Editing Kingdom (biology) (section)

== Beyond traditional kingdoms ==
{{anchor|Modern view}}While the concept of kingdoms continues to be used by some taxonomists, there has been a movement away from traditional kingdoms, as they are no longer seen as providing a [[Cladistics|cladistic]] classification, where there is emphasis in arranging organisms into [[Clade|natural groups]].<ref name="SimpsonRoger2004"/>

=== Three domains of life ===
{{main|Three-domain system|Domain (biology)}}

{{PhylomapB||caption=A [[phylogenetic tree]] based on [[rRNA]] data showing Woese's [[three-domain system]]. All smaller branches can be considered kingdoms.|size = 440px}}
Based on RNA studies, [[Carl Woese]] thought life could be divided into three large divisions and referred to them as the "three primary kingdom" model or "urkingdom" model.<ref name="Balch_Magrum_Fox_Wolfe_Woese">{{cite journal|last1=Balch |first1=W.E. |last2=Magrum |first2=L.J. |last3=Fox |first3=G.E. |last4=Wolfe |first4=C.R. |last5=Woese |first5=C.R. |name-list-style=amp |date=August 1977|title=An ancient divergence among the bacteria|journal=[[Journal of Molecular Evolution]] |volume=9|issue=4 |pages=305–311 |doi=10.1007/BF01796092 |pmid=408502 |bibcode=1977JMolE...9..305B |s2cid=27788891}}</ref>

In 1990, the name "domain" was proposed for the highest rank.<ref name="Woese"/> This term represents a synonym for the category of dominion (lat. dominium), introduced by Moore in 1974.<ref name=Moore1974>{{cite journal|last=Moore |first=R.T. |year=1974|title=Proposal for the recognition of super ranks |journal=Taxon |volume=23|issue=4 |pages=650–652 |doi=10.2307/1218807 |jstor=1218807 |url=http://www.iapt-taxon.org/historic/Congress/IBC_1975/Prop034bis-037.pdf}}</ref> Unlike Moore, Woese et al. (1990) did not suggest a Latin term for this category, which represents a further argument supporting the accurately introduced term dominion.<ref name=Luketa2012>{{cite journal |last=Luketa |first=S. |year=2012|title=New views on the megaclassification of life |journal=[[Protistology]] |volume=7|issue=4 |pages=218–237 |url=http://protistology.ifmo.ru/num7_4/luketa_protistology_7-4.pdf}}</ref>

Woese divided the prokaryotes (previously classified as the Kingdom Monera) into two groups, called [[bacteria|Eubacteria]] and [[Archaea|Archaebacteria]], stressing that there was as much genetic difference between these two groups as between either of them and all eukaryotes.

{{clade
   |label1=[[Life]]
   |1={{clade
      |1=Domain [[Bacteria]] ([[Eubacteria]])
      |2=Domain [[Archaea]] ([[Archaebacteria]])
      |3=Domain [[Eukaryote|Eukarya]] ([[Eukaryota]])
   }}
}}

According to genetic data, although eukaryote groups such as plants, fungi, and animals may look different, they are more closely related to each other than they are to either the Eubacteria or Archaea. It was also found that the eukaryotes are more closely related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research.<ref name="DagenEtAl2010">{{cite journal |last1=Dagan |first1=T. |last2=Roettger |first2=M. |last3=Bryant |last4=Martin |first4=W. |year=2010|title=Genome Networks Root the Tree of Life between Prokaryotic Domains|journal=[[Genome Biology and Evolution]] |volume=2|pages=379–92 |doi=10.1093/gbe/evq025 |pmid=20624742 |pmc=2997548 |name-list-style=amp}}</ref> There is no consensus on how many kingdoms exist in the classification scheme proposed by Woese.

=== Eukaryotic supergroups ===
{{anchor|Kingdoms of the Eukaryota}}
{{Main|Supergroup (biology)}}

In 2004, a review article by Simpson and Roger noted that the Protista were "a [[Wastebasket taxon|grab-bag]] for all [[eukaryote]]s that are not animals, plants or fungi". They held that only monophyletic groups should be accepted as formal ranks in a classification and that – while this approach had been impractical previously (necessitating "literally dozens of eukaryotic 'kingdoms{{'"}}) – it had now become possible to divide the eukaryotes into "just a few major groups that are probably all monophyletic".<ref name="SimpsonRoger2004">{{cite journal |title=The real 'kingdoms' of eukaryotes |last1=Simpson |first1=Alastair G.B. |last2=Roger|first2=Andrew J. |journal=[[Current Biology]] |volume=14|issue=17 |pages=R693–R696 |doi=10.1016/j.cub.2004.08.038 |pmid=15341755|year=2004|s2cid=207051421 |doi-access=free}}</ref>

On this basis, the diagram opposite (redrawn from their article) showed the real "kingdoms" (their quotation marks) of the eukaryotes.<ref name="SimpsonRoger2004" /> A classification which followed this approach was produced in 2005 for the International Society of Protistologists, by a committee which "worked in collaboration with specialists from many societies". It divided the eukaryotes into the same six "supergroups".<ref name=Adl2005>{{cite journal |vauthors=Adl SM, ((Simpson AGB)), 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 Ø, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MF |display-authors=6 |title=The new higher-level classification of eukaryotes with emphasis on the taxonomy of protists |journal=[[Journal of Eukaryotic Microbiology]] |year=2005|volume=52|issue=5 |pages=399–451 |doi=10.1111/j.1550-7408.2005.00053.x |pmid=16248873 |s2cid=8060916 |doi-access=free|url=http://doc.rero.ch/record/14409/files/PAL_E1847.pdf}}</ref> The published classification deliberately did not use formal taxonomic ranks, including that of "kingdom".

{{clade
|label1=[[Life]]
|1={{clade
|1={{clade
   |label1=Domain [[Bacteria]]
   |1={{clade |1= [[prokaryotic]] [[Bacteria]] }}
   }}
|2={{clade
   |label1=Domain [[Archaea]]
   |1={{clade |1= [[prokaryotic]] [[Archaea]]ns }}
   }}
|3={{clade
|label1=Domain [[Eukaryota]]
   |1={{clade
      |label1= [[Excavata]]
      |1= various [[flagellate]] protozoa
      |label2=[[Amoebozoa]]
      |2= most lobose [[amoeboid]]s and [[slime mould]]s
      |label3=[[Opisthokonta]]
      |3= [[animal]]s, [[fungus|fungi]], [[choanoflagellate]]s, etc.
      |label4=[[Rhizaria]]
      |4= [[Foraminifera]], [[Radiolaria]], and various other [[amoeboid]] protozoa
      |label5=[[Chromalveolate|Chromalveolata]]
      |5= [[Heterokont|Stramenopiles]] ([[Brown Algae]], [[Diatoms]], [[Ochrophyte|etc.]]), [[haptophyte|Haptophyta]], [[cryptomonad|Cryptophyta]] (or cryptomonads), and [[alveolate|Alveolata]]
      |label6=[[Archaeplastida]] (or [[Primoplantae]])
      |6= [[Embryophyte|Land plants]], [[green alga]]e, [[red alga]]e, and [[glaucophyte]]s
      }}
   }}
}}
}}

[[File:Eukaryote Phylogeny.png|alt=Eukaryotic tree of life showing the diversity of eukaryotic cells.|thumb|400px|One hypothesis of eukaryotic relationships depicted by Alastair Simpson]]In this system the multicellular animals ([[Metazoa]]) are descended from the same ancestor as both the unicellular [[choanoflagellate]]s and the fungi which form the [[Opisthokonta]].<ref name=Adl2005/> Plants are thought to be more distantly related to animals and fungi.

However, in the same year as the International Society of Protistologists' classification was published (2005), doubts were being expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata,<ref>{{cite journal |last1=Harper |first1=J.T. |last2=Waanders |first2=E. |last3=Keeling |first3=P.J. |year=2005|title=On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes|journal=[[International Journal of Systematic and Evolutionary Microbiology]] |volume=55|issue=Pt 1 |pmid=15653923 |pages=487–496 |name-list-style=amp |doi=10.1099/ijs.0.63216-0 |df=dmy-all |doi-access=free}}</ref> and a review in 2006 noted the lack of evidence for several of the six proposed supergroups.<ref name="parfrey">{{cite journal |last1=Parfrey |first1=Laura W. |last2=Barbero |first2=Erika |last3=Lasser |first3=Elyse|last4=Dunthorn |first4=Micah |year=2006|last5=Bhattacharya |first5=Debashish |last6=Patterson |first6=David J. |last7=Katz |first7=Laura A. |name-list-style=amp |title=Evaluating support for the current classification of eukaryotic diversity|journal=[[PLOS Genetics]] |volume=2|issue=12 |pages=e220 |doi=10.1371/journal.pgen.0020220 |pmid=17194223 |pmc=1713255 |doi-access=free}}</ref>

{{As of|2019}}, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a [[clade]] dubbed the [[SAR supergroup]],<ref name="Burki2007p4">{{Harvnb|Burki|Shalchian-Tabrizi|Minge|Skjæveland |2007|p=4}}</ref> so that Rhizaria is not one of the main eukaryote groups.<ref name="CavalierSmith2009"/><ref name="Burki2007">{{cite journal |last1=Burki |first1=Fabien |last2=Shalchian-Tabrizi |first2=Kamran |last3=Minge |first3=Marianne |last4=Skjæveland |first4=Åsmund |last5=Nikolaev |first5=Sergey I. |last6=Jakobsen |first6=Kjetill S. |last7=Pawlowski |first7=Jan |name-list-style=amp |editor1-last=Butler |year=2007 |editor1-first=Geraldine |title=Phylogenomics reshuffles the eukaryotic supergroups |journal=[[PLOS ONE]] |volume=2 |issue=8 |pages=e790 |doi=10.1371/journal.pone.0000790 |pmid=17726520 |pmc=1949142 |bibcode=2007PLoSO...2..790B |doi-access=free}}</ref><ref name="Burki2008">{{cite journal |last1=Burki |first1=Fabien |last2=Shalchian-Tabrizi|first2=Kamran |last3=Pawlowski |first3=Jan |year=2008|title=Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes |journal=[[Biology Letters]] |pmid=18522922 |volume=4|issue=4|pmc=2610160|pages=366–369 |doi=10.1098/rsbl.2008.0224 |name-list-style=amp}}</ref><ref name="Burki2009">{{cite journal |last1=Burki |first1=F. |last2=Inagaki |year=2009|first2=Y. |last3=Brate |first3=J. |last4=Archibald|first4=J.M. |last5=Keeling |first5=P.J. |last6=Cavalier-Smith |first6=T. |last7=Sakaguchi |first7=M. |last8=Hashimoto |first8=T. |last9=Horak |first9=A. |last10=Kumar |first10=S. |last11=Klaveness |first11=D.|author-link11=Dag Klaveness (limnologist)|last12=Jakobsen |first12=K.S. |last13=Pawlowski |first13=J. |last14=Shalchian-Tabrizi |first14=K. |title=Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic Chromalveolates|journal=[[Genome Biology and Evolution]] |volume=1|pages=231–238 |doi=10.1093/gbe/evp022 |pmc=2817417 |pmid=20333193 |display-authors=8}}</ref><ref name="Hackett2007">{{cite journal |last1=Hackett |first1=J.D. |last2=Yoon |first2=H.S. |last3=Li |first3=S. |last4=Reyes-Prieto |first4=A.|last5=Rummele |first5=S.E. |last6=Bhattacharya |first6=D. |name-list-style=amp|year=2007|title=Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with chromalveolates |journal=[[Molecular Biology and Evolution]] |volume=24|issue=8|pages=1702–1713 |doi=10.1093/molbev/msm089 |pmid=17488740 |doi-access=free}}</ref> {{clear}}

=== Prokaryotic kingdoms ===
{{main|Bacterial taxonomy#Subdivisions}}
The ''Prokaryotic Code'' treats Bacteria and Archaea each as a domain. Since 2024, each domain each contains 4 kingdoms, for a total of 8.<ref name="valid-dom-kingdom">{{cite journal |last1=Göker |first1=Markus |last2=Oren |first2=Aharon |title=Valid publication of names of two domains and seven kingdoms of prokaryotes |journal=International Journal of Systematic and Evolutionary Microbiology |date=22 January 2024 |volume=74 |issue=1 |doi=10.1099/ijsem.0.006242|pmid=38252124 }}</ref>

=== Comparison of top level classification ===
{{further|Tree of life (biology)#Developments since 1990}}

Some authors have added [[non-cellular life]] to their classifications. This can create a "superdomain" called "Acytota", also called "Aphanobionta", of non-cellular life; with the other superdomain being "[[cytota]]" or cellular life.<ref name="pmidhttps://pubmed.ncbi.nlm.nih.gov/26305806/">{{cite journal|author=Trifonov EN, Kejnovsky E |title=Acytota - associated kingdom of neglected life. |journal=J Biomol Struct Dyn |year=2016|volume=34|issue= 8 |pages=1641–8 |pmid=26305806 |doi=10.1080/07391102.2015.1086959 |pmc= |s2cid=38178747 |url=https://pubmed.ncbi.nlm.nih.gov/26305806/}}</ref><ref name="Biological systematics : the state of the art p. ">{{cite book |title=Biological systematics: The state of the art |publication-place=London|isbn=0-412-36440-9 |oclc=27895507 |page= |last1=Minelli |first1=Alessandro |year=1993|publisher=[[Chapman & Hall]]}}</ref> (see section below for further discussion)

The [[eocyte hypothesis]] proposes that the [[eukaryote]]s emerged from a phylum within the [[archaea]] called the [[Thermoproteota]] (formerly known as eocytes or Crenarchaeota).<ref name=Archibald>{{cite journal|first1=John M. |last1=Archibald|title=The eocyte hypothesis and the origin of eukaryotic cells |journal=[[PNAS]] |volume=105|issue=51 |pages=20049–20050 |date=23 December 2008|doi=10.1073/pnas.0811118106|pmid=19091952|bibcode=2008PNAS..10520049A|pmc=2629348|doi-access=free }}</ref><ref name=Lake>{{cite journal |first1=James A. |last1=Lake |first2=Eric |last2=Henderson |first3=Melanie |last3=Oakes |first4=Michael W. |last4=Clark|title=Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes|journal=[[PNAS]] |volume=81|pages=3786–3790 |date=June 1984|issue=12 |doi=10.1073/pnas.81.12.3786 |pmid=6587394|pmc=345305|bibcode=1984PNAS...81.3786L |doi-access=free}}</ref>

{{biological classification with acellular}}