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{{redirect|Eukaryotic cell|the journal|Eukaryotic Cell (journal)}}{{pp-move-indef|small=yes}}{{automatic taxobox| name=Eukaryotes
Orosirian – Holocene>Present {{long fossil range0|earliest=2700}}| image=Eukaryota diversity 2.jpgOsmia bicornis>Red mason bee, Boletus edulis, chimpanzee, Isotricha intestinalis, Ranunculus asiaticus, and Volvox carteri| taxon=EukaryotaÉdouard Chatton>Chatton, 1925) Robert Whittaker & Lynn Margulis>Margulis, 1978Kingdom (biology)#Kingdoms of the Eukaryota>SupergroupsADL SM, SIMPSON AG, LANE CE, LUKEš J, BASS D, BOWSER SS, BROWN MW, BURKI F, DUNTHORN M, HAMPL V, HEISS A, HOPPENRATH M, LARA E, LE GALL L, LYNN DH, MCMANUS H, MITCHELL EA, MOZLEY-STANRIDGE SE, PARFREY LW, PAWLOWSKI J, RUECKERT S, SHADWICK L, SHADWICK L, SCHOCH CL, SMIRNOV A, SPIEGEL FW > DISPLAY-AUTHORS = 6 JOURNAL = THE JOURNAL OF EUKARYOTIC MICROBIOLOGY ISSUE = 5 DATE = SEPTEMBER 2012 PMC = 3483872 URL = HTTP://WWW.PARU.CAS.CZ/DOCS/DOCUMENTS/93-ADL-JEM-2012.PDF DEADURL = YES Kingdom (biology)>kingdoms| subdivision =

Kingdom Plantae – Plants
  • HacrobiaJOURNAL, Sakaguchi M, Takishita K, Matsumoto T, Hashimoto T, Inagaki Y, Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads, Gene, 441, 1–2, 126–31, July 2009, 18585873, 10.1016/j.gene.2008.05.010,weblink
  • SAR (Stramenopiles + Alveolata + Rhizaria)
  • Discoba
  • Loukozoa
  • Amoebozoa
  • Opisthokonta


Kingdom Animalia – Animals Kingdom Fungi

Eukaryotic organisms that cannot be classified under the kingdoms Plantae, Animalia or Fungi are sometimes grouped in the kingdom Protista.{{!}}- style="background:#e0d0b0;" {{!}}}}Eukaryotes ({{IPAc-en|j|uː|ˈ|k|ær|i|oʊ|t|,_|-|ə|t}}) are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound organelles.BOOK, Youngson, Robert M., vanc, Collins Dictionary of Human Biology, 2006, HarperCollins, Glasgow, 978-0-00-722134-9, BOOK, Nelson, David L., Cox, Michael M., vanc, 2005, Lehninger Principles of Biochemistry, 4th, New York, W.H. Freeman, 978-0-7167-4339-2, BOOK, Martin, E.A., 2nd, Macmillan Dictionary of Life Sciences, 1983, Macmillan Press, London, 978-0-333-34867-3, Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek (wikt:εὖ|εὖ) (eu, "well" or "true") and (wikt:κάρυον|κάρυον) (karyon, "nut" or "kernel").{{OEtymD|eukaryotic|accessdate=}} Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes.Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. These act as sex cells (gametes). Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.The domain Eukaryota appears to be monophyletic, and makes up one of the domains of life in the three-domain system. The two other domains, Bacteria and Archaea, are prokaryotesNEWS,weblink Scientists Unveil New 'Tree of Life', The New York Times, 11 April 2016, 2016-04-11, Zimmer, Carl, vanc, and have none of the above features. Eukaryotes represent a tiny minority of all living things. However, due to their generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes.JOURNAL, Whitman WB, Coleman DC, Wiebe WJ, Prokaryotes: the unseen majority, Proceedings of the National Academy of Sciences of the United States of America, 95, 12, 6578–6583, June 1998, 9618454, 33863, 10.1073/pnas.95.12.6578,weblink 1998PNAS...95.6578W, Eukaryotes evolved approximately 1.6–2.1 billion years ago, during the Proterozoic eon.

History

File:Konstantin Mereschkowski cr.jpg|thumb|upright|Konstantin Mereschkowski proposed a symbiotic origin for cells with nuclei.]]The concept of the eukaryote has been attributed to the French biologist Edouard Chatton (1883–1947). The terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1937 work Titres et Travaux ScientifiquesBOOK, Chatton, Édouard, Titres Et Travaux Scientifiques (1906-1937) De Edouard Chatton, 1937, Impr. E. Sottano., Sète, , Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in only one paragraph, and the idea was effectively ignored until Chatton's statement was rediscovered by Stanier and van Niel.JOURNAL, Sapp J, The prokaryote-eukaryote dichotomy: meanings and mythology, Microbiology and Molecular Biology Reviews, 69, 2, 292–305, June 2005, 15944457, 1197417, 10.1128/MMBR.69.2.292-305.2005, In 1905 and 1910, the Russian biologist Konstantin Mereschkowski (1855–1921) argued that plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic (heterotrophic) host that was itself formed by symbiosis between an amoeba-like host and a bacterium-like cell that formed the nucleus. Plants had thus inherited photosynthesis from cyanobacteria.JOURNAL, Martin WF, Garg S, Zimorski V, Endosymbiotic theories for eukaryote origin, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 370, 1678, 20140330, September 2015, 26323761, 4571569, 10.1098/rstb.2014.0330, In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in eukaryotic cells in her paper, On the origin of mitosing cells.JOURNAL, Sagan L, On the origin of mitosing cells, Journal of Theoretical Biology, 14, 3, 255–274, March 1967, 11541392, 10.1016/0022-5193(67)90079-3, Lynn Margulis, In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA. This helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts. In 1977, Woese and George Fox introduced a "third form of life", which they called the Archaebacteria; in 1990, Woese, Otto Kandler and Mark L. Wheelis renamed this the Archaea.In 1979, G. W. Gould and G. J. Dring suggested that the eukaryotic cell's nucleus came from the ability of Gram-positive bacteria to form endospores. In 1987 and later papers, Thomas Cavalier-Smith proposed instead that the membranes of the nucleus and endoplasmic reticulum first formed by infolding a prokaryote's plasma membrane. In the 1990s, several other biologists proposed endosymbiotic origins for the nucleus, effectively reviving Mereschkowski's theory.

Cell features

Eukaryotic cells are typically much larger than those of prokaryotes having a volume of around 10,000 times greater than the prokaryotic cell.JOURNAL, Deep-sea microorganisms and the origin of the eukaryotic cell,weblink Masashi, Yamaguchi, Cedric O'Driscoll, Worman, Jpn. J. Protozool., 47, 1,2, 2014, 29–48, They have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.

Internal membrane

(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.BOOK, Evolutionary Integration of Chloroplast Metabolism with the Metabolic Networks of the Cells, Burnap, Robert L., Vermaas, Willem F.J., vanc, Functional Genomics and Evolution of Photosynthetic Systems, Springer, 2011, 978-9400715332, 215,weblink Linka, Marc, Weber, Andreas P.M., Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle.BOOK, Marsh, Mark, Endocytosis, Oxford University Press, 2001, vii, 978-0-19-963851-2, It is probable that most other membrane-bound organelles are ultimately derived from such vesicles. Alternatively some products produced by the cell can leave in a vesicle through exocytosis.The nucleus is surrounded by a double membrane (commonly referred to as a nuclear membrane or nuclear envelope), with pores that allow material to move in and out.JOURNAL, Hetzer MW, The nuclear envelope, Cold Spring Harbor Perspectives in Biology, 2, 3, a000539, March 2010, 20300205, 2829960, 10.1101/cshperspect.a000539, Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum.WEB, Endoplasmic Reticulum (Rough and Smooth),weblink British Society for Cell Biology, 12 November 2017, In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.WEB, Golgi Apparatus,weblink British Society for Cell Biology, 12 November 2017, Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm.WEB, Lysosome,weblink British Society for Cell Biology, 12 November 2017, Peroxisomes are used to break down peroxide, which is otherwise toxic. Many protozoans have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. In higher plants, most of a cell's volume is taken up by a central vacuole, which mostly contains water and primarily maintains its osmotic pressure.

Mitochondria and plastids

(File:Mitochondrion structure.svg|thumb|upright=1.4|Simplified structure of a mitochondrion) Mitochondria are organelles found in all but one{{refn|group=note|name="Only1"|To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria.JOURNAL, 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, A Eukaryote without a Mitochondrial Organelle, Current Biology, 26, 10, 1274–1284, May 2016, 27185558, 10.1016/j.cub.2016.03.053, }} eukaryote. Mitochondria provide energy to the eukaryote cell by converting sugars into ATP.WEB,weblink Re: Are there eukaryotic cells without mitochondria?, 1 May 2006, madsci.org, Steve, Mack, They have two surrounding membranes, each a phospholipid bi-layer; the inner of which is folded into invaginations called cristae where aerobic respiration takes place.The outer mitochondrial membrane is freely permeable and allows almost anything to enter into the intermembrane space while the inner mitochondrial membrane is semi permeable so allows only some required things into the mitochondrial matrix.Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA.BOOK, Watson, James, Hopkins, Nancy, Roberts, Jeffery, Steitz, Joan Argetsinger, Weiner, Alan, vanc, Molecular Biology of the Gene, 1988, The Benjamin/Cummings Publishing Company, Inc., Menlo Park, CA, 978-0-8053-9614-0, 1154, Fourth, 28: The Origins of Life, They are now generally held to have developed from endosymbiotic prokaryotes, probably proteobacteria.Some eukaryotes, such as the metamonads such as Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes, and thus have lost their mitochondria secondarily. They obtain energy by enzymatic action on nutrients absorbed from the environment. The metamonad Monocercomonoides has also acquired, by lateral gene transfer, a cytosolic sulfur mobilisation system which provides the clusters of iron and sulfur required for protein synthesis. The normal mitochondrial iron-sulfur cluster pathway has been lost secondarily.WEB,weblink Scientists Shocked To Discover Eukaryote With NO Mitochondria, 13 May 2016, Davis, Josh L., IFL Science, 2016-05-13, Plants and various groups of algae also have plastids. Plastids also have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion.BOOK, Sato, N., 2006, 75–102, The Structure and Function of Plastids, 23, R.R. Wise, J.K. Hoober, Springer Netherlands, Origin and Evolution of Plastids: Genomic View on the Unification and Diversity of Plastids, 978-1-4020-4060-3, 10.1007/978-1-4020-4061-0_4, Advances in Photosynthesis and Respiration, The capture and sequestering of photosynthetic cells and chloroplasts occurs in many types of modern eukaryotic organisms and is known as kleptoplasty.Endosymbiotic origins have also been proposed for the nucleus, and for eukaryotic flagella.BOOK, Margulis L, Symbiotic planet: a new look at evolution, Basic Books, New York, 1998, 978-0-465-07271-2, 39700477, {{page needed|date=November 2017}}

Cytoskeletal structures

File:Chlamydomonas TEM 09.jpg|thumb|left|Longitudinal section through the flagellum of Chlamydomonas reinhardtiiChlamydomonas reinhardtiiMany eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Flagella and cilia are sometimes referred to as undulipodia,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}} 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 submembraneous cortical layers and bundles, as well. Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the network.Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups 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.BOOK, Vorobjev IA, Nadezhdina ES, The centrosome and its role in the organization of microtubules, 106, 227–293, 1987, 3294718, 10.1016/S0074-7696(08)61714-3, 978-0-12-364506-7, International Review of Cytology, The significance of cytoskeletal structures is underlined in the determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis and chemokinesis. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema.

Cell wall

The cells of plants and algae, fungi and most chromalveolates have a cell wall, a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.BOOK, Howland, John L., vanc, 2000, The Surprising Archaea: Discovering Another Domain of Life, 69–71, Oxford University Press, Oxford, 978-0-19-511183-5, The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.JOURNAL, Fry, Stephen C., The Structure and Functions of Xyloglucan, Journal of Experimental Botany, 40, 1, 1989, 1–11, 10.1093/jxb/40.1.1,

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 cellplant cellAll animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Due to the lack of a cell wall, animal cells can transform into a variety of shapes. A phagocytic cell can even engulf other structures.

Plant cell

Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:
  • A large central vacuole (enclosed by a membrane, the tonoplast), which maintains the cell's turgor and controls movement of molecules between the cytosol and sapJOURNAL, Raven, J.A., vanc, July 1987, The role of vacuoles, New Phytologist, 106, 3, 357–422, 10.1111/j.1469-8137.1987.tb00149.x,
  • A primary cell wall containing cellulose, hemicellulose and pectin, deposited by the protoplast on the outside of the cell membrane; this contrasts with the cell walls of fungi, which contain chitin, and the cell envelopes of prokaryotes, in which peptidoglycans are the main structural molecules
  • The plasmodesmata, pores in the cell wall that link adjacent cells and allow plant cells to communicate with adjacent cells.BOOK, Oparka K, 2005, Plasmodesmata, Blackwell Publishing, Oxford, UK, Animals have a different but functionally analogous system of gap junctions between adjacent cells.
  • Plastids, especially chloroplasts, organelles that contain chlorophyll, the pigment that gives plants their green color and allows them to perform photosynthesis
  • Bryophytes and seedless vascular plants only have flagellae and centrioles in the sperm cells.BOOK, Raven PH, Evert RF, Eichorm SE, 1999, Biology of Plants, W.H. Freeman, New York, Sperm of cycads and Ginkgo are large, complex cells that swim with hundreds to thousands of flagellae.JOURNAL, Silflow CD, Lefebvre PA, Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii, Plant Physiology, 127, 4, 1500–1507, December 2001, 11743094, 1540183, 10.1104/pp.010807,
  • Conifers (Pinophyta) and flowering plants (Angiospermae) lack the flagellae and centrioles 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 – spitzenkörperspitzenkörperThe cells of fungi are most similar to animal cells, with the following exceptions:BOOK, Deacon J, Fungal Biology, Blackwell Publishers, Cambridge, Massachusetts, 2005, 978-1-4051-3066-0, 4 and passim,
  • A cell wall that contains chitin
  • Less compartmentation between cells; the hyphae of higher fungi have porous partitions called septa, which allow the passage of cytoplasm, organelles, and, sometimes, nuclei. Primitive fungi have few or no septa, so each organism is essentially a giant multinucleate supercell; these fungi are described as coenocytic.
  • Only the most primitive fungi, chytrids, have flagella.

Other eukaryotic cells

Some groups of eukaryotes have unique organelles, such as the cyanelles (unusual chloroplasts) of the glaucophytes,JOURNAL, Keeling PJ, Diversity and evolutionary history of plastids and their hosts, American Journal of Botany, 91, 10, 1481–1493, October 2004, 21652304, 10.3732/ajb.91.10.1481,weblink the haptonema of the haptophytes, or the ejectosomes of the cryptomonads. Other structures, such as pseudopodia, are found in various eukaryote groups in different forms, such as the lobose amoebozoans or the reticulose foraminiferans.WEB,weblink David J. Patterson, Amoebae: Protists Which Move and Feed Using Pseudopodia, Tree of Life Web Project, 12 November 2017,

Reproduction

(File:Evolsex-dia1a.png|thumb|upright=1.4|This diagram illustrates the twofold cost of sex. If each individual were to contribute to the same number of offspring (two), (a) the sexual population remains the same size each generation, where the (b) asexual population doubles in size each generation.)Cell division generally takes place asexually by mitosis, a process that allows each daughter nucleus to receive one copy of each chromosome. Most eukaryotes also have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell and a diploid phase, wherein two copies of each chromosome are present in each cell. The diploid phase is formed by fusion of two haploid gametes to form a zygote, which may divide by mitosis or undergo chromosome reduction by meiosis. There is considerable variation in this pattern. Animals have no multicellular haploid phase, but each plant generation can consist of haploid and diploid multicellular phases.Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times.JOURNAL, Lane N, Energetics and genetics across the prokaryote-eukaryote divide, Biology Direct, 6, 1, 35, June 2011, 21714941, 3152533, 10.1186/1745-6150-6-35, The evolution of sexual reproduction may be a primordial and fundamental characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger proposed that facultative sex was present in the common ancestor of all eukaryotes.JOURNAL, Dacks J, Roger AJ, The first sexual lineage and the relevance of facultative sex, Journal of Molecular Evolution, 48, 6, 779–783, June 1999, 10229582, 10.1007/PL00013156, 1999JMolE..48..779D, 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.JOURNAL, Ramesh MA, Malik SB, Logsdon JM, A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis, Current Biology, 15, 2, 185–191, January 2005, 15668177, 10.1016/j.cub.2005.01.003, JOURNAL, Malik SB, Pightling AW, Stefaniak LM, Schurko AM, Logsdon JM, An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis, PLOS One, 3, 8, e2879, August 2007, 18663385, 2488364, 10.1371/journal.pone.0002879, Hahn, 2008PLoSO...3.2879M, Matthew W, Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, it was inferred that core meiotic genes, and hence sex, were likely present in a common ancestor of all eukaryotes. Eukaryotic species once thought to be asexual, such as parasitic protozoa of the genus Leishmania, have been shown to have a sexual cycle.JOURNAL, Akopyants NS, Kimblin N, Secundino N, Patrick R, Peters N, Lawyer P, Dobson DE, Beverley SM, Sacks DL, Demonstration of genetic exchange during cyclical development of Leishmania in the sand fly vector, Science, 324, 5924, 265–268, April 2009, 19359589, 2729066, 10.1126/science.1169464, 2009Sci...324..265A, 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.JOURNAL, Lahr DJ, Parfrey LW, Mitchell EA, Katz LA, Lara E, The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms, Proceedings: Biological Sciences, 278, 1715, 2081–2090, July 2011, 21429931, 3107637, 10.1098/rspb.2011.0289,

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 & prokaryotes)File:Eukaryota tree.svg|thumb|upright=1.4|One hypothesis of eukaryotic relationships. The Opisthokonta group includes both animals (Metazoa) and fungi. Plants (Plantae) are placed in ArchaeplastidaArchaeplastida(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 antiquity, the two lineages of animals and plants were recognized. They were given the taxonomic rank of Kingdom by Linnaeus. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980s.JOURNAL, Moore RT, 1980, Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts, Botanica Marina, 23, 361–373, The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word protozoa to refer to organisms such as ciliates,JOURNAL, Goldfuß, Ueber die Classification der Zoophyten, Isis, oder, Encyclopädische Zeitung von Oken, 1818, 2, 6, 1008–1019,weblink On the classification of zoophytes, German, 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.] and this group was expanded until it encompassed all single-celled eukaryotes, and given their own kingdom, the Protista, by Ernst Haeckel in 1866.JOURNAL, Scamardella, JM, Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista, 1999, International Microbiology, 2, 207–221,weblink yes,weblink" title="web.archive.org/web/20110614000656weblink">weblink 14 June 2011, JOURNAL, Rothschild LJ, Protozoa, Protista, Protoctista: what's in a name?, Journal of the History of Biology, 22, 2, 277–305, 1989, 11542176, 10.1007/BF00139515, Lynn J. Rothschild, The eukaryotes thus came to be composed of four kingdoms: The protists were understood to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really started with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, uniting all the eukaryote kingdoms under the eukaryote domain.JOURNAL, Woese CR, Kandler O, Wheelis ML, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proceedings of the National Academy of Sciences of the United States of America, 87, 12, 4576–4579, June 1990, 2112744, 54159, 10.1073/pnas.87.12.4576,weblink 1990PNAS...87.4576W, 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 grouping in the Archaea. The basal groupings are the Opimoda, Diphoda, the Discoba, and the Loukozoa. The Eukaryote root is usually assessed to be near or even in Discoba.A classification produced in 2005 for the International Society of Protistologists,JOURNAL, 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, 6, The new higher level classification of eukaryotes with emphasis on the taxonomy of protists, The Journal of Eukaryotic Microbiology, 52, 5, 399–451, 2005, 16248873, 10.1111/j.1550-7408.2005.00053.x, which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. However, in the same year (2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata,JOURNAL, Harper JT, Waanders E, Keeling PJ, On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes, International Journal of Systematic and Evolutionary Microbiology, 55, Pt 1, 487–496, January 2005, 15653923, 10.1099/ijs.0.63216-0,weblinkweblink" title="web.archive.org/web/20081217052013weblink">weblink 17 December 2008, and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.JOURNAL, Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA, Evaluating support for the current classification of eukaryotic diversity, PLoS Genetics, 2, 12, e220, December 2006, 17194223, 1713255, 10.1371/journal.pgen.0020220, A revised classification in 2012 recognizes five supergroups.{| class="wikitable"
Archaeplastida (or Primoplantae) >Embryophyte>Land plants, green algae, red algae, and glaucophytes
SAR supergroup >Heterokont>Stramenopiles (brown algae, diatoms, etc.), Alveolata, and Rhizaria (Foraminifera, Radiolaria, and various other amoeboid protozoa).
Excavata >| Various flagellate protozoa
Amoebozoa >| Most lobose amoeboids and slime molds
Opisthokonta >Animals, fungus>fungi, choanoflagellates, etc.
There are also smaller groups of eukaryotes whose position is uncertain or seems to fall outside the major groups â€“ in particular, Haptophyta, Cryptophyta, Centrohelida, Telonemia, Picozoa, Apusomonadida, Ancyromonadida, Breviatea, and the genus Collodictyon.JOURNAL, Khadidja, Romari, Daniel, Vaulot, vanc, 2004, Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences, Limnol Oceanogr, 49, 3, 784–798, 10.4319/lo.2004.49.3.0784, 2004LimOc..49..784R, Overall, it seems that, although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. As Roger & Simpson said in 2009 "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."JOURNAL, Roger AJ, Simpson AG, Evolution: revisiting the root of the eukaryote tree, Current Biology, 19, 4, R165–67, February 2009, 19243692, 10.1016/j.cub.2008.12.032, In an article published in Nature Microbiology in April 2016 the authors, "reinforced once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represent a tiny percentage of the world's biodiversity." They classified eukaryote "based on the inheritance of their information systems as opposed to lipid or other cellular structures." Jillian F. Banfield of the University of California, Berkeley and fellow scientists used a super computer to generate a diagram of a new tree of life based on DNA from 3000 species including 2,072 known species and 1,011 newly reported microbial organisms, whose DNA they had gathered from diverse environments.JOURNAL, 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, April 2016, A new view of the tree of life, Nature Microbiology, 1, 5, 16048, 10.1038/nmicrobiol.2016.48, 27572647, As the capacity to sequence DNA became easier, Banfield and team were able to do metagenomic sequencing â€“ "sequencing whole communities of organisms at once and picking out the individual groups based on their genes alone."WEB,weblink Wealth of unsuspected new microbes expands tree of life, Berkeley News, 11 April 2016, 2016-04-11, Sanders, Robert,

Phylogeny

The rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true crown), which was usually divided by the form of the mitochondrial cristae; see crown eukaryotes. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive; but this is now considered an artifact of long-branch attraction, and they are known to have lost them secondarily.JOURNAL, Tovar J, Fischer A, Clark CG, The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica, Molecular Microbiology, 32, 5, 1013–1021, June 1999, 10361303, 10.1046/j.1365-2958.1999.01414.x, JOURNAL, 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, An anaerobic mitochondrion that produces hydrogen, Nature, 434, 7029, 74–79, March 2005, 15744302, 10.1038/nature03343, 2005Natur.434...74B,weblink {{As of|2011}}, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup, so that Rhizaria is not one of the main eukaryote groups; also that the Amoebozoa and Opisthokonta are each monophyletic and form a clade, often called the unikonts.JOURNAL, Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J, Phylogenomics reshuffles the eukaryotic supergroups, PLOS One, 2, 8, e790, August 2007, 17726520, 1949142, 10.1371/journal.pone.0000790, Butler, 2007PLoSO...2..790B, Geraldine, JOURNAL, Burki F, Shalchian-Tabrizi K, Pawlowski J, Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes, Biology Letters, 4, 4, 366–369, August 2008, 18522922, 2610160, 10.1098/rsbl.2008.0224, JOURNAL, Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K, Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates, Genome Biology and Evolution, 1, 231–238, July 2009, 20333193, 2817417, 10.1093/gbe/evp022, JOURNAL, Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rümmele SE, Bhattacharya D, Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates, Molecular Biology and Evolution, 24, 8, 1702–1713, August 2007, 17488740, 10.1093/molbev/msm089, Rummele SE, Bhattacharya D, JOURNAL, Cavalier-Smith T, Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree, Biology Letters, 6, 3, 342–345, June 2010, 20031978, 2880060, 10.1098/rsbl.2009.0948, Thomas Cavalier-Smith, Beyond this, there does not appear to be a consensus.It has been estimated that there may be 75 distinct lineages of eukaryotes.JOURNAL, Jagus R, Bachvaroff TR, Joshi B, Place AR, Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists, Comparative and Functional Genomics, 2012, 1–21, 2012, 22778692, 3388326, 10.1155/2012/134839, Most of these lineages are protists.The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000–220,050 Mb in the dinoflagellate Prorocentrum micans, showing that the genome of the ancestral eukaryote has undergone considerable variation during its evolution. The last common ancestor of all eukaryotes is believed to have been a phagotrophic protist with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. Later endosymbiosis led to the spread of plastids in some lineages.

Five supergroups

A global tree of eukaryotes from a consensus of phylogenetic evidence (in particular, phylogenomics), rare genomic signatures, and morphological characteristics is presented in Adl et al. 2012 and Burki 2014/2016 with the Cryptophyta and picozoa having emerged within the Archaeplastida.JOURNAL, Burki F, The eukaryotic tree of life from a global phylogenomic perspective, Cold Spring Harbor Perspectives in Biology, 6, 5, a016147, May 2014, 24789819, 10.1101/cshperspect.a016147, 3996474, JOURNAL, Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ, Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista, Proceedings: Biological Sciences, 283, 1823, 20152802, January 2016, 26817772, 4795036, 10.1098/rspb.2015.2802,weblink JOURNAL, Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Rohwer FL, Mylnikov AP, Keeling PJ, A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction, Current Biology, 27, 23, 3717–24.e5, December 2017, 29174886, 10.1016/j.cub.2017.10.051, JOURNAL, Bodył A, Did some red alga-derived plastids evolve via kleptoplastidy? A hypothesis, Biological Reviews of the Cambridge Philosophical Society, 93, 1, 201–222, February 2018, 28544184, 10.1111/brv.12340, JOURNAL, Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AG, Roger AJ, Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group, Genome Biology and Evolution, 10, 2, 427–433, February 2018, 29360967, 5793813, 10.1093/gbe/evy014, JOURNAL, Lax G, Eglit Y, Eme L, Bertrand EM, Roger AJ, Simpson AG, Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes, Nature, 564, 7736, 410–414, November 2018, 30429611, 10.1038/s41586-018-0708-8, A similar inclusion of Glaucophyta, Cryptista (and also, unusually, Haptista) has also been made. {{Clade|{{clade|1={{clade|1=Hemimastigophora| label2=Diaphoretickes| 2={{clade|label1=Archaeplastida + Cryptista|1={{clade| 1={{cladeRed 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)
}}|3=Cryptista

}}| 2={{clade| 1={{clade
Haptista (File:Raphidiophrys contractilis.jpg>60 px)|2=Ancoracysta}}|label2=TSAR
|2={{clade
|1=Telonemia
SAR supergroup>SAR| 2={{clade| label1=Halvaria| 1={{cladeStramenopiles (File:Ochromonas.png>40 px)Alveolata (File:Ceratium furca.jpg>80 px)
}}
Rhizaria (File:Ammonia tepida.jpg>60 px)
}}
}}
}}
}}}}Discoba (File:Euglena mutabilis - 400x - 1 (10388739803) (cropped).jpg>55px)| label3=Amorphea| 3={{cladeAmoebozoa (File:Chaos carolinensis Wilson 1900.jpg>60 px)|label2=Obazoa| 2={{cladeApusomonadida (File:Apusomonas.png>60 px)| label2=Opisthokonta| 2={{cladeHolomycota (inc. fungi) (File:Asco1013.jpg>60 px)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, but in other ones it is nested inside the Archaeplastida.JOURNAL, Kim E, Graham LE, EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata, PLOS One, 3, 7, e2621, July 2008, 18612431, 2440802, 10.1371/journal.pone.0002621, Redfield, yes, 2008PLoSO...3.2621K, Rosemary Jeanne, However, several recent studies have concluded that Haptophyta and Cryptophyta do not form a monophyletic group.JOURNAL, Baurain D, Brinkmann H, Petersen J, Rodríguez-Ezpeleta N, Stechmann A, Demoulin V, Roger AJ, Burger G, Lang BF, Philippe H, Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles, Molecular Biology and Evolution, 27, 7, 1698–1709, July 2010, 20194427, 10.1093/molbev/msq059, yes, The former could be a sister group to the SAR group, the latter cluster with the Archaeplastida (plants in the broad sense).JOURNAL, Burki F, Okamoto N, Pombert JF, Keeling PJ, The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins, Proceedings: Biological Sciences, 279, 1736, 2246–2254, June 2012, 22298847, 3321700, 10.1098/rspb.2011.2301, yes, The division of the eukaryotes into two primary clades, bikonts (Archaeplastida + SAR + Excavata) and unikonts (Amoebozoa + Opisthokonta), derived from an ancestral biflagellar organism and an ancestral uniflagellar organism, respectively, had been suggested earlier.JOURNAL, Cavalier-Smith, T, vanc, Thomas Cavalier-Smith, Protist phylogeny and the high-level classification of Protozoa, European Journal of Protistology, 2006, 39, 4, 338–348, 10.1078/0932-4739-00002, JOURNAL, Burki F, Pawlowski J, Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts, Molecular Biology and Evolution, 23, 10, 1922–1930, October 2006, 16829542, 10.1093/molbev/msl055,weblink A 2012 study produced a somewhat similar division, although noting that the terms "unikonts" and "bikonts" were not used in the original sense.JOURNAL, Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K, Collodictyon – an ancient lineage in the tree of eukaryotes, Molecular Biology and Evolution, 29, 6, 1557–1568, June 2012, 22319147, 3351787, 10.1093/molbev/mss001, Dag Klaveness (limnologist), 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.JOURNAL, Ren R, Sun Y, Zhao Y, Geiser D, Ma H, Zhou X, Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes, Genome Biology and Evolution, 8, 9, 2683–2701, September 2016, 27604879, 5631032, 10.1093/gbe/evw196, JOURNAL, Derelle R, Torruella G, Klimeš V, Brinkmann H, Kim E, Vlček Č, Lang BF, Eliáš M, Bacterial proteins pinpoint a single eukaryotic root, Proceedings of the National Academy of Sciences of the United States of America, 112, 7, E693–699, February 2015, 25646484, 4343179, 10.1073/pnas.1420657112, 2015PNAS..112E.693D, JOURNAL, Yang J, Harding T, Kamikawa R, Simpson AG, Roger AJ, Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids, Genome Biology and Evolution, 9, 5, 1161–1174, May 2017, 28453770, 5421314, 10.1093/gbe/evx086, JOURNAL, Cavalier-Smith T, Fiore-Donno AM, Chao E, Kudryavtsev A, Berney C, Snell EA, Lewis R, Multigene phylogeny resolves deep branching of Amoebozoa, Molecular Phylogenetics and Evolution, 83, 293–304, February 2015, 25150787, 10.1016/j.ympev.2014.08.011, JOURNAL, 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, Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi, Current Biology, 25, 18, 2404–2410, September 2015, 26365255, 10.1016/j.cub.2015.07.053, The main remaining controversies are the root, and the exact positioning of the Rhodophyta and the bikonts Rhizaria, Haptista, Cryptista, Picozoa and Telonemia, many of which may be endosymbyotic eukaryote-eukaryote hybrids. Archaeplastida acquired chloroplasts probably by endosymbiosis of a prokaryotic ancestor related to a currently extant cyanobacterium, Gloeomargarita lithophora.JOURNAL, Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D, An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids, Current Biology, 27, 3, 386–391, February 2017, 28132810, 5650054, 10.1016/j.cub.2016.11.056, JOURNAL, de Vries J, Archibald JM, Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?, Current Biology, 27, 3, R103–105, February 2017, 28171752, 10.1016/j.cub.2016.12.006, JOURNAL, López-García P, Eme L, Moreira D, Symbiosis in eukaryotic evolution, Journal of Theoretical Biology, 434, 20–33, December 2017, 28254477, 5638015, 10.1016/j.jtbi.2017.02.031, {hide}Clade|{{clade|label1=Diphoda|1={{Clade
|2=Discoba
|label1=Diaphoretickes
|1={{clade
|1={{clade
Archaeplastida >sublabel1= (+ Gloeomargarita lithophora)
|1={{Clade
| 1=Glaucophyta|2={{clade|1=Rhodophyta
| 2=Viridiplantae
{edih}
}}|label2=Hacrobia| 2={hide}clade|1=Haptista| 2=Cryptista
{edih}
}}
SAR supergroup>SAR| 2={hide}clade|label1=Halvaria| 1={{clade| 1=Stramenopiles| 2=Alveolata
{edih}| 2=Rhizaria
}}
}}}}|label2=Opimoda|2={hide}clade|1=Metamonada|2={{clade|1=Ancyromonas|2={{clade|1=Malawimonas| label2=Podiata|2={{clade|label1=CRuMsVarisulca>Diphyllatea, Rigifilida, Mantamonas|label2=Amorphea|2={{clade| 1=Amoebozoa|label2=Obazoa|2={{clade|1=Breviata|2={{clade|1=Apusomonadida| 2=Opisthokonta
{edih}
}} }}}}}}}}}}}}|style=font-size:80%; line-height:80%|label1=Eukaryotes}}

Cavalier-Smith's tree

Thomas Cavalier-Smith 2010,JOURNAL, Cavalier-Smith T, Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree, Biology Letters, 6, 3, 342–345, June 2010, 20031978, 2880060, 10.1098/rsbl.2009.0948, 2013,JOURNAL, Cavalier-Smith T, Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa, European Journal of Protistology, 49, 2, 115–178, May 2013, 23085100, 10.1016/j.ejop.2012.06.001, 2014,JOURNAL, Cavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM, Lewis R, Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution, 81, 71–85, December 2014, 25152275, 10.1016/j.ympev.2014.08.012, 2017JOURNAL, Cavalier-Smith T, Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences, Protoplasma, 255, 1, 297–357, January 2018, 28875267, 5756292, 10.1007/s00709-017-1147-3, and 2018JOURNAL, Cavalier-Smith T, Chao EE, Lewis R, Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria, Protoplasma, 255, 5, 1517–1574, April 2018, 29666938, 6133090, 10.1007/s00709-018-1241-1, 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 endosymbyotic event of capturing a red-algae. He et alJOURNAL, He D, Fiz-Palacios O, Fu CJ, Fehling J, Tsai CC, Baldauf SL, An alternative root for the eukaryote tree of life, Current Biology, 24, 4, 465–470, February 2014, 24508168, 10.1016/j.cub.2014.01.036, specifically supports rooting eukaryotic tree between a monophyletic Discoba (Discicristata + Jakobida) and a Amorphea-Diaphoretickes clade.{hide}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=Tsukubamonas globosa
|2=Jakobea
{edih}
|label2=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
}}
}}
|label2=Scotokaryota
|sublabel2=Opimoda
|2={{Clade
|1=Malawimonas
|2={{Clade
|1=Metamonada
|label2=Podiata
|2={{Clade
|1=Ancyromonadida
|2={{Clade
|1={{Clade
|1=Mantamonas plastica
|2=Diphyllatea
}}
|label2=Amorphea
|2={{Clade
|1=Amoebozoa
|label2=Obazoa
|2={{Clade
|1=Breviatea
|2={{Clade
|1=Apusomonadida
|2=Opisthokonta
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}

Origin of eukaryotes

File:Eocyte hypothesis.png|thumb|upright=1.4|The three-domains tree and the Eocyte hypothesisEocyte hypothesisFile:Collapsed tree labels simplified.png|thumb|upright=1.4|Phylogenetic tree showing a possible relationship between the eukaryotes and other forms of life;JOURNAL, Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P, Toward automatic reconstruction of a highly resolved tree of life, Science, 311, 5765, 1283–1287, March 2006, 16513982, 10.1126/science.1123061, 2006Sci...311.1283C, 10.1.1.381.9514, eukaryotes are colored red, archaea green and bacteriabacteria(File:Phylogenetic Tree of Life.png|thumb|upright=1.4|Eocyte tree.)

Fossils

The origin of the eukaryotic cell is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The timing of this series of events is hard to determine; Knoll (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarchs are known from at least 1.65 billion years ago, and the possible alga Grypania has been found as far back as 2.1 billion years ago.JOURNAL, Knoll AH, Javaux EJ, Hewitt D, Cohen P, Eukaryotic organisms in Proterozoic oceans, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1470, 1023–1038, June 2006, 16754612, 1578724, 10.1098/rstb.2006.1843, The Geosiphon-like fossil fungus Diskagma has been found in paleosols 2.2 billion years old.JOURNAL, Retallack GJ, Krull ES, Thackray GD, Parkinson DH, Problematic urn-shaped fossils from a Paleoproterozoic (2.2 Ga) paleosol in South Africa., Precambrian Research, 2013, 235, 71–87, 10.1016/j.precamres.2013.05.015, 2013PreR..235...71R, Organized living structures have been found in the black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, dated at 2.1 billion years old. Eukaryotic life could have evolved at that time.JOURNAL, 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, Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago, Nature, 466, 7302, 100–104, July 2010, 20596019, 10.1038/nature09166, 2010Natur.466..100A, Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of a red alga, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back perhaps to 1.6 to 1.7 billion years ago.JOURNAL, Bengtson S, Belivanova V, Rasmussen B, Whitehouse M, The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older, Proceedings of the National Academy of Sciences of the United States of America, 106, 19, 7729–7734, May 2009, 19416859, 2683128, 10.1073/pnas.0812460106, 2009PNAS..106.7729B, Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of steranes in Australian shales indicates that eukaryotes were present in these rocks dated at 2.7 billion years old,JOURNAL, Brocks JJ, Logan GA, Buick R, Summons RE, Archean molecular fossils and the early rise of eukaryotes, Science, 285, 5430, 1033–1036, August 1999, 10446042, 10.1126/science.285.5430.1033, 10.1.1.516.9123, JOURNAL, Peter Ward (paleontologist), Ward P, Mass extinctions: the microbes strike back, New Scientist, 40–43, 9 Feb 2008,weblink although it was suggested they could originate from samples contamination.JOURNAL, French KL, Hallmann C, Hope JM, Schoon PL, Zumberge JA, Hoshino Y, Peters CA, George SC, Love GD, Brocks JJ, Buick R, Summons RE, Reappraisal of hydrocarbon biomarkers in Archean rocks, Proceedings of the National Academy of Sciences of the United States of America, 112, 19, 5915–5920, May 2015, 25918387, 10.1073/pnas.1419563112, 4434754, 2015PNAS..112.5915F, 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.JOURNAL, 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, 6, Tracking the rise of eukaryotes to ecological dominance with zinc isotopes, Geobiology, 16, 4, 341–352, June 2018, 29869832, 10.1111/gbi.12289, In April 2019, biologists reported that the very large medusavirus, or a relative, may have been responsible, at least in part, for the evolutionary emergence of complex eukaryotic cells from simpler prokaroytic cells.JOURNAL, Yoshikawa G, Blanc-Mathieu R, Song C, Kayama Y, Mochizuki T, Murata K, Ogata H, Takemura M, Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water, Journal of Virology, 93, 8, April 2019, 30728258, 6450098, 10.1128/JVI.02130-18,weblink EurekAlert!, 30 April 2019,

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 eubacterium, and the nucleus from an archaeon,JOURNAL, Martin W, Archaebacteria (Archaea) and the origin of the eukaryotic nucleus, Current Opinion in Microbiology, 8, 6, 630–637, December 2005, 16242992, 10.1016/j.mib.2005.10.004, from a virus,JOURNAL, Takemura M, Poxviruses and the origin of the eukaryotic nucleus, Journal of Molecular Evolution, 52, 5, 419–425, May 2001, 11443345, 10.1007/s002390010171, 2001JMolE..52..419T, JOURNAL, Bell PJ, Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?, Journal of Molecular Evolution, 53, 3, 251–256, September 2001, 11523012, 10.1007/s002390010215, 2001JMolE..53..251L, or from a pre-cell.JOURNAL, Wächtershäuser G, From pre-cells to Eukarya – a tale of two lipids, Molecular Microbiology, 47, 1, 13–22, January 2003, 12492850, 10.1046/j.1365-2958.2003.03267.x, JOURNAL, Wächtershäuser G, From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1474, 1787–1806; discussion 1806–1808, October 2006, 17008219, 1664677, 10.1098/rstb.2006.1904,
  • Eukaryotes developed from Archaea, and acquired their eubacterial characteristics through the endosymbiosis of a proto-mitochondrion of eubacterial origin.BOOK, Lane, Nick, Nick Lane, The Vital Question: Why is Life the Way it is?, 2016, Profile Books, 978-1-781-25037-2, paperback, 157–91, The Vital Question,
  • Eukaryotes and Archaea developed separately from a modified eubacterium.
(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.JOURNAL, Egel R, Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life, Life, 2, 1, 170–212, January 2012, 25382122, 4187143, 10.3390/life2010170, )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.JOURNAL, Hartman H, Fedorov A, The origin of the eukaryotic cell: a genomic investigation, Proceedings of the National Academy of Sciences of the United States of America, 99, 3, 1420–1425, February 2002, 11805300, 122206, 10.1073/pnas.032658599, 2002PNAS...99.1420H,
  • The universal common ancestor (UCA) of the current tree of life was a complex organism that survived a mass extinction event rather than an early stage in the evolution of life. Eukaryotes and in particular akaryotes (Bacteria and Archaea) evolved through reductive loss, so that similarities result from differential retention of original features.
Assuming no other group is involved, there are three possible phylogenies for the Bacteria, Archaea and Eukaryota in which each is monophyletic. These are labelled 1 to 3 in the table below. The eocyte hypothesis is a modification of hypothesis 2 in which the Archaea are paraphyletic. (The table and the names for the hypotheses are based on Harish and Kurland, 2017.){| class="wikitable"|+ Alternative hypotheses for the base of the tree of life! 1 – Two empires !! 2 – Three domains !! 3 – Gupta !! 4 – Eocytestyle=line-height:100%|label1=UCA |1={{clade
|1={{clade
|1=Archaea
|2=Bacteria
{edih}
|2=Eukaryota
}}
}}style=line-height:100%|label1=UCA |1={{clade
|1={{clade
|1=Eukaryota
|2=Archaea
{edih}
|2=Bacteria
}}
}}style=line-height:100%|label1=UCA |1={{clade
|1={{clade
|1=Eukaryota
|2=Bacteria
{edih}
|2=Archaea
}}
}}style=line-height:100%|label1=UCA |1={{clade
|1={{clade
|1={{clade
|1=Eukaryota
|2=Archaea-Crenarchaeota
{edih}
|2=Archaea-Euryarchaeota
}}
|2=Bacteria
}}
}}In recent years, most researchers have favoured either the three domains (3D) or the eocyte hypotheses. An rRNA analyses supports the eocyte scenario, apparently with the Eukaryote root in Excavata. A cladogram supporting the eocyte hypothesis, positioning eukaryotes within Archaea, based on phylogenomic analyses of the Asgard archaea, is:JOURNAL, Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, 521, 7551, 173–179, May 2015, 25945739, 4444528, 10.1038/nature14447, 2015Natur.521..173S, JOURNAL, 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, Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, 541, 7637, 353–358, January 2017, 28077874, 10.1038/nature21031, 2017Natur.541..353Z, JOURNAL, Liu Y, Zhou Z, Pan J, Baker BJ, Gu JD, Li M, Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota, The ISME Journal, 12, 4, 1021–1031, April 2018, 29445130, 5864231, 10.1038/s41396-018-0060-x, {hide}Clade|{{Clade
| label1=TACK
| 1={{Clade
| 1=Korarchaeota
| 2={{Clade
| 1=Crenarchaeota
| 2={{Clade
| 1={{Clade |1=Aigarchaeota|2=Geoarchaeota{edih}
| 2={{Clade |1=Thaumarchaeota |2=Bathyarchaeota}} }} }} }}
| label2=Asgard
| 2={{Clade
|1=Lokiarchaeota |2=Odinarchaeota |3=Thorarchaeota
| 4={{Clade |1=Heimdallarchaeota
| label2=(+α─Proteobacteria)
|2=Eukaryota }} }} }}|style=font-size:80%; line-height:80%|label1=Proteoarchaeota}}
In this scenario, the Asgard group is seen as a sister taxon of the TACK group, which comprises Crenarchaeota (formerly named eocytes), Thaumarchaeota, and others.In 2017, there has been 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).JOURNAL, Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P, Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes, PLoS Genetics, 13, 6, e1006810, June 2017, 28604769, 5484517, 10.1371/journal.pgen.1006810, 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.JOURNAL, Harish A, Kurland CG, Empirical genome evolution models root the tree of life, Biochimie, 138, 137–155, July 2017, 28478110, 10.1016/j.biochi.2017.04.014, JOURNAL, Harish A, Kurland CG, Akaryotes and Eukaryotes are independent descendants of a universal common ancestor, Biochimie, 138, 168–183, July 2017, 28461155, 10.1016/j.biochi.2017.04.013, 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.JOURNAL, Harish A, Tunlid A, Kurland CG, Rooted phylogeny of the three superkingdoms, Biochimie, 95, 8, 1593–1604, August 2013, 23669449, 10.1016/j.biochi.2013.04.016,

Endomembrane system and mitochondria

The origins of the endomembrane system and mitochondria are also unclear.BOOK, Jékely G, 607, 38–51, 2007, 17977457, 10.1007/978-0-387-74021-8_3, 978-0-387-74020-1, Advances in Experimental Medicine and Biology, Eukaryotic Membranes and Cytoskeleton, Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios, 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.JOURNAL, Cavalier-Smith T, The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, International Journal of Systematic and Evolutionary Microbiology, 52, Pt 2, 297–354, March 2002, 11931142, 10.1099/00207713-52-2-297,weblink 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).JOURNAL, Martin W, Müller M, The hydrogen hypothesis for the first eukaryote, Nature, 392, 6671, 37–41, March 1998, 9510246, 10.1038/32096, 1998Natur.392...37M, In a study using genomes to construct supertrees, Pisani et al. (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy between an archaea closely related to Thermoplasmatales and an α-proteobacterium, likely a symbiosis driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont.JOURNAL, Pisani D, Cotton JA, McInerney JO, Supertrees disentangle the chimerical origin of eukaryotic genomes, Molecular Biology and Evolution, 24, 8, 1752–1760, August 2007, 17504772, 10.1093/molbev/msm095,

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.|360px}}Autogenous models propose that a proto-eukaryotic cell containing a nucleus existed first, and later acquired mitochondria.According to this model, a large prokaryote developed invaginations in its plasma membrane in order to obtain enough surface area to service its cytoplasmic volume. As the invaginations differentiated in function, some became separate compartments â€“ giving rise to the endomembrane system, including the endoplasmic reticulum, golgi apparatus, nuclear membrane, and single membrane structures such as lysosomes.JOURNAL, Ayala J, Transport and internal organization of membranes: vesicles, membrane networks and GTP-binding proteins, Journal of Cell Science, 107 ( Pt 4), 107, 753–763, April 1994, 8056835,weblink Mitochondria are proposed to come from the endosymbiosis of an aerobic proteobacterium, and it is assumed that all the eukaryotic lineages that did not acquire mitochondria became extinct.WEB, Martin, William F., vanc, The Origin of Mitochondria,weblink Scitable, Nature education, 2013-03-27, Chloroplasts came about from another endosymbiotic event involving cyanobacteria. Since all eukaryotes have mitochondria, but not all have chloroplasts, the serial endosymbiosis theory proposes that mitochondria came first.

Chimeric models

Chimeric models claim that two prokaryotic cells existed initially – an archaeon and a bacterium. The closest living relatives of these appears to be Asgardarchaeota and (distantly related) the alphaproteobacteria.JOURNAL, Dacks JB, Field MC, Evolutionary origins and specialisation of membrane transport, Current Opinion in Cell Biology, 53, 70–76, August 2018, 29929066, 6141808, 10.1016/j.ceb.2018.06.001, JOURNAL, Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ, Deep mitochondrial origin outside the sampled alphaproteobacteria, Nature, 557, 7703, 101–105, May 2018, 29695865, 10.1038/s41586-018-0059-5,weblink The Scientist, These cells underwent a merging process, either by a physical fusion or by endosymbiosis, thereby leading to the formation of a eukaryotic cell. Within these chimeric models, some studies further claim that mitochondria originated from a bacterial ancestor while others emphas ize the role of endosymbiotic processes behind the origin of mitochondria.The inside-out hypothesis, developed by cousins David and Buzz Baum, suggest the fusion between a free-living mitochondria-like bacteria and an archaea into an eykaryotic cell happened gradually over a long period of time, instead of phagocytosis in a single gulp. In this scenario an archaea would trap aerobic bacteria with cell protrusions, and then keeping 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 archaea wouldn't have to provide them with all the required nutrients. But eventually the archaea would engulf the bacteria completely, creating the internal membrane structures and nucleus membrane in the process.JOURNAL, Baum DA, Baum B, An inside-out origin for the eukaryotic cell, BMC Biology, 12, 76, October 2014, 25350791, 4210606, 10.1186/s12915-014-0076-2,weblink University of Wisconsin-Madison, It is assumed the archaean group called halophiles went through a similar procedure, where they acquired as much as a thousand genes from a bacterium, way more than through the conventional horizontal gene transfer that often occurs in the microbial world, but that the two microbes separated again before they had fused into a single eukaryote-like cell.WEB, Lucas, Brouwers, vanc, 12 April 2013,weblink How genetic plunder transformed a microbe into a pink, salt-loving scavenger, Scientific American, Based on the process of mutualistic symbiosis, the hypotheses can be categorized as – the serial endosymbiotic theory (SET),BOOK, Margulis L, Origin of Eukaryotic Cells., 1970, Yale University Press, New Haven, London, BOOK, Margulis L, Symbiosis in Cell Evolution., 1993, W.H. Freeman, New York, JOURNAL, Margulis L, Dolan MF, Guerrero R, The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists, Proceedings of the National Academy of Sciences of the United States of America, 97, 13, 6954–6959, June 2000, 10860956, 34369, 10.1073/pnas.97.13.6954, 2000PNAS...97.6954M, the hydrogen hypothesis (mostly a process of symbiosis where hydrogen transfer takes place among different species), and the syntrophy hypothesis.JOURNAL, Moreira D, Lopez-Garcia P, Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis, Journal of Molecular Evolution, 47, 5, 517–530, November 1998, 9797402, 10.1007/PL00006408, 1998JMolE..47..517M, JOURNAL, López-García P, Moreira D, Selective forces for the origin of the eukaryotic nucleus, BioEssays, 28, 5, 525–533, May 2006, 16615090, 10.1002/bies.20413, An expanded version of the hypothesis that the eukaryotic cell was created by physical interactions between two prokarytic organisms is that the last common ancestor of eukaryotes got its genome from a whole population or comminity 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 for their own benefit, occasionally leading to horizontal gene transfer between them. This accumulation of beneficial genes gave rise to the genome of the eukaryotic cell, which contained all the genes required for independence.Researchers Rethink the Ancestry of Complex Cells - Quanta MagazineAccording to serial endosymbiotic theory (championed by Lynn Margulis), a union between a motile anaerobic bacterium (like Spirochaeta) and a thermoacidophilic crenarchaeon (like Thermoplasma which is sulfidogenic in nature) gave rise to the present day eukaryotes. This union established a motile organism capable of living in the already existing acidic and sulfurous waters. Oxygen is known to cause toxicity to organisms that lack the required metabolic machinery. Thus, the archaeon provided the bacterium with a highly beneficial reduced environment (sulfur and sulfate were reduced to sulfide). In microaerophilic conditions, oxygen was reduced to water thereby creating a mutual benefit platform. The bacterium on the other hand, contributed the necessary fermentation products and electron acceptors along with its motility feature to the archaeon thereby gaining a swimming motility for the organism. From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the motile features of eukaryotic cells. Endosymbiotic unifications of the ancestors of alpha-proteobacteria and cyanobacteria, led to the origin of mitochondria and plastids respectively. For example, Thiodendron has been known to have originated via an ectosymbiotic process based on a similar syntrophy of sulfur existing between the two types of bacteria – Desulphobacter and Spirochaeta. However, such an association based on motile symbiosis have never been observed practically. Also there is no evidence of archaeans and spirochetes adapting to intense acid-based environments.BOOK, Latorre A, Durban A, Moya A, Pereto J,weblink The role of symbiosis in eukaryotic evolution, Origins and Evolution of Life: An Astrobiological Perspective, Gargaud, Muriel, López-Garcìa, Purificación, Martin, Hervé, vanc, 2011, Cambridge, Cambridge University Press, 326–339, 978-0-521-76131-4, In the hydrogen hypothesis, the symbiotic linkage of an anaerobic and autotrophic methanogenic archaeon (host) with an alpha-proteobacterium (the symbiont) gave rise to the eukaryotes. The host utilized hydrogen (H2) and carbon dioxide ({{CO2}}) to produce methane while the symbiont, capable of aerobic respiration, expelled H2 and {{CO2}} as byproducts of anaerobic fermentation process. The host's methanogenic environment worked as a sink for H2, which resulted in heightened bacterial fermentation. Endosymbiotic gene transfer (EGT) acted as a catalyst for the host to acquire the symbionts' carbohydrate metabolism and turn heterotrophic in nature. Subsequently, the host's methane forming capability was lost. Thus, the origins of the heterotrophic organelle (symbiont) are identical to the origins of the eukaryotic lineage. In this hypothesis, the presence of H2 represents the selective force that forged eukaryotes out of prokaryotes.{{citation needed |date=March 2017}}The syntrophy hypothesis was developed in contrast to the hydrogen hypothesis and proposes the existence of two symbiotic events. According to this theory, the origin of eukaryotic cells was based on metabolic symbiosis (syntrophy) between a methanogenic archaeon and a delta-proteobacterium. This syntrophic symbiosis was initially facilitated by H2 transfer between different species under anaerobic environments. In earlier stages, an alpha-proteobacterium became a member of this integration, and later developed into the mitochondrion. Gene transfer from a delta-proteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus. The archaeon constituted the genetic apparatus, while the delta-proteobacterium contributed towards the cytoplasmic features. This theory incorporates two selective forces at the time of nucleus evolution – (a) presence of metabolic partitioning to avoid the harmful effects of the co-existence of anabolic and catabolic cellular pathways, and (b) prevention of abnormal protein biosynthesis due to a vast spread of introns in the archaeal genes after acquiring the mitochondrion and losing methanogenesis.{{citation needed |date=March 2017}}

6+ serial endosymbiosis scenario

Pitts and Galbanón propose a complex scenario of 6+ serial endosymbiotic events of Archaea and bacteria in which mitochondria and an asgard related archaeota were acquired at a late stage of eukaryogenesis, possibly in combination, as a secondary endosymbiote.JOURNAL, Pittis AA, Gabaldón T, Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry, Nature, 531, 7592, 101–104, March 2016, 26840490, 4780264, 10.1038/nature16941, 2016Natur.531..101P, BOOK,weblink Evolution since Coding: Cradles, Halos, Barrels, and Wings, Burton, Zachary F., vanc, 1 August 2017, Academic Press, 9780128130346, The findings have been rebuked as an artefact.JOURNAL, Martin WF, Roettger M, Ku C, Garg SG, Nelson-Sathi S, Landan G, Late Mitochondrial Origin Is an Artifact, Genome Biology and Evolution, 9, 2, 373–379, February 2017, 28199635, 5516564, 10.1093/gbe/evx027,

See also

{{Wikipedia books}}

References

{{Reflist}}{{NCBI-scienceprimer}}{{dead link|date=March 2017}}

Notes

{{reflist|group=note}}

External links

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