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{{Short description|Domain of life whose cells have nuclei}}
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* Eukarya {{au|[[Lynn Margulis|Margulis]] 1996}}<ref name="Margulis 1996"/>
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The '''eukaryotes''' ({{IPAc-en|j|uː|ˈ|k|ær|i|oʊ|t|s|,_|-|ə|t|s}} {{respell|yoo|KARR|ee|ohts|,_|-|əts}})<ref>{{Cite Merriam-Webster|eukaryote|accessdate=2024-05-12}}</ref> constitute the [[Domain (biology)|domain]] of '''Eukarya
The eukaryotes seemingly emerged
Eukaryotic cells contain [[organelle|membrane-bound organelles]] such as the [[cell nucleus|nucleus]], the [[endoplasmic reticulum]], and the [[Golgi apparatus]]. Eukaryotes may be either [[Unicellular organism|unicellular]] or [[Multicellular organism|multicellular]]. In comparison, prokaryotes are typically unicellular. Unicellular eukaryotes are sometimes called [[protist]]s. Eukaryotes can reproduce both [[asexual reproduction|asexually]] through [[mitosis]] and [[Sexual reproduction|sexually]] through [[meiosis]] and [[gamete]] fusion ([[fertilization]]).
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Mitochondria contain [[Mitochondrial DNA|their own DNA]], which has close structural similarities to [[bacterial DNA]], from which it originated, 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, California |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>
Some eukaryotes, such as the [[metamonad]]s ''[[Giardia]]'' and ''[[Trichomonas]]'', and the amoebozoan ''[[Pelomyxa]]'', appear to lack mitochondria, but all contain mitochondrion-derived organelles, like [[hydrogenosome]]s or [[mitosome]]s, having lost their mitochondria secondarily.<ref name="Karn"/> They obtain energy by enzymatic action in the cytoplasm.<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><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=3 |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 |bibcode=2016CBio...26.1274K }}</ref>
=== Plastids ===
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Eukaryotes 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, with two copies of each chromosome in each cell. The diploid phase is formed by fusion of two haploid gametes, such as [[Egg cell|eggs]] and [[spermatozoa]], to form a [[zygote]]; this may grow into a body, with its cells dividing by [[mitosis]], and at some stage produce haploid gametes through [[meiosis]], a division that reduces the number of chromosomes and creates [[genetic variability]].<ref>{{cite book |last=Hamilton |first=Matthew B. |name-list-style=vanc |title=Population genetics |url=https://archive.org/details/populationgeneti00hami |url-access=limited |year=2009 |publisher=[[Wiley-Blackwell]] |isbn=978-1-4051-3277-0 |page=[https://archive.org/details/populationgeneti00hami/page/n69 55]}}</ref> There is considerable variation in this pattern. Plants have both [[alternation of generations|haploid and diploid multicellular phases]].<ref>{{cite journal |last1=Taylor |first1=TN |last2=Kerp |first2=H |last3=Hass |first3=H |name-list-style=vanc |year=2005 |title=Life history biology of early land plants: Deciphering the gametophyte phase |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=102 |issue=16 |pages=5892–5897 |doi=10.1073/pnas.0501985102 |pmid=15809414 |pmc=556298 |doi-access=free }}</ref> Eukaryotes have lower metabolic rates and longer generation times than prokaryotes, because they are larger and therefore have a smaller surface area to volume ratio.<ref name="Lane2011">{{cite journal |vauthors=Lane N |authorlink=Nick Lane |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 |doi-access=free }}</ref>
The [[evolution of sexual reproduction]] may be a primordial characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and [[Andrew J. Roger|Roger]] have proposed that facultative sex was present in the group's common ancestor.<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 |bibcode=2005CBio...15..185R }}</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, core meiotic genes, and hence sex, were likely present in the common ancestor of eukaryotes.<ref name=Ramesh/><ref name=Malik/> Species once thought to be asexual, such as ''[[Leishmania]]'' parasites, 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> Amoebae, previously regarded as asexual, are anciently sexual; present-day asexual groups likely arose recently.<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>
== Evolution ==
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[[File:Symbiogenesis 2 mergers.svg|thumb|upright=1.5|In the theory of [[symbiogenesis]], a merger of an [[archaea]]n and an aerobic bacterium created the eukaryotes, with aerobic [[Mitochondrion|mitochondria]]; a second merger added [[chloroplast]]s, creating the [[Viridiplantae|green plants]].<ref name=latorre/>]]
The origin of the eukaryotic cell, or ''eukaryogenesis'', is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The [[last eukaryotic common ancestor]] (LECA) is the hypothetical origin of all living eukaryotes,<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> and was most likely a [[Population|biological population]], not a single individual.<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 |bibcode=2019NatEE...3..338O |hdl-access=free |s2cid=67790751 |hdl=10261/201794 }}</ref> The LECA is believed to have been a protist with a nucleus, at least one [[centriole]] and [[flagellum]], facultatively aerobic mitochondria, sex ([[meiosis]] and [[syngamy]]), a dormant [[cyst]] with a cell wall of [[chitin]] or [[cellulose]], and [[peroxisome]]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 |bibcode=2020CBio...30.R510L }}</ref><ref name="RedAlgalDerivedPlastids">{{cite journal |vauthors=Strassert JF, Irisarri I, Williams TA, Burki F |title=A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids |journal=Nature Communications |volume=12 |issue=1 |pages=1879 |date=March 2021 |pmid=33767194 |pmc=7994803 |doi=10.1038/s41467-021-22044-z |bibcode=2021NatCo..12.1879S |doi-access=free }}</ref><ref name="Koumandou Wickstead Ginger van der Giezen 2013">{{cite journal |last1=Koumandou |first1=V. Lila |last2=Wickstead |first2=Bill |last3=Ginger |first3=Michael L. |last4=van der Giezen |first4=Mark |last5=Dacks |first5=Joel B. |last6=Field |first6=Mark C. |name-list-style=vanc |title=Molecular paleontology and complexity in the last eukaryotic common ancestor |journal=Critical Reviews in Biochemistry and Molecular Biology |volume=48 |issue=4 |year=2013 |doi=10.3109/10409238.2013.821444 |pages=373–396|pmid=23895660 |pmc=3791482 }}</ref>
An [[Symbiogenesis|endosymbiotic union]] between a motile [[anaerobic organism|anaerobic]] archaean and an aerobic [[Alphaproteobacteria|alphaproteobacterium]] gave rise to the LECA and all eukaryotes, with [[mitochondrion|mitochondria]]. A second, much later endosymbiosis with a cyanobacterium gave rise to the ancestor of plants, with [[chloroplast]]s.<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>
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=== Fossils ===
The timing of the origin of eukaryotes is hard to determine but the discovery of ''Qingshania magnificia'', the earliest multicelluar eukaryote from North China which lived during 1.635 billion years ago, suggests that the crown group eukaryotes would have originated from the late [[Paleoproterozoic]] ([[Statherian]]); the earliest unequivocal unicellular eukaryotes which lived during approximately 1.65 billion years ago are also discovered from North China: ''Tappania plana'', ''Shuiyousphaeridium macroreticulatum'', ''Dictyosphaera macroreticulata'', ''Germinosphaera alveolata'', and ''Valeria lophostriata''.<ref>{{Cite journal|last1=Miao |first1=L. |last2=Yin |first2=Z. |last3=Knoll |first3=A. H. |last4=Qu |first4=Y. |last5=Zhu |first5=M. |title=1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China |year=2024 |journal=Science Advances |volume=10 |issue=4 |pages=eadk3208 |doi=10.1126/sciadv.adk3208 |doi-access=free |pmid=38266082 |pmc=10807817 |bibcode=2024SciA...10K3208M }}</ref>
Some [[acritarch]]s are known from at least 1.65 billion years ago, and a fossil, ''[[Grypania]]'', which may be an alga, is as much as 2.1 billion years old.<ref name="Han">{{cite journal |vauthors=Han TM, Runnegar B |title=Megascopic eukaryotic algae from the 2.1-billion-year-old negaunee iron-formation, Michigan |journal=Science |volume=257 |issue=5067 |pages=232–5 |date=July 1992 |pmid=1631544 |doi=10.1126/science.1631544 |bibcode=1992Sci...257..232H |url=}}</ref><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 [[Incertae sedis|"problematic"]]<ref name="Retallack 2013"/><!--in case adj is challenged--> fossil ''[[Diskagma]]'' has been found in [[paleosol]]s 2.2 billion years old.<ref name="Retallack 2013">{{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>
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[[File:Diskagma butonii.jpg|thumb|left|Reconstruction of the problematic<ref name="Retallack 2013"/> ''[[Diskagma buttonii]]'', a terrestrial fossil less than 1mm high, from rocks around 2.2 billion years old]]
Structures proposed to represent "large colonial organisms" have been found in the [[black shale]]s of the [[Palaeoproterozoic]] such as the [[Francevillian B Formation]], in [[Gabon]], dubbed the "[[Francevillian biota]]" which is dated at 2.1 billion years old.<ref name="El Albani Bengtson Canfield 2010">{{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 |display-authors=3 |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><ref name="El Albani 2023">{{cite journal |title=A search for life in Palaeoproterozoic marine sediments using Zn isotopes and geochemistry |last=El Albani |first=Abderrazak |journal=Earth and Planetary Science Letters |year=2023 |volume=623 |page=118169 |doi=10.1016/j.epsl.2023.118169|bibcode=2023E&PSL.61218169E |s2cid=258360867 |doi-access=free |url=https://hal.science/hal-04095643/file/El%20Albani%20et%20al._EPSL_2023.pdf }}</ref> However, the status of these structures as fossils is contested, with other authors suggesting that they might represent [[pseudofossil]]s.<ref name="Ossa Ossa Pons Bekker Hofmann 2023">{{cite journal | last1=Ossa Ossa | first1=Frantz | last2=Pons | first2=Marie-Laure | last3=Bekker | first3=Andrey | last4=Hofmann | first4=Axel | last5=Poulton | first5=Simon W. | last6=Andersen | first6=Morten B. | last7=Agangi | first7=Andrea | last8=Gregory | first8=Daniel | last9=Reinke | first9=Christian | last10=Steinhilber | first10=Bernd | last11=Marin-Carbonne | first11=Johanna | last12=Schoenberg | first12=Ronny | display-authors=5 | title=Zinc enrichment and isotopic fractionation in a marine habitat of the c. 2.1 Ga Francevillian Group: A signature of zinc utilization by eukaryotes? | journal=Earth and Planetary Science Letters | volume=611 | date=2023 | doi=10.1016/j.epsl.2023.118147 | page=118147| doi-access=free | bibcode=2023E&PSL.61118147O | url=https://eprints.whiterose.ac.uk/197720/8/1-s2.0-S0012821X23001607-main.pdf }}</ref> The oldest fossils than can unambiguously be assigned to eukaryotes are from the Ruyang Group of China, dating to approximately 1.8-1.6 billion years ago.<ref>{{Cite journal |last1=Fakhraee |first1=Mojtaba |last2=Tarhan |first2=Lidya G. |last3=Reinhard |first3=Christopher T. |last4=Crowe |first4=Sean A. |last5=Lyons |first5=Timothy W. |last6=Planavsky |first6=Noah J. |date=May 2023 |title=Earth's surface oxygenation and the rise of eukaryotic life: Relationships to the Lomagundi positive carbon isotope excursion revisited
The presence of [[sterane]]s, eukaryotic-specific [[Biomarker (petroleum)|biomarkers]], 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 magazine |vauthors=Ward P |title=Mass extinctions: the microbes strike back |magazine=[[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 |authorlink=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> but these Archaean biomarkers have been 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> The oldest valid biomarker records are only around 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 |url=https://resolver.caltech.edu/CaltechAUTHORS:20170407-083556533 }}</ref> The nature of steranes as eukaryotic biomarkers is further complicated by the production of [[sterol]]s 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 |authorlink3=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 |doi-access=free }}</ref>
Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive increase in the [[Abiogenesis#Zinc world|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=3 |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 |bibcode=2018Gbio...16..341I |doi-access=free }}</ref>
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