journal|vauthors=Hug 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|date=April 2016|title=A new view of the tree of life|journal=Nature Microbiology|volume=1|issue=5|pages=16048|doi=10.1038/nmicrobiol.2016.48|pmid=27572647|doi-access=free}}<!--|access-date=2016-04-11 --></ref>]]

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 [[Most recent common ancestor|last common ancestor]] of all living eukaryotes,<ref name="Gabaldón"/> and was most likely a [[Population|biological population]].<ref name="O'Malley Leger Wideman Ruiz-Trillo pp. 338–344">{{cite journal | vauthors = O'Malley MA, Leger MM, Wideman JG, Ruiz-Trillo I | title = Concepts of the last eukaryotic common ancestor | journal = Nature Ecology & Evolution | volume = 3 | issue = 3 | pages = 338–344 | date = March 2019 | pmid = 30778187 | doi = 10.1038/s41559-019-0796-3 | publisher = Springer Science and Business Media LLC | hdl-access = free | s2cid = 67790751 | hdl = 10261/201794 }}</ref>

Eukaryotes have a number of features that differentiate them from prokaryotes, including an [[endomembrane system]], and unique biochemical pathways such as [[sterane]] synthesis.<ref name=sterane/> 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.<ref name="pmid11805300">{{cite journal | vauthors = Hartman H, Fedorov A | title = The origin of the eukaryotic cell: a genomic investigation | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 3 | pages = 1420–5 | date = February 2002 | pmid = 11805300 | pmc = 122206 | doi = 10.1073/pnas.032658599 | bibcode = 2002PNAS...99.1420H | doi-access = free }}</ref>

====Fossils====
The timing of this series of events is hard to determine; [[Andrew H. Knoll|Knoll]] (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some [[acritarch]]s 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.<ref>{{cite journal | vauthors = Knoll AH, Javaux EJ, Hewitt D, Cohen P | title = Eukaryotic organisms in Proterozoic oceans | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 361 | issue = 1470 | pages = 1023–1038 | date = June 2006 | pmid = 16754612 | pmc = 1578724 | doi = 10.1098/rstb.2006.1843 }}</ref> The ''[[Geosiphon]]''-like fossil [[fungus]] ''[[Diskagma]]'' has been found in paleosols 2.2 billion years old.<ref>{{cite journal | vauthors = Retallack GJ, Krull ES, Thackray GD, Parkinson DH |title= Problematic urn-shaped fossils from a Paleoproterozoic (2.2 Ga) paleosol in South Africa. |journal= Precambrian Research |year=2013 |volume=235 |pages=71–87 |doi=10.1016/j.precamres.2013.05.015|bibcode=2013PreR..235...71R }}</ref>

Organized living structures have been found in the [[black shale]]s of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time.<ref>{{cite journal | vauthors = 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 | s2cid = 4331375 | title = Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago | journal = Nature | volume = 466 | issue = 7302 | pages = 100–104 | date = July 2010 | pmid = 20596019 | doi = 10.1038/nature09166 | bibcode = 2010Natur.466..100A }}</ref> Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a [[red algae#Fossil record|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.<ref>{{cite journal | vauthors = Bengtson S, Belivanova V, Rasmussen B, Whitehouse M | title = The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 19 | pages = 7729–7734 | date = May 2009 | pmid = 19416859 | pmc = 2683128 | doi = 10.1073/pnas.0812460106 | bibcode = 2009PNAS..106.7729B | doi-access = free }}</ref>

The presence of eukaryotic-specific [[Biomarker (petroleum)|biomarkers]] ([[sterane]]s) in [[Australia]]n [[shale]]s previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old,<ref name=sterane>{{cite journal | vauthors = Brocks JJ, Logan GA, Buick R, Summons RE | title = Archean molecular fossils and the early rise of eukaryotes | journal = Science | volume = 285 | issue = 5430 | pages = 1033–1036 | date = August 1999 | pmid = 10446042 | doi = 10.1126/science.285.5430.1033 | bibcode = 1999Sci...285.1033B | citeseerx = 10.1.1.516.9123 }}</ref><ref>{{cite journal |vauthors=Ward P |title=Mass extinctions: the microbes strike back |journal=[[New Scientist]] |pages=40–43 |date=9 February 2008 |url=https://www.newscientist.com/channel/life/mg19726421.900-mass-extinctions-the-microbes-strike-back.html |author-link=Peter Ward (paleontologist) |access-date=27 August 2017 |archive-date=8 July 2008 |archive-url=https://web.archive.org/web/20080708222803/http://www.newscientist.com/channel/life/mg19726421.900-mass-extinctions-the-microbes-strike-back.html |url-status=live }}</ref> 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.<ref>{{cite journal | vauthors = French KL, Hallmann C, Hope JM, Schoon PL, Zumberge JA, Hoshino Y, Peters CA, George SC, Love GD, Brocks JJ, Buick R, Summons RE | title = Reappraisal of hydrocarbon biomarkers in Archean rocks | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 19 | pages = 5915–5920 | date = May 2015 | pmid = 25918387 | doi = 10.1073/pnas.1419563112 | pmc = 4434754 | bibcode = 2015PNAS..112.5915F | doi-access = free }}</ref> Currently, putatively the oldest biomarker records are only ~800 million years old.<ref>{{cite journal | vauthors = Brocks JJ, Jarrett AJ, Sirantoine E, Hallmann C, Hoshino Y, Liyanage T | title = The rise of algae in Cryogenian oceans and the emergence of animals | journal = Nature | volume = 548 | issue = 7669 | pages = 578–581 | date = August 2017 | pmid = 28813409 | doi = 10.1038/nature23457 | s2cid = 205258987 | bibcode = 2017Natur.548..578B }}</ref> In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago,<ref>{{cite journal | vauthors = Gold DA, Caron A, Fournier GP, Summons RE | title = Paleoproterozoic sterol biosynthesis and the rise of oxygen | journal = Nature | volume = 543 | issue = 7645 | pages = 420–423 | date = March 2017 | pmid = 28264195 | doi = 10.1038/nature21412 | hdl-access = free | s2cid = 205254122 | bibcode = 2017Natur.543..420G | hdl = 1721.1/128450 }}</ref> 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.<ref>{{cite journal | vauthors = Wei JH, Yin X, Welander PV | title = Sterol Synthesis in Diverse Bacteria | journal = Frontiers in Microbiology | volume = 7 | pages = 990 | date = 2016-06-24 | pmid = 27446030 | pmc = 4919349 | doi = 10.3389/fmicb.2016.00990 | doi-access = free | author-link3 = Paula V. Welander }}</ref><ref>{{cite journal | vauthors = Hoshino Y, Gaucher EA | title = Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 118 | issue = 25 | pages = e2101276118 | date = June 2021 | pmid = 34131078 | pmc = 8237579 | doi = 10.1073/pnas.2101276118 | bibcode = 2021PNAS..11801276H }}</ref>

Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive uptick in the zinc composition of marine sediments {{Ma|800}} 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).<ref name="pmid29869832">{{cite journal | vauthors = Isson TT, Love GD, Dupont CL, Reinhard CT, Zumberge AJ, Asael D, Gueguen B, McCrow J, Gill BC, Owens J, Rainbird RH, Rooney AD, Zhao MY, Stueeken EE, Konhauser KO, John SG, Lyons TW, Planavsky NJ | display-authors = 6 | title = Tracking the rise of eukaryotes to ecological dominance with zinc isotopes | journal = Geobiology | volume = 16| issue = 4| pages = 341–352| date = June 2018 | pmid = 29869832 | doi = 10.1111/gbi.12289 | doi-access = free }}</ref>

In April 2019, biologists reported that the very large [[medusavirus]], or a relative, may have been responsible, at least in part, for the [[Evolution|evolutionary emergence]] of complex eukaryotic cells from simpler [[Prokaryote|prokaryotic cells]].<ref name="pmid30728258">{{cite journal | vauthors = Yoshikawa G, Blanc-Mathieu R, Song C, Kayama Y, Mochizuki T, Murata K, Ogata H, Takemura M | title = Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water | journal = Journal of Virology | volume = 93 | issue = 8 | date = April 2019 | pmid = 30728258 | pmc = 6450098 | doi = 10.1128/JVI.02130-18 | url = https://eurekalert.org/pub_releases/2019-04/tuos-ngv043019.php | access-date =  | archive-date = 30 April 2019 | archive-url = https://web.archive.org/web/20190430141716/https://eurekalert.org/pub_releases/2019-04/tuos-ngv043019.php | url-status = live }}
* {{cite press release |date=30 April 2019 |title=New giant virus may help scientists better understand the emergence of complex life |website=[[EurekAlert!]] |url=https://www.eurekalert.org/pub_releases/2019-04/tuos-ngv043019.php}}</ref>

====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,<ref>{{cite journal | vauthors = Martin W | title = Archaebacteria (Archaea) and the origin of the eukaryotic nucleus | journal = Current Opinion in Microbiology | volume = 8 | issue = 6 | pages = 630–637 | date = December 2005 | pmid = 16242992 | doi = 10.1016/j.mib.2005.10.004 }}</ref> [[Viral Eukaryogenesis|from a virus]],<ref>{{cite journal | vauthors = Takemura M | s2cid = 21200827 | title = Poxviruses and the origin of the eukaryotic nucleus | journal = Journal of Molecular Evolution | volume = 52 | issue = 5 | pages = 419–425 | date = May 2001 | pmid = 11443345 | doi = 10.1007/s002390010171 | bibcode = 2001JMolE..52..419T }}</ref><ref>{{cite journal | vauthors = Bell PJ | s2cid = 20542871 | title = Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? | journal = Journal of Molecular Evolution | volume = 53 | issue = 3 | pages = 251–256 | date = September 2001 | pmid = 11523012 | doi = 10.1007/s002390010215 | bibcode = 2001JMolE..53..251L }}</ref> or from a [[pre-cell]].<ref>{{cite journal | vauthors = Wächtershäuser G | s2cid = 37944519 | title = From pre-cells to Eukarya – a tale of two lipids | journal = Molecular Microbiology | volume = 47 | issue = 1 | pages = 13–22 | date = January 2003 | pmid = 12492850 | doi = 10.1046/j.1365-2958.2003.03267.x | doi-access = free }}</ref><ref>{{cite journal | vauthors = Wächtershäuser G | title = From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 361 | issue = 1474 | pages = 1787–1806; discussion 1806–1808 | date = October 2006 | pmid = 17008219 | pmc = 1664677 | doi = 10.1098/rstb.2006.1904 }}</ref>
* Eukaryotes developed from Archaea, and acquired their bacterial characteristics through the [[Symbiogenesis|endosymbiosis]] of a [[proto-mitochondrion]] of bacterial origin.<ref>{{cite book | vauthors = Lane N |author-link=Nick Lane |title=The Vital Question: Why is Life the Way it is? |date=2016 |publisher=Profile Books |isbn=978-1-781-25037-2 |edition=paperback |pages=157–91|title-link=The Vital Question }}</ref>
* Eukaryotes and Archaea developed separately from a modified bacterium.

[[File:Primordial biogenesis.svg|thumb|upright=1.4|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.<ref name=Egel>{{cite magazine| vauthors = Egel R | title = Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life | magazine = Life | volume = 2 | issue = 1 | pages = 170–212 | date = January 2012 | pmid = 25382122 | pmc = 4187143 | doi = 10.3390/life2010170 | doi-access = free }}</ref>]]

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.<ref name="pmid11805300"/>
* 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.<ref name=HariTunlKurl13/>

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&nbsp;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.<ref name=Harish17/>)

{| class="wikitable"
|+ Alternative hypotheses for the base of the tree of life
! 1 – Two empires  !! 2 – Three domains !! 3 – Gupta !! 4 – Eocyte
|-
| {{clade
     |style=line-height:100%
     |label1=<br/>&nbsp;[[Last universal common ancestor|UCA]]&nbsp;
     |1={{clade
       |label1=&emsp;
       |1={{clade
          |label1=&emsp;
          |1=&nbsp;[[Archaea]]
          |2=&nbsp;[[Bacteria]]
          }}
       |2=&nbsp;'''Eukaryota'''
       }}
     }}
| {{clade
     |style=line-height:100%
     |label1=<br/>&nbsp;[[Last universal common ancestor|UCA]]&nbsp;
     |1={{clade
       |label1=&emsp;
       |1={{clade
          |label1=&emsp;
          |1=&nbsp;'''Eukaryota'''
          |2=&nbsp;[[Archaea]]
          }}
       |2=&nbsp;[[Bacteria]]
       }}
     }}
| {{clade
     |style=line-height:100%
     |label1=<br/>&nbsp;[[Last universal common ancestor|UCA]]&nbsp;
     |1={{clade
       |label1=&emsp;
       |1={{clade
          |label1=&emsp;
          |1=&nbsp;'''Eukaryota''' 
          |2=&nbsp;[[Bacteria]]
          }}
       |2=&nbsp;[[Archaea]]
       }}
     }}
| {{clade
     |style=line-height:100%
     |label1=<br/>&nbsp;[[Last universal common ancestor|UCA]]&nbsp;
     |1={{clade
       |label1=&nbsp;[[Archaea]]&nbsp;
       |1={{clade
          |label1=&emsp;
          |1={{clade
             |1=&nbsp;'''Eukaryota'''
             |2=&nbsp;Archaea-[[Crenarchaeota]]
             }}
          |2=&nbsp;Archaea-[[Euryarchaeota]]
          }}
       |2=&nbsp;[[Bacteria]]
       }}
     }}
|}

In recent years, most researchers have favoured either the three domains (3D) or the [[eocyte hypothesis]]. An [[Ribosomal RNA|rRNA]] analysis supports the eocyte scenario, apparently with the Eukaryote root in [[Excavata]].<ref name=tree_life_2016/><ref name=Cavalier-Smith2010b/><ref name=Cavalier-Smith2013/><ref name=cavalier2014/><ref name=Cavalier-Smith_2018/> A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the [[Asgard (archaea)|Asgard]] archaea, is:<ref name=SpangSaw2015>{{cite journal | vauthors = Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ | date = May 2015 | title = Complex archaea that bridge the gap between prokaryotes and eukaryotes | journal = Nature | volume = 521 | issue = 7551 | pages = 173–179 | pmid = 25945739 | pmc = 4444528 | doi = 10.1038/nature14447 | bibcode = 2015Natur.521..173S }}</ref><ref name=Zaremba-NiedzwiedzkaCaceres2017>{{cite journal | vauthors = Zaremba-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 | date = January 2017 | title = Asgard archaea illuminate the origin of eukaryotic cellular complexity | journal = Nature | volume = 541 | issue = 7637 | pages = 353–358 | pmid = 28077874 | doi = 10.1038/nature21031 | bibcode = 2017Natur.541..353Z | osti = 1580084 | s2cid = 4458094 | url = https://escholarship.org/uc/item/0qh5400s | url-status = live | access-date = 28 June 2019 | archive-date = 5 December 2019 | archive-url = https://web.archive.org/web/20191205195537/https://escholarship.org/uc/item/0qh5400s}}</ref><ref name=Liu_2018>{{cite journal | vauthors = Liu Y, Zhou Z, Pan J, Baker BJ, Gu JD, Li M | date = April 2018 | title = Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota | journal = The ISME Journal | volume = 12 | issue = 4 | pages = 1021–1031 | pmid = 29445130 | pmc = 5864231 | doi = 10.1038/s41396-018-0060-x }}</ref><ref name=":1"/>


{{clade 
 | style=font-size:80%; line-height:80%
 | label1=&nbsp;[[Archaea]]&nbsp;
 | 1={{clade
    | label1=&nbsp;[[TACK]]&nbsp;
    | 1={{clade
       | label1=&emsp; 
       | 1=&nbsp;"[[Korarchaeota]]"
       | 2={{clade
          | label1=&emsp; 
          | 1=&nbsp;[[Thermoproteota]]
          | 2={{clade
             | label1=&nbsp; 
             | 1={{clade
                | 1=&nbsp;"[[Aigarchaeota]]"
                | 2=&nbsp;"[[Geoarchaeota]]"
                }}
             | 2={{clade
                | 1=&nbsp;[[Nitrososphaerota]]
                | 2=&nbsp;"[[Bathyarchaeota]]"
                }}
             }}
          }}
       }}
    | label2=&nbsp;[[Asgard (archaea)|Asgard]]&nbsp;
    | 2={{clade
       | label1=&emsp; 
       | 1=&nbsp;"[[Lokiarchaeota]]"
       | 2=&nbsp;"[[Odinarchaeota]]"
       | 3=&nbsp;"[[Thorarchaeota]]"
       | 4={{clade
          | label1=&emsp; 
          | 1=&nbsp;"[[Heimdallarchaeota]]"
          | 2=&nbsp;'''Eukaryota'''<br/>&nbsp;(<small>+[[Alphaproteobacteria]]</small>)
          }}
       }}
    |label3=&nbsp;"[[Proteoarchaeota]]"&nbsp;
    }}
 }}


In this scenario, the Asgard group is seen as a sister taxon of the [[TACK]] group, which comprises [[Thermoproteota]] (formerly named [[Eocyte hypothesis|eocytes]] or Crenarchaeota), [[Nitrososphaerota]] (formerly Thaumarchaeota), and others. This group is reported contain many of the eukaryotic signature proteins and produce vesicles.<ref name="NAT-20200115"/>

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).<ref>{{cite journal | vauthors = Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P | title = Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes | journal = PLOS Genetics | volume = 13 | issue = 6 | pages = e1006810 | date = June 2017 | pmid = 28604769 | pmc = 5484517 | doi = 10.1371/journal.pgen.1006810 }}</ref> 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.<ref name=HariKurl17>{{cite journal |author2-link=Charles Kurland| vauthors = Harish A, Kurland CG | title = Empirical genome evolution models root the tree of life | journal = Biochimie | volume = 138 | pages = 137–155 | date = July 2017 | pmid = 28478110 | doi = 10.1016/j.biochi.2017.04.014 }}</ref><ref name=Harish17>{{cite journal | vauthors = Harish A, Kurland CG | title = Akaryotes and Eukaryotes are independent descendants of a universal common ancestor | journal = Biochimie | volume = 138 | pages = 168–183 | date = July 2017 | pmid = 28461155 | doi = 10.1016/j.biochi.2017.04.013 }}</ref> 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.<ref name=HariTunlKurl13>{{cite journal | vauthors = Harish A, Tunlid A, Kurland CG | title = Rooted phylogeny of the three superkingdoms | journal = Biochimie | volume = 95 | issue = 8 | pages = 1593–1604 | date = August 2013 | pmid = 23669449 | doi = 10.1016/j.biochi.2013.04.016 }}</ref> On the other hand, the researchers who came up with Asgard re-affirmed their hypothesis with additional Asgard samples.<ref>{{cite journal | vauthors = Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, Guy L, Ettema TJ | display-authors = 6 | title = Asgard archaea are the closest prokaryotic relatives of eukaryotes | journal = PLOS Genetics | volume = 14 | issue = 3 | pages = e1007080 | date = March 2018 | pmid = 29596421 | doi = 10.1371/journal.pgen.1007080 | pmc = 5875740 }}</ref> 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,<ref name="pmid31384702">{{cite journal |vauthors=MacLeod F, Kindler GS, Wong HL, Chen R, Burns BP |title=Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes |journal=AIMS Microbiology |volume=5 |issue=1 |pages=48–61 |date=2019 |pmid=31384702 |pmc=6646929 |doi=10.3934/microbiol.2019.1.48 }}</ref> 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.<ref name="NYT-2020115">{{cite news |vauthors=Zimmer C |title=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. |url=https://www.nytimes.com/2020/01/15/science/cells-eukaryotes-archaea.html |date=15 January 2020 |work=[[The New York Times]] |access-date=18 January 2020 |archive-date=16 January 2020 |archive-url=https://web.archive.org/web/20200116011824/https://www.nytimes.com/2020/01/15/science/cells-eukaryotes-archaea.html |url-status=live }}</ref><ref name="NAT-20200115">{{cite journal | vauthors = Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K | display-authors = 6 | title = Isolation of an archaeon at the prokaryote-eukaryote interface | journal = Nature | volume = 577 | issue = 7791 | pages = 519–525 | date = January 2020 | pmid = 31942073 | doi = 10.1038/s41586-019-1916-6 | doi-access = free | pmc = 7015854 | bibcode = 2020Natur.577..519I }}</ref>

====Endomembrane system and mitochondria====
The origins of the endomembrane system and mitochondria are also unclear.<ref>{{cite book | vauthors = Jékely G | volume = 607 | pages = [https://archive.org/details/eukaryoticmembra00gasp/page/38 38–51] | year = 2007 | pmid = 17977457 | doi = 10.1007/978-0-387-74021-8_3 | isbn = 978-0-387-74020-1 | series = Advances in Experimental Medicine and Biology | title = Eukaryotic Membranes and Cytoskeleton | chapter = Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios | chapter-url = https://archive.org/details/eukaryoticmembra00gasp/page/38 | publisher = New York, N.Y. : Springer Science+Business Media; Austin, Tex. : Landes Bioscience }}</ref> 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.<ref>{{cite journal | vauthors = Cavalier-Smith T | title = The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 52 | issue = Pt 2 | pages = 297–354 | date = March 2002 | pmid = 11931142 | doi = 10.1099/00207713-52-2-297 | url = http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=11931142 | access-date = 10 June 2008 | archive-date = 29 July 2017 | archive-url = https://web.archive.org/web/20170729113756/http://ijs.microbiologyresearch.org/content/journal/ijsem | url-status = live }}</ref> 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).<ref name="ReferenceA">{{cite journal | vauthors = Martin W, Müller M | s2cid = 338885 | title = The hydrogen hypothesis for the first eukaryote | journal = Nature | volume = 392 | issue = 6671 | pages = 37–41 | date = March 1998 | pmid = 9510246 | doi = 10.1038/32096 | bibcode = 1998Natur.392...37M }}</ref>

In a study using genomes to construct [[supertree]]s, 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.<ref>{{cite journal | vauthors = Pisani D, Cotton JA, McInerney JO | title = Supertrees disentangle the chimerical origin of eukaryotic genomes | journal = Molecular Biology and Evolution | volume = 24 | issue = 8 | pages = 1752–1760 | date = August 2007 | pmid = 17504772 | doi = 10.1093/molbev/msm095 | doi-access = free }}</ref> 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.<ref>{{cite journal | vauthors = Brueckner J, Martin WF | title = Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes | journal = Genome Biology and Evolution | volume = 12 | issue = 4 | pages = 282–292 | date = April 2020 | pmid = 32142116 | doi = 10.1093/gbe/evaa047 | doi-access = free | pmc = 7151554 }}</ref>

====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.

=====Autogenous models=====
{{Plain image with caption|Serial endosymbiosis.svg|An autogenous model for the origin of eukaryotes.|upright=1.9}}

Autogenous models propose that a proto-eukaryotic cell containing a [[Cell nucleus|nucleus]] existed first, and later acquired [[Mitochondrion|mitochondria]].<ref name="latorre" /> According to this model, a large [[prokaryote]] developed [[invaginations]] in its [[plasma membrane]] in order to obtain enough [[surface area to volume ratio|surface area]] to service its [[cytoplasmic]] volume. As the invaginations differentiated in function, some became separate compartments&nbsp;– giving rise to the [[endomembrane system]], including the [[endoplasmic reticulum]], [[golgi apparatus]], [[nuclear membrane]], and single membrane structures such as [[lysosome]]s.<ref>{{cite journal | vauthors = Ayala J | title = Transport and internal organization of membranes: vesicles, membrane networks and GTP-binding proteins | journal = Journal of Cell Science | volume = 107 | issue = Pt 4 | pages = 753–763 | date = April 1994 | doi = 10.1242/jcs.107.4.753 | pmid = 8056835 | url = http://jcs.biologists.org/content/107/4/753.long | access-date = 27 March 2013 | archive-url = https://web.archive.org/web/20120429004318/http://jcs.biologists.org/content/107/4/753.long | archive-date = 29 April 2012 | url-status = dead }}</ref>

[[Mitochondria]] are proposed to come from the [[endosymbiosis]] of an aerobic [[proteobacterium]] after an 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 doesn’t explain why  anaerobic variants of mitochondria have evolved.<ref>{{cite web|vauthors=Martin WF|title=The Origin of Mitochondria|url=http://www.nature.com/scitable/topicpage/the-origin-of-mitochondria-14232356|work=Scitable|publisher=Nature education|access-date=2013-03-27|archive-date=16 June 2013|archive-url=https://web.archive.org/web/20130616015444/http://www.nature.com/scitable/topicpage/the-origin-of-mitochondria-14232356|url-status=live|quote= 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.}}</ref>

=====Chimeric models=====
[[Chimera (genetics)|Chimeric models]] claim that two prokaryotic cells existed initially – an [[Archaea|archaeon]] and a [[Bacteria|bacterium]]. The closest living relatives of these appears to be [[Asgard (archaea)|Asgardarchaeota]] and (distantly related) the [[alphaproteobacteria]] called the [[proto-mitochondrion]].<ref name="pmid29929066">{{cite journal |vauthors=Dacks JB, Field MC |title=Evolutionary origins and specialisation of membrane transport |journal=Current Opinion in Cell Biology |volume=53 |pages=70–76 |date=August 2018 |pmid=29929066 |pmc=6141808 |doi=10.1016/j.ceb.2018.06.001}}</ref><ref name="pmid29695865">{{cite journal |vauthors=Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ |s2cid=13740626 |title=Deep mitochondrial origin outside the sampled alphaproteobacteria |journal=Nature |volume=557 |issue=7703 |pages=101–105 |date=May 2018 |pmid=29695865 |doi=10.1038/s41586-018-0059-5 |bibcode=2018Natur.557..101M | url = https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345 |access-date=21 April 2019 |archive-date=21 April 2019 |archive-url=https://web.archive.org/web/20190421155631/https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345 |url-status=live }}
* {{cite magazine |author=Shawna Williams |date=Apr 25, 2018 |title=Mitochondria's Bacterial Origins Upended |magazine=The Scientist |url=https://www.the-scientist.com/daily-news/mitochondrias-bacterial-origins-upended-33345 |url-access=subscription}}</ref> These cells underwent a merging process, either by a physical fusion or by [[Endosymbiont|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 [[phagocytosis#In protists|phagocytotic]] event. In this scenario, an archaeon would trap aerobic bacteria with [[Bleb (cell biology)|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.<ref name="pmid25350791">{{cite journal | vauthors = Baum DA, Baum B | title = An inside-out origin for the eukaryotic cell | journal = BMC Biology | volume = 12 | pages = 76 | date = October 2014 | pmid = 25350791 | pmc = 4210606 | doi = 10.1186/s12915-014-0076-2}}
* {{cite press release |author=Terry Devitt |date=December 12, 2014 |title=New theory suggests alternate path led to rise of the eukaryotic cell |website=University of Wisconsin-Madison |url=https://news.wisc.edu/new-theory-suggests-alternate-path-led-to-rise-of-the-eukaryotic-cell/ |archive-url=https://web.archive.org/web/20190421155635/https://news.wisc.edu/new-theory-suggests-alternate-path-led-to-rise-of-the-eukaryotic-cell/ |archive-date=21 April 2019 |url-status=live}}</ref>

It is assumed the archaean group called [[halophile]]s 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.<ref>{{cite journal | vauthors = Brouwers L |date=12 April 2013 |url=https://blogs.scientificamerican.com/thoughtomics/how-genetic-plunder-transformed-a-microbe-into-a-pink-salt-loving-scavenger/ |title=How genetic plunder transformed a microbe into a pink, salt-loving scavenger |volume=109 |issue=50 |pages=20537–20542 |journal=Scientific American |access-date=21 April 2019 |archive-url=https://web.archive.org/web/20181010003645/https://blogs.scientificamerican.com/thoughtomics/how-genetic-plunder-transformed-a-microbe-into-a-pink-salt-loving-scavenger/ |archive-date=10 October 2018 |url-status=dead }}</ref>

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.<ref>{{cite web |url=https://www.quantamagazine.org/rethinking-the-ancestry-of-the-eukaryotes-20190409/ | vauthors = Wilcox C |date=April 9, 2019 |title=Rethinking the ancestry of the eukaryotes |website=Quanta Magazine |access-date=8 May 2019 |archive-url=https://web.archive.org/web/20190509210556/https://www.quantamagazine.org/rethinking-the-ancestry-of-the-eukaryotes-20190409/ |archive-date=9 May 2019 |url-status=dead }}</ref><ref name="McCutcheon">{{cite journal | vauthors = McCutcheon JP | title = The Genomics and Cell Biology of Host-Beneficial Intracellular Infections | journal = Annual Review of Cell and Developmental Biology | volume = 37 | issue = 1 | pages = 115–142 | date = October 2021 | pmid = 34242059 | doi = 10.1146/annurev-cellbio-120219-024122 | s2cid = 235786110 }}</ref><ref name="Callier">{{cite journal | vauthors = Saygin D, Tabib T, Bittar HE, Valenzi E, Sembrat J, Chan SY, Rojas M, Lafyatis R | display-authors = 6 | title = Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension | journal = Pulmonary Circulation | volume = 10 | issue = 1 | date = 8 June 2022 | pmid = 32166015 | doi = 10.1146/knowable-060822-2 | doi-access = free }}</ref>

=====The serial endosymbiotic hypothesis=====
{{Main|Symbiogenesis}}
According to [[Symbiogenesis|serial endosymbiotic theory]] (championed by [[Lynn Margulis]]), a union between a motile [[anaerobic organism|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 [[Metabolism|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 (biochemistry)|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. [[Spirochete]]s 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 [[plastid]]s respectively. For example, ''Thiodendron'' has been known to have originated via an [[Ectosymbiosis|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.<ref name=latorre>{{cite book |vauthors=Latorre A, Durban A, Moya A, Pereto J |chapter-url=https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |chapter=The role of symbiosis in eukaryotic evolution |title=Origins and Evolution of Life: An astrobiological perspective |veditors=Gargaud M, López-Garcìa P, Martin H |year=2011 |location=Cambridge |publisher=Cambridge University Press |pages=326–339 |isbn=978-0-521-76131-4 |access-date=27 August 2017 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055723/https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |url-status=live }}</ref>

=====The hydrogen hypothesis=====
In the [[hydrogen hypothesis]], the symbiotic linkage of an anaerobic and [[autotroph]]ic [[methanogen]]ic archaeon (host) with an alphaproteobacterium (the symbiont) gave rise to the eukaryotes. The host used [[hydrogen]] (H<sub>2</sub>) and [[carbon dioxide]] ({{CO2}}) to produce [[methane]] while the symbiont, capable of aerobic respiration, expelled H<sub>2</sub> and {{CO2}} as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H<sub>2</sub>, which resulted in heightened bacterial fermentation.

[[Endosymbiotic gene transfer]] acted as a catalyst for the host to acquire the symbionts' [[carbohydrate]] metabolism and turn [[heterotroph]]ic 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 (evolution)|lineage]]. In this hypothesis, the presence of H<sub>2</sub> represents the selective force that forged eukaryotes out of prokaryotes.<ref name="ReferenceA" />

=====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 H<sub>2</sub> 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 [[cytoplasm]]ic 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 [[Anabolism|anabolic]] and [[Catabolism|catabolic]] cellular pathways, and
* prevention of abnormal [[protein biosynthesis]] due to a vast spread of [[intron]]s in the archaeal genes after acquiring the mitochondrion and losing [[methanogenesis]].{{citation needed |date=March 2017}}

=====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.<ref>{{cite journal |vauthors=Pittis AA, Gabaldón T |title=Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry |journal=Nature |volume=531 |issue=7592 |pages=101–104 |date=March 2016 |pmid=26840490 |pmc=4780264 |doi=10.1038/nature16941 |bibcode=2016Natur.531..101P}}</ref><ref>{{cite book |url=https://books.google.com/books?id=mXzGDgAAQBAJ&pg=PA133 |title=Evolution since coding: Cradles, halos, barrels, and wings |vauthors=Burton ZF |date=1 August 2017 |publisher=Academic Press |isbn=978-0-12-813034-6 |access-date=27 November 2018 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055722/https://books.google.com/books?id=mXzGDgAAQBAJ&lpg=PA133 |url-status=live }}</ref> The findings have been rebuked as an artifact.<ref>{{cite journal |vauthors=Martin WF, Roettger M, Ku C, Garg SG, Nelson-Sathi S, Landan G |title=Late mitochondrial origin is an artifact |journal=Genome Biology and Evolution |volume=9 |issue=2 |pages=373–379 |date=February 2017 |pmid=28199635 |pmc=5516564 |doi=10.1093/gbe/evx027}}</ref>

== See also ==
{{Portal|Biology}}
* [[Eukaryote hybrid genome]]
* [[Evolution of sexual reproduction]]
* [[List of sequenced eukaryotic genomes]]
* ''[[Parakaryon myojinensis]]''
* [[Prokaryote]]
* [[Nitrososphaerota]]
* [[Vault (organelle)]]

==Notes==
{{Reflist|group=note}}

== References ==
<!-- SystBiol56:389. -->
{{Reflist|refs=

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}}

{{NCBI-scienceprimer}}

== External links ==
{{Wikispecies|Eukaryota}}
* [http://www.tolweb.org/Eukaryotes/3 "Eukaryotes"] ([[Tree of Life Web Project]])
* {{EOL}}
* [https://www.theatlantic.com/science/archive/2020/11/how-do-single-celled-organisms-have-sex/617072/ Attraction and sex among our microbial Last Eukaryotic Common Ancestors], The Atlantic, November 11, 2020

{{Eukaryota}}
{{Excavata}}
{{Plant classification}}
{{Cryptophyta and haptophyta}}
{{Heterokont}}
{{Alveolata}}
{{Amoebozoa}}
{{Opisthokont protists}}
<!--{{Animalia}} -->
{{Fungi classification}}
{{Life on Earth}}
{{Organisms et al.}}
{{Taxonbar|from=Q19088}}
{{Authority control}}

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