Editing Three-domain system (section)

==Alternatives==
[[File:3 domains.png|thumb|330px|Alternative versions of the three domains of life's phylogeny]]
Parts of the three-domain theory have been challenged by scientists including [[Ernst Mayr]], [[Thomas Cavalier-Smith]], and [[Radhey S. Gupta]].<ref name=Gupta1998>{{cite journal | last1=Gupta | first1=Radhey S. | year=1998 | title=Life's Third Domain (''Archaea''): An Established Fact or an Endangered Paradigm?: A New Proposal for Classification of Organisms Based on Protein Sequences and Cell Structure.| journal=Theoretical Population Biology | volume=54 | issue=2| pages=91–104 | doi=10.1006/tpbi.1998.1376 | pmid=9733652| bibcode=1998TPBio..54...91G }}</ref><ref>{{cite journal | last1=Mayr | first1=E. | year=1998 | title=Two empires or three? | journal=Proc. Natl. Acad. Sci. USA | volume=95 | issue=17| pages=9720–9723 | doi=10.1073/pnas.95.17.9720 | pmid=9707542 | pmc=33883| bibcode=1998PNAS...95.9720M | doi-access=free }}</ref><ref>{{cite journal | last1=Cavalier-Smith | first1=Thomas |author-link=Thomas Cavalier-Smith | year=2002 | title=The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | pmid=11837318| journal=Int J Syst Evol Microbiol | volume=52 | issue=1| pages=7–76 | doi=10.1099/00207713-52-1-7| doi-access=free }}</ref>

Recent work has proposed that Eukaryota may have actually branched off from the domain Archaea. According to Spang ''et al.'', [[Lokiarchaeota]] forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.<ref>{{cite journal | last1=Spang | first1=Anja | year=2015 |  title=Complex archaea that bridge the gap between prokaryotes and eukaryotes | journal=Nature | volume=521 | issue=7551 | pages=173–179 | doi=10.1038/nature14447 | pmid=25945739 | pmc=4444528| bibcode=2015Natur.521..173S }}</ref> This work suggests a [[two-domain system]] as opposed to the three-domain system.<ref name=":02" /><ref name=":3" /><ref name="Gabaldón">{{cite journal |last1=Gabaldón |first1=Toni |title=Origin and Early Evolution of the Eukaryotic Cell |journal=Annual Review of Microbiology |date=8 October 2021 |volume=75 |issue=1 |pages=631–647 |doi=10.1146/annurev-micro-090817-062213 |pmid=34343017 |s2cid=236916203 |url=https://doi.org/10.1146/annurev-micro-090817-062213 |access-date=11 August 2022 |language=en |issn=0066-4227 |quote="A rooted version of this three-domain tree placed Archaea and Eukarya as sister clades, suggesting that eukaryotes were very distantly related to archaea and not more related to any specific group. More recently, phylogenetic analyses using more sophisticated models and expanded gene data sets have provided increasing support for an alternative tree topology in which the eukaryotic clade branches within Archaea, rather than next to it." }}</ref> Exactly how and when Archaea, Bacteria, and Eucarya developed and how they are related continues to be debated.<ref name="Callier">{{cite journal |last1=Callier |first1=Viviane |title=Mitochondria and the origin of eukaryotes |journal=Knowable Magazine |date=8 June 2022 |doi=10.1146/knowable-060822-2 |doi-access=free |url=https://knowablemagazine.org/article/living-world/2022/mitochondria-origin-eukaryotes |access-date=18 August 2022}}</ref><ref name="Gabaldón"/><ref name="McCutcheon">{{cite journal |last1=McCutcheon |first1=John P. |title=The Genomics and Cell Biology of Host-Beneficial Intracellular Infections |journal=Annual Review of Cell and Developmental Biology |date=6 October 2021 |volume=37 |issue=1 |pages=115–142 |doi=10.1146/annurev-cellbio-120219-024122 |pmid=34242059 |s2cid=235786110 |language=en |issn=1081-0706|doi-access=free }}</ref>