Editing Paraphyly (section)

=== Examples ===

[[File:Wasps are Paraphyletic.svg|thumb|upright=1.8|[[Wasp]]s are paraphyletic, consisting of the [[clade]] [[Apocrita]] without [[ant]]s and [[bee]]s, which are not usually considered to be wasps; the [[sawflies]] ("[[Symphyta]]") too are paraphyletic, as the Apocrita are nested inside the Symphytan clades.]]

The [[prokaryotes]] (single-celled life forms without cell nuclei) are a paraphyletic grouping, because they exclude the [[eukaryotes]], a descendant group. [[Bacteria]] and [[Archaea]] are prokaryotes, but archaea and eukaryotes share a common ancestor that is not ancestral to the bacteria. The prokaryote/eukaryote distinction was proposed by [[Edouard Chatton]] in 1937<ref>{{Cite journal|first=Jan |last=Sapp |title=The prokaryote–eukaryote dichotomy: meanings and mythology |journal=Microbiology and Molecular Biology Reviews |date=June 2005|pages=292–305 |volume=69 |issue=2 |doi=10.1128/MMBR.69.2.292-305.2005 |pmid=15944457 |pmc=1197417}}</ref> and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. The botanical code (the ICBN, now the [[International Code of Nomenclature for algae, fungi, and plants|ICN]]) abandoned consideration of bacterial nomenclature in 1975; currently, prokaryotic nomenclature is regulated under the [[International Code of Nomenclature of Bacteria|ICNB]] with a starting date of 1 January 1980 (in contrast to a 1753 start date under the ICBN/ICN).<ref>{{Cite book|title=Biology of the prokaryotes |editor-first=Joseph W. |editor-last=Lengeler |editor2-first=Gerhart |editor2-last=Drews |editor3-first=Hans Günter |editor3-last= Schlegel |contribution=Prokaryotic Diversity and Systematics |first1=E. |last1=Stackebrabdt |first2=B. |last2=Tindell |first3=W. |last3=Ludwig |first4=M. |last4=Goodfellow| year=1999 |location=Stuttgart |publisher=Georg Thieme Verlag |page=679}}</ref>

Among plants, [[dicotyledon]]s (in the traditional sense) are paraphyletic because the group excludes [[monocotyledon]]s. "Dicotyledon" has not been used as a botanic classification for decades, but is allowed as a synonym of Magnoliopsida.<ref group=note>The history of flowering plant classification can be found under [[Flowering plant#Phylogeny|History of the classification of flowering plants]].</ref> Phylogenetic analysis indicates that the [[monocot]]s are a development from a [[dicot]] ancestor. Excluding monocots from the dicots makes the latter a paraphyletic group.<ref name="Simpson 2006 139–140">{{harvnb|Simpson|2006|pp=139–140}}. "It is now thought that the possession of two cotyledons is an ancestral feature for the taxa of the flowering plants and not an apomorphy for any group within. The 'dicots' ... are paraphyletic ...."</ref>

Among animals, several familiar groups are not, in fact, clades. The order [[Artiodactyla]] ([[even-toed ungulate]]s) as traditionally defined is paraphyletic because it excludes [[Cetacea]]ns (whales, dolphins, etc.). Under the ranks of the [[ICZN Code]], the two taxa are separate orders. Molecular studies, however, have shown that the Cetacea descend from artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetaceans the Artiodactyls are paraphyletic.<ref name="O'Leary, 2001">{{cite journal |first=Maureen A. |last=O'Leary |year=2001 |title=The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization |journal=[[American Zoologist]] |volume=41 |issue=3 |pages=487–506 |citeseerx=10.1.1.555.8631 |doi=10.1093/icb/41.3.487 |doi-access=free}}</ref>
The class [[reptile|Reptilia]] is paraphyletic because it excludes birds (class [[Aves]]). Under a traditional classification, these two taxa are separate classes. However birds are sister taxon to a group of dinosaurs (part of [[Diapsida]]), both of which are "reptiles".<ref name="Romer & Parson">[[Alfred Romer|Romer, A. S.]] & Parsons, T. S. (1985): ''The Vertebrate Body.'' (6th ed.) Saunders, Philadelphia.</ref>

[[Osteichthyes]], bony fish, are paraphyletic when circumscribed to include only [[Actinopterygii]] (ray-finned fish) and [[Sarcopterygii]] (lungfish, etc.), and to exclude [[tetrapod]]s; more recently, Osteichthyes is treated as a clade, including the tetrapods.<ref name="Sharkey_2007"/><ref name=Betancur>{{cite journal|author=Betancur-R, Ricardo |display-authors=etal |year=2013 |title=The Tree of Life and a New Classification of Bony Fishes |journal=PLOS Currents Tree of Life |volume=5 |issue=Edition 1 |url=http://currents.plos.org/treeoflife/article/the-tree-of-life-and-a-new-classification-of-bony-fishes/pdf |doi=10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 |pmid=23653398 |pmc=3644299 |hdl=2027.42/150563 |archive-url=https://web.archive.org/web/20131013102547/http://currents.plos.org//treeoflife/article/the-tree-of-life-and-a-new-classification-of-bony-fishes/pdf |archive-date=13 October 2013 |doi-access=free }}</ref>

The "[[wasp]]s" are paraphyletic, consisting of the narrow-waisted [[Apocrita]] without the [[ant]]s and [[bee]]s.<ref name="Johnson et al, 2013">{{cite journal |author1=Johnson, Brian R. |author2=Borowiec, Marek L. |author3=Chiu, Joanna C. |author4=Lee, Ernest K. |author5=Atallah, Joel |author6=Ward, Philip S. |year=2013 |title=Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps |journal=[[Current Biology]] |volume=23 |issue=20 |pages=2058–2062 |url=http://www.cell.com/current-biology/pdf/S0960-9822(13)01056-7.pdf |pmid=24094856 |doi=10.1016/j.cub.2013.08.050 |doi-access=free |bibcode=2013CBio...23.2058J |s2cid=230835 |s2cid-access=free}}</ref> The sawflies ([[Symphyta]]) are similarly paraphyletic, forming all of the [[Hymenoptera]] except for the Apocrita, a clade deep within the sawfly tree.<ref name="Sharkey_2007">{{cite journal |last1=Sharkey |first1=M. J. |title=Phylogeny and classification of Hymenoptera |journal=Zootaxa |date=2007 |volume=1668 |pages=521–548 |url=http://www.mapress.com/zootaxa/2007f/zt01668p548.pdf |quote=Symphyta and Apocrita have long been considered as suborders of Hymenoptera but since recognition of the paraphyletic nature of the Symphyta (Köningsmann 1977, Rasnitsyn 1988) and the advent of cladistic methods the subordinal classification should be avoided. Likewise the woodwasps are thought to be non-monophyletic, forming a grade that is ancestral relative to Apocrita and Orussidae. The traditional hymenopteran classification is faulty, by cladistic criteria, in the same way as pre-cladistic vertebrate classifications in which groups sharing plesiomorphic characterswere recognized as natural, e.g., fishes were once grouped together as 'Pisces', which excluded tetrapods.|doi=10.11646/zootaxa.1668.1.25 }}</ref>
[[Crustacean]]s are not a clade because the [[Hexapoda]] (insects) are excluded. The modern clade that spans all of them is the [[Pancrustacea]].<ref name=Zrzavy1997>{{cite journal |last1=Zrzavý |first1=J. |last2=Štys |first2=P. |title=The basic body plan of arthropods: insights from evolutionary morphology and developmental biology |journal=Journal of Evolutionary Biology |date=May 1997 |volume=10 |issue=3 |pages=353–367 |doi=10.1046/j.1420-9101.1997.10030353.x}}</ref><ref name=Andrew2011>{{cite journal |last=Andrew |first=David R. |year=2011 |title=A new view of insect–crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics |journal=[[Arthropod Structure & Development]] |volume=40 |issue=3 |pages=289–302 |doi=10.1016/j.asd.2011.02.001 |pmid=21315832 |bibcode=2011ArtSD..40..289A }}</ref><ref name="Bjoern2012">{{cite journal |last1=Bjoern |first1=M. |last2=von Reumont |first2=Ronald A. |last3=Jenner |first3=Matthew A. |last4=Wills |first4=Emiliano |last5=Dell'Ampio |first5=Günther |last6=Pass |first6=Ingo |last7=Ebersberger |first7=Benjamin |last8=Meyer |first8=Stefan |last9=Koenemann |first9=Thomas M. Iliffe |year=2012 |title=Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda |url=http://eprints.cs.univie.ac.at/3232/ |format=[[Portable Document Format|PDF]] proofs |journal=[[Molecular Biology and Evolution]] |volume=29 |issue=3 |pages=1031–1045 |doi=10.1093/molbev/msr270 |pmid=22049065 |doi-access=free}}</ref>

One of the goals of modern taxonomy over the past fifty years has been to eliminate paraphyletic taxa from formal classifications.<ref>Schuh, Randall T. "The Linnaean system and its 250-year persistence." The Botanical Review 69, no. 1 (2003): 59.</ref><ref>{{cite journal |author=Brower, Andrew V.Z. |title=Dead on arrival: a postmortem assessment of "phylogenetic nomenclature", 20+ years on |date=2020 |journal=Cladistics |volume=36 |issue=6 |pages=627–637 |doi=10.1111/cla.12432|s2cid=224927279 |doi-access=free }}</ref> Below is a partial list of obsolete taxa and informal groups that have been found to be paraphyletic.

{| class="wikitable sortable"
|-
! Paraphyletic group !! Excluded clades !! Corresponding monophyletic taxon !! References and notes
|-
| [[Prokaryote|Prokaryota]] || [[Eukaryota]] || [[organism|Cellular organisms]] || <ref name="Berg_360">{{Cite book |last=Berg |first=Linda |title=Introductory Botany: Plants, People, and the Environment |publisher=Thomson Corporation |year=2008 |isbn=978-0-03-075453-1 |edition=2nd |location=Belmont CA |page=360}}</ref>
|-
| [[Protista]] || [[Animal]]ia, [[Plant]]ae, [[Fungi]] || [[Eukaryote|Eukaryota]] ||<ref>{{cite journal |last1=Schlegel |first1=Martin |last2=Hülsmann |first2=Norbert |date=2 August 2007 |title=Protists – A textbook example for a paraphyletic taxon |journal=Organisms Diversity & Evolution |volume=7 |issue=2 |pages=166–172 |doi=10.1016/j.ode.2006.11.001 |issn=1439-6092}}</ref>
|-
|[[Chromista]]
|[[Archaeplastida]], [[Provora]]
|[[Diaphoretickes]]
|<ref>{{cite journal |last1=Cavalier-Smith |first1=Thomas |last2=Allsopp |first2=M. T. |last3=Chao |first3=E. E. |date=November 1994 |title=Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic? |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=91 |issue=24 |pages=11368–11372 |bibcode=1994PNAS...9111368C |doi=10.1073/pnas.91.24.11368 |pmc=45232 |pmid=7972066 |doi-access=free}}</ref>
|-
| [[Invertebrate]]s || [[Vertebrate|Vertebrata]] || [[Animal]]ia || <ref name="Agassiz2013">{{cite book |author=Agassiz, Louis |author-link=Louis Agassiz |url=https://books.google.com/books?id=O6fDAgAAQBAJ&pg=PT115 |title=Essay on Classification |date=21 March 2013 |publisher=Courier |isbn=978-0-486-15135-9 |pages=115–}}</ref>
|-
| [[Platyzoa]] || [[Lophotrochozoa]], [[Mesozoa]] || [[Spiralia]] || <ref>{{cite web |title=Gnathifera - Richard C. Brusca |url=http://rickbrusca.com/http___www.rickbrusca.com_index.html/Invertebrates,_3rd_Ed._files/Ch%2016%20Gnathifera.pdf}}</ref>
|-
| [[Fish]] || [[Tetrapoda]] || [[Vertebrate|Vertebrata]] || <ref name="treeoflife">Tree of life web project – [http://tolweb.org/Chordata/2499 Chordates] {{webarchive|url=https://web.archive.org/web/20070224172716/http://tolweb.org/Chordata/2499|date=24 February 2007}}.</ref>
|-
| [[Reptile|Reptilia]] || [[Bird|Aves]] || [[Sauropsida]] || <ref name="tudge">{{RefTudgeVariety}}</ref>
|-
| [[Lizard]]s || [[Snake|Serpentes]], [[Amphisbaenia]] || [[Squamata]] || <ref>{{cite journal |last1=Reeder |first1=Tod W. |last2=Townsend |first2=Ted M. |last3=Mulcahy |first3=Daniel G. |last4=Noonan |first4=Brice P. |last5=Wood |first5=Perry L. |last6=Sites |first6=Jack W. |last7=Wiens |first7=John J. |date=2015 |title=Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa |journal=PLOS ONE |volume=10 |issue=3 |pages=e0118199 |bibcode=2015PLoSO..1018199R |doi=10.1371/journal.pone.0118199 |pmc=4372529 |pmid=25803280 |doi-access=free}}</ref>
|-
| [[Plagiaulacida]]ns || [[Cimolodonta]], [[Arginbaataridae]] || [[Multituberculata]] || <ref>{{cite journal |author1=Kielan-Jaworowska, Z. |author2=Hurum, J. |name-list-style=amp |year=2001 |title=Phylogeny and Systematics of Multituberculate Animals |url=http://doc.rero.ch/record/14775/files/PAL_E1903.pdf |journal=Palaeontology |volume=44 |issue=3 |pages=389–429 |bibcode=2001Palgy..44..389K |doi=10.1111/1475-4983.00185 |s2cid=83592270}}</ref>
|-
| [[Pelycosaur]]s || [[Therapsida]] || [[Synapsida]] || <ref name="Benton">{{cite book |last=Benton |first=Michael J. |title=Vertebrate palaeontology |publisher=Blackwell Science |year=2004 |isbn=978-0-632-05637-8 |edition=3rd |location=Oxford}}</ref>
|- 
| [[Even-toed ungulate]]s || [[Cetacea]] || [[Artiodactyl]]a || <ref name="O'Leary, 2001" /><ref name="MamEv">{{cite book |author1=Savage, R. J. G. |url=https://archive.org/details/mammalevolutioni0000sava |title=Mammal Evolution: an illustrated guide |author2=Long, M. R. |publisher=Facts on File |year=1986 |isbn=0-8160-1194-X |location=New York |pages=[https://archive.org/details/mammalevolutioni0000sava/page/208 208] |url-access=registration |name-list-style=amp}}</ref>
|-
| [[Archaeoceti]] || [[Neoceti]] || [[Cetacea]] || <ref name="Thewissen-2002">{{Cite journal |last1=Thewissen |first1=J. G. M. |last2=Williams |first2=E. M. |year=2002 |title=The Early Radiations of Cetacea (Mammalia): Evolutionary Pattern and Developmental Correlations |journal=Annual Review of Ecology and Systematics |volume=33 |pages=73–90 |doi=10.1146/annurev.ecolsys.33.020602.095426 |oclc=4656321698}}</ref>
|-
| [[Prosimian|Prosimii]] || [[Simian|Simiiformes]] || [[Primate]]s || <ref>{{Cite journal |last1=Groves |first1=C. P. |year=1998 |title=Systematics of tarsiers and lorises |journal=Primates |volume=39 |issue=1 |pages=13–27 |doi=10.1007/BF02557740 |s2cid=10869981}}<!--page 13--></ref>
|-
| [[Crustacean|Crustacea]] || [[Hexapoda]] || [[Pancrustacea]]|| <ref name="Andrew2011" /><ref name="Bjoern2012" /><ref name="Zrzavy1997" />
|-
| [[Wasps]] || [[Ant|Formicidae]], [[Bee|Anthophila]]|| [[Apocrita]] || <ref name="Johnson et al, 2013" />
|-
| [[Sawfly|Symphyta]] || [[Apocrita]] || [[Hymenoptera]] || <ref name="Sharkey_2007" />
|-
| [[Parasitica]] || [[Aculeata]] || [[Apocrita]] || <ref>Parasitic Hymenoptera (Parasitica). RL Zuparko, Encyclopedia of Entomology, 2004</ref>
|-
| [[Nautiloidea]] || [[Ammonoidea]], [[Coleoidea]] || [[Cephalopoda]] || <ref name="Lindgren2004">{{Cite journal |last1=Lindgren |first1=A. R. |last2=Giribet |first2=G. |last3=Nishiguchi |first3=M. K. |year=2004 |title=A combined approach to the phylogeny of Cephalopoda (Mollusca) |journal=Cladistics |volume=20 |issue=5 |pages=454–486 |doi=10.1111/j.1096-0031.2004.00032.x |pmid=34892953 |s2cid=85975284 |doi-access=free}}</ref>
|-
| [[Charophyta]]|| [[Embryophyte|Embryophyta]]|| [[Streptophyta]] || <ref name="Becker2009">{{Cite journal |last1=Becker |first1=B. |last2=Marin |first2=B. |year=2009 |title=Streptophyte algae and the origin of embryophytes |journal=Annals of Botany |volume=103 |issue=7 |pages=999–1004 |doi=10.1093/aob/mcp044 |pmc=2707909 |pmid=19273476}}</ref>
|-
| [[Dicotyledon]]s || [[Monocotyledon]]s || [[Flowering plant|Angiospermae]]|| <ref name="Simpson 2006 139–140" />
|-
| [[Moth]]s || [[Butterfly|Papilionoidea]] || [[Lepidoptera]] || <ref name="scoble">{{cite book |last=Scoble |first=M.J. |title=The Lepidoptera: form, function and diversity |publisher=Oxford University Press |year=1995 |location=Oxford |pages=404<!--is that length of book or a page ref?-->}}</ref>
|-
| [[Jellyfish]] || various [[Hydrozoa|hydrozoans]] || [[Medusozoa]] || <ref name="Zou2012">{{Cite journal |last1=Zou |first1=H. |last2=Zhang |first2=J. |last3=Li |first3=W. |last4=Wu |first4=S. |last5=Wang |first5=G. |year=2012 |title=Mitochondrial Genome of the Freshwater Jellyfish Craspedacusta sowerbyi and Phylogenetics of Medusozoa |journal=PLOS ONE |volume=7 |issue=12 |pages=e51465 |bibcode=2012PLoSO...751465Z |doi=10.1371/journal.pone.0051465 |pmc=3519871 |pmid=23240028 |doi-access=free}}</ref><ref>{{cite journal |last=Marques |first=Antonio C. |author2=Allen G. Collins |date=March 2004 |title=Cladistic analysis of Medusozoa and cnidarian evolution |journal=Invertebrate Biology |volume=123 |pages=23–42 |doi=10.1111/j.1744-7410.2004.tb00139.x |number=1}}</ref><ref>{{cite journal |author1=Zapata |display-authors=etal |date=2015 |title=Phylogenomic analyses support traditional relationships within Cnidaria |journal=PLOS ONE |volume=10 |issue=10 |page=e0139068 |bibcode=2015PLoSO..1039068Z |doi=10.1371/journal.pone.0139068 |pmc=4605497 |pmid=26465609 |doi-access=free}}</ref>
|-
| [[Rotifer]]a || [[Acanthocephala]] || [[Syndermata]] || <ref>{{cite book |author1=Ruppert, Edward E. |url=https://archive.org/details/isbn_9780030259821 |title=Invertebrate zoology: a functional evolutionary approach |author2=Fox, Richard S. |author3=Barnes, Robert D. |publisher=[[Cengage|Thomson-Brooks/Cole]] |year=2004 |isbn=0-03-025982-7 |edition=7th |place=Belmont, CA |pages=788ff. – see particularly p. 804 |chapter=23 GNATHIFERA |lccn=2003107287 |oclc=752875516 |url-access=registration}}</ref><ref name="shimek">{{cite web |author=Shimek, Ronald |date=January 2006 |title=Nano-Animals, Part I: Rotifers |url=http://reefkeeping.com/issues/2006-01/rs/index.php |access-date=27 July 2008 |publisher=Reefkeeping.com}}</ref>
|-
| [[Monkey]]s || [[Hominoidea]]
|| [[Simiiformes]] ||<ref>{{cite AV media |url=https://www.youtube.com/watch?v=4A-dMqEbSk8 |title=Turns out we DID come from monkeys! |date=2010-01-16 |last=AronRa |access-date=2018-11-12}}</ref><ref>{{Cite web |title=Early Primate Evolution: The First Primates |url=http://anthro.palomar.edu/earlyprimates/early_2.htm |url-status=dead |archive-url=https://web.archive.org/web/20180110174441/https://www2.palomar.edu/anthro/earlyprimates/early_2.htm |archive-date=10 January 2018 |access-date=2017-08-12 |website=anthro.palomar.edu}}</ref>
|-
|[[Antelope]]s
|[[Bovini]], [[Caprinae|Caprini]], [[Ovibovini]]
|[[Bovid]]ae
| <ref>{{cite book |last1=Wilson |first1=Don E. |url=https://books.google.com/books?id=JgAMbNSt8ikC&pg=PA699 |title=Mammal Species of the World: A Taxonomic and Geographic Reference, Volume 1 |last2=Reeder |first2=DeeAnn M. |publisher=Johns Hopkins University Press |year=2005 |isbn=0-8018-8221-4 |edition=3rd |location=Belmont, CA |url-access=registration |name-list-style=amp}}, p. 699.</ref>
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