paraphyly

The term paraphyly, or paraphyletic, derives from the two Ancient Greek words {{wikt-lang|grc|παρά}} ({{grc-transl|παρά}}), meaning "beside, near", and {{wikt-lang|grc|φῦλον}} ({{grc-transl|φῦλον}}), meaning "genus, species",{{Cite book |title=Abrégé du dictionnaire grec français |last=Bailly |first=Anatole |date=1 January 1981 |publisher=Hachette |isbn=978-2-01-003528-9 |location=Paris |oclc=461974285 }}{{Cite web |url=http://www.tabularium.be/bailly/ |title=Greek-French dictionary online |last=Bailly |first=Anatole |website=www.tabularium.be |access-date=8 March 2018}} and refers to the situation in which one or several monophyletic subgroups of organisms (e.g., genera, species) are left apart from all other descendants of a unique common ancestor.

Conversely, the term monophyly, or monophyletic, builds on the Ancient Greek prefix {{wikt-lang|grc|μόνος}} ({{grc-transl|μόνος}}), meaning "alone, only, unique", and refers to the fact that a monophyletic group includes organisms consisting of all the descendants of a unique common ancestor.

By comparison, the term polyphyly, or polyphyletic, uses the Ancient Greek prefix {{wikt-lang|grc|πολύς}} ({{grc-transl|πολύς}}), meaning "many, a lot of", and refers to the fact that a polyphyletic group includes organisms arising from multiple ancestral sources.

File:Monophyly, paraphyly, polyphyly.svg of the primates, showing a monophyly (the simians, in yellow), a paraphyly (the prosimians, in blue, including the red patch), and a polyphyly (the night-active primates, the lorises and the tarsiers, in red). "Monkeys" too are paraphyletic if apes and humans are excluded. ]]

{{further|Cladistics}}

Groups that include all the descendants of a common ancestor are said to be monophyletic. A paraphyletic group is a monophyletic group from which one or more subsidiary clades (monophyletic groups) are excluded to form a separate group. Philosopher of science Marc Ereshefsky has argued that paraphyletic taxa are the result of anagenesis in the excluded group or groups.{{cite book|url=https://books.google.com/books?id=ucilIjrex5cC&pg=PA9 |title=Handbook of Plant Science|isbn=978-0-470-05723-0|last1=Roberts|first1=Keith|date=10 December 2007|publisher=John Wiley & Sons }} A cladistic approach normally does not grant paraphyletic assemblages the status of "groups", nor does it reify them with explanations, as in cladistics they are not seen as the actual products of evolutionary events.{{Cite book |last=Williams |first=David M. |title=Cladistics: A Guide to Biological Classification |last2=Ebach |first2=Malte C. |date=2020-08-06 |publisher=Cambridge University Press |isbn=978-1-108-88267-5 |language=en}}

A group whose identifying features evolved convergently in two or more lineages is polyphyletic (Greek πολύς [polys], "many"). More broadly, any taxon that is not paraphyletic or monophyletic can be called polyphyletic. Empirically, the distinction between polyphyletic groups and paraphyletic groups is rather arbitrary, since the character states of common ancestors are inferences, not observations.{{citation needed|date=April 2023}}

These terms were developed during the debates of the 1960s and 1970s accompanying the rise of cladistics.

Paraphyletic groupings are considered problematic by many taxonomists, as it is not possible to talk precisely about their phylogenetic relationships, their characteristic traits and literal extinction.{{Cite book|url=https://books.google.com/books?id=XcYSZTPkXTQC&pg=PA166 |title=The Symbolic Species Evolved |last1=Schilhab |first1=Theresa |last2=Stjernfelt |first2=Frederik |last3=Deacon |first3=Terrence |year=2012 |publisher=Springer |isbn=978-94-007-2335-1}}{{Cite journal |last=Villmoare |first=Brian |date=2018 |title=Early Homo and the role of the genus in paleoanthropology |journal=American Journal of Physical Anthropology |volume=165 |pages=72–89 |doi=10.1002/ajpa.23387|pmid=29380889 |doi-access=free }} Related terms are stem group, chronospecies, budding cladogenesis, anagenesis, or 'grade' groupings. Paraphyletic groups are often relics from outdated hypotheses of phylogenic relationships from before the rise of cladistics.{{cite journal |last1=Dominguez |first1=Eduardo |last2=Wheeler |first2=Quentin D. |date=1997 |title=Forum – Taxonomic Stability is Ignorance |journal=Cladistics |volume=13 |issue=4 |pages=367–372 |doi=10.1111/j.1096-0031.1997.tb00325.x|pmid=34911226 |s2cid=55540349 |doi-access=free }}

File:Wasps are Paraphyletic.svgs are paraphyletic, consisting of the clade Apocrita without ants and bees, 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{{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}} and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. The botanical code (the ICBN, now the ICN) abandoned consideration of bacterial nomenclature in 1975; currently, prokaryotic nomenclature is regulated under the ICNB with a starting date of 1 January 1980 (in contrast to a 1753 start date under the ICBN/ICN).{{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}}

Among plants, dicotyledons (in the traditional sense) are paraphyletic because the group excludes monocotyledons. "Dicotyledon" has not been used as a botanic classification for decades, but is allowed as a synonym of Magnoliopsida.The history of flowering plant classification can be found under History of the classification of flowering plants. Phylogenetic analysis indicates that the monocots are a development from a dicot ancestor. Excluding monocots from the dicots makes the latter a paraphyletic group.{{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 ...."

Among animals, several familiar groups are not, in fact, clades. The order Artiodactyla (even-toed ungulates) as traditionally defined is paraphyletic because it excludes Cetaceans (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.{{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}}

The class 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".Romer, A. S. & Parsons, T. S. (1985): The Vertebrate Body. (6th ed.) Saunders, Philadelphia.

Osteichthyes, bony fish, are paraphyletic when circumscribed to include only Actinopterygii (ray-finned fish) and Sarcopterygii (lungfish, etc.), and to exclude tetrapods; more recently, Osteichthyes is treated as a clade, including the tetrapods.{{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 }}

The "wasps" are paraphyletic, consisting of the narrow-waisted Apocrita without the ants and bees.{{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}} The sawflies (Symphyta) are similarly paraphyletic, forming all of the Hymenoptera except for the Apocrita, a clade deep within the sawfly tree.{{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 }}

Crustaceans are not a clade because the Hexapoda (insects) are excluded. The modern clade that spans all of them is the Pancrustacea.{{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}}{{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 }}{{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=PDF proofs |journal=Molecular Biology and Evolution |volume=29 |issue=3 |pages=1031–1045 |doi=10.1093/molbev/msr270 |pmid=22049065 |doi-access=free}}

One of the goals of modern taxonomy over the past fifty years has been to eliminate paraphyletic taxa from formal classifications.Schuh, Randall T. "The Linnaean system and its 250-year persistence." The Botanical Review 69, no. 1 (2003): 59.{{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 }} Below is a partial list of obsolete taxa and informal groups that have been found to be paraphyletic.

{{main|Paraspecies}}

Species have a special status in systematics as being an observable feature of nature itself and as the basic unit of classification.{{cite journal |last1=Queiroz |first1=Kevin |last2=Donoghue |first2=Michael J. |title=Phylogenetic Systematics and the Species Problem |journal=Cladistics |date=December 1988 |volume=4 |issue=4 |pages=317–338 |doi= 10.1111/j.1096-0031.1988.tb00518.x |pmid=34949064 |s2cid=40799805 }} Some articulations of the phylogenetic species concept require species to be monophyletic, but paraphyletic species are common in nature, to the extent that they do not have a single common ancestor. Indeed, for sexually reproducing taxa, no species has a "single common ancestor" organism. Paraphyly is common in speciation, whereby a mother species (a paraspecies) gives rise to a daughter species without itself becoming extinct.{{cite book |first1=James S.| last1= Albert | first2= Roberto E.| last2= Reis |title=Historical Biogeography of Neotropical Freshwater Fishes |url=https://books.google.com/books?id=_Suu7a-ERdMC&pg=PA308 |access-date=28 June 2011 |date=8 March 2011 |publisher= University of California Press |page=308 |isbn=978-0-520-26868-5| via= Google Books}} Research indicates as many as 20 percent of all animal species and between 20 and 50 percent of plant species are paraphyletic.{{cite journal |last1= Ross |first1= Howard A. |title= The incidence of species-level paraphyly in animals: A re-assessment |journal=Molecular Phylogenetics and Evolution |date= July 2014 |volume=76 |pages=10–17 |doi=10.1016/j.ympev.2014.02.021 |pmid=24583289}}{{cite journal |last1=Crisp |first1=M.D. |last2=Chandler |first2=G.T. |title=Paraphyletic species |journal= Telopea |date=1 July 1996 |volume= 6 |issue=4 |pages=813–844 |doi=10.7751/telopea19963037 |url= http://plantnet.rbgsyd.nsw.gov.au/emuwebnswlive/objects/common/webmedia.php?irn=75865&reftable=ebibliography |access-date=22 January 2015|doi-access=free }} Accounting for these facts, some taxonomists argue that paraphyly is a trait of nature that should be acknowledged at higher taxonomic levels.{{cite book |title=Framework for Post-Phylogenetic Systematics |last=Zander |first=Richard |year=2013 |publisher=Zetetic Publications, Amazon CreateSpace |location=St. Louis |url= https://www.academia.edu/9137481 }}{{cite journal | last1=Aubert | first1=D. | year=2015 | title=A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics | journal= Phytoneuron | volume=66 | pages=1–54 }}

Cladists advocate a phylogenetic species concept {{cite journal| last1= Nixon| first1= Kevin C.| first2= Quentin D. |last2= Wheeler| title= An amplification of the phylogenetic species concept| journal= Cladistics |volume= 6| number= 3 |year= 1990| pages= 211–23| doi= 10.1111/j.1096-0031.1990.tb00541.x| s2cid= 84095773| doi-access= free}} that does not consider species to exhibit the properties of monophyly or paraphyly, concepts under that perspective which apply only to groups of species.{{cite book| last1= Brower| first1= Andrew V. Z. |first2= Randall T.| last2= Schuh| year= 2021| title= Biological Systematics: principles and applications| edition= 3rd| publisher= Cornell University Press| place= Ithaca, New York| isbn= 978-1-5017-5277-3}} They consider Zander's extension of the "paraphyletic species" argument to higher taxa to represent a category error{{cite journal| last= Schmidt-Lebuhn| first= Alexander N. |title= Fallacies and false premises—a critical assessment of the arguments for the recognition of paraphyletic taxa in botany| journal= Cladistics |volume= 28| number= 2 |year= 2012| pages= 174–87| doi= 10.1111/j.1096-0031.2011.00367.x | pmid= 34861757 | s2cid= 83900580 | doi-access= free }}

{{anchor|Cladistics generally discourages paraphyletic groups}}

When the appearance of significant traits has led a subclade on an evolutionary path very divergent from that of a more inclusive clade, it often makes sense to study the paraphyletic group that remains without considering the larger clade. For example, the Neogene evolution of the Artiodactyla (even-toed ungulates, like deer, cows, pigs and hippopotamuses - Cervidae, Bovidae, Suidae and Hippopotamidae, the families that contain these various artiodactyls, are all monophyletic groups) has taken place in environments so different from that of the Cetacea (whales, dolphins, and porpoises) that the Artiodactyla are often studied in isolation even though the cetaceans are a descendant group. The prokaryote group is another example; it is paraphyletic because it is composed of two Domains (Eubacteria and Archaea) and excludes (the eukaryotes). It is very useful because it has a clearly defined and significant distinction (absence of a cell nucleus, a plesiomorphy) from its excluded descendants.{{citation needed|date=October 2020}}

Also, some systematists recognize paraphyletic groups as being involved in evolutionary transitions, the development of the first tetrapods from their ancestors for example. Any name given to these hypothetical ancestors to distinguish them from tetrapods—"fish", for example—necessarily picks out a paraphyletic group, because the descendant tetrapods are not included.{{cite web|author1=Kazlev, M.A. |author2=White, T. |name-list-style=amp |title=Amphibians, Systematics, and Cladistics |url=http://palaeos.com/vertebrates/tetrapoda/amphibians.html |publisher=Palaeos website |access-date=16 August 2012}} Other systematists consider reification of paraphyletic groups to obscure inferred patterns of evolutionary history.{{cite journal |last=Patterson |first=Colin |title=Morphology and interrelationships of primitive actinopterygian fishes |journal=American Zoologist |volume=22 |issue=2 |year=1982 |pages=241–259|doi=10.1093/icb/22.2.241 |doi-access=free }}

The term "evolutionary grade" is sometimes used for paraphyletic groups.{{Cite book | first=Richard | last=Dawkins | author-link=Richard Dawkins | title=The Ancestor's Tale, A Pilgrimage to the Dawn of Life | chapter=Mammal-like Reptiles | publisher=Houghton Mifflin | location=Boston| year=2004| isbn=978-0-618-00583-3 | title-link=The Ancestor's Tale }}

Moreover, the concepts of monophyly, paraphyly, and polyphyly have been used in deducing key genes for barcoding of diverse group of species.{{cite journal |doi=10.1016/j.gene.2019.143967 |pmid=31279710 |title=Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group |journal=Gene |volume=713 |pages=143967 |year=2019 |last1=Parhi |first1=J. |author2=Tripathy, P.S. |author3=Priyadarshi, H. |author4=Mandal S.C. |author5=Pandey P.K. |s2cid=195828782 }}

{{main|Tree model}}

The concept of paraphyly has also been applied to historical linguistics, where the methods of cladistics have found some utility in comparing languages. For instance, the Formosan languages form a paraphyletic group of the Austronesian languages because they consist of the nine branches of the Austronesian family that are not Malayo-Polynesian and are restricted to the island of Taiwan.Greenhill, Simon J. and Russell D. Gray. (2009.) "Austronesian Language and Phylogenies: Myths and Misconceptions About Bayesian Computational Methods", in Austronesian Historical Linguistics and Culture History: a Festschrift for Robert Blust, edited by Alexander Adelaar and Andrew Pawley. Canberra: Pacific Linguistics, Research School of Pacific and Asian Studies, The Australian National University.

• Glossary of scientific naming
• Polyphyly

{{reflist|group=note}}

{{reflist|30em}}

• {{Cite book |author=Simpson, Michael George |year=2006 |title=Plant systematics |publisher=Academic Press |place=Burlington; San Diego; London |isbn=978-0-12-644460-5 |ref=none}}
• [https://www.jstor.org/stable/41059863?seq=1#page_scan_tab_contents Paraphyletic groups as natural units of biological classification]

{{Wiktionary|paraphyletic}}

• {{Commons category-inline|Paraphyly}}
• {{Cite journal|author=Funk, D. J. |author2=Omland, K. E. |year=2003 |title=Species-level paraphyly and polyphyly: Frequency, cause and consequences, with insights from animal mitochondrial DNA |journal=Annual Review of Ecology, Evolution, and Systematics |volume=34 |pages=397–423 |doi=10.1146/annurev.ecolsys.34.011802.132421 |s2cid=33951905 |s2cid-access=free |ref=none}}

{{Phylogenetics}}

Category:Phylogenetics

Category:Paraphyletic groups