In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. The arrangement of the members of a paraphyletic group is called a paraphyly. The term is commonly used in phylogenetics (a subfield of biology) and in linguistics.
The term was coined to apply to well-known taxa like Reptilia (reptiles) which, as commonly named and traditionally defined, is paraphyletic with respect to mammals and birds. Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor, including all extant reptiles as well as the extinct synapsids, except for mammals and birds. Other commonly recognized paraphyletic groups include fish, monkeys, and lizards.
If many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, or monophyletic group, which is any group of species that includes a common ancestor and all of its descendants. Formally, a paraphyletic group is the relative complement of one or more subclades within a clade: removing one or more subclades leaves a paraphyletic group.
The term paraphyly, or paraphyletic, derives from the two Ancient Greek words παρά (pará), meaning "beside, near", and φῦλον (phûlon), meaning "genus, species", 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 μόνος (mónos), 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 πολύς (polús), meaning "many, a lot of", and refers to the fact that a polyphyletic group includes organisms arising from multiple ancestral sources.
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. Ereshefsky has argued that paraphyletic taxa are the result of anagenesis in the excluded group or groups.
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.
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. Related terminology that may be encountered are stem group, chronospecies, budding cladogenesis, anagenesis, or 'grade' groupings. Paraphyletic groups are often a relic from previous erroneous assessments about phylogenic relationships, or from before the rise of cladistics.
The prokaryotes (single-celled life forms without cell nuclei), 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 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 January 1, 1980 (in contrast to a 1753 start date under the ICBN/ICN).
Among plants, dicotyledons (in the traditional sense) are paraphyletic because the group excludes monocotyledons. "Dicotyledon" has not been used as an ICBN classification for decades, but is allowed as a synonym of Magnoliopsida.[note 1] Phylogenetic analysis indicates that the monocots are a development from a dicot ancestor. Excluding monocots from the dicots makes the latter a paraphyletic group.
Among animals, several familiar groups are not, in fact, clades. The order Artiodactyla (even-toed ungulates) is paraphyletic because it excludes Cetaceans (whales, dolphins, etc.). In the ICZN Code, the two taxa are orders of equal rank. Molecular studies, however, have shown that the Cetacea descend from artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls must be paraphyletic. The class Reptilia as traditionally defined is paraphyletic because it excludes birds (class Aves) and mammals. In the ICZN Code, the three taxa are classes of equal rank. However, mammals hail from the synapsids (which were once described as "mammal-like reptiles") and birds are descended from the dinosaurs (a group of Diapsida), both of which are reptiles. Alternatively, reptiles are paraphyletic because they gave rise to (only) birds. Birds and reptiles together make Sauropsids. Osteichthyes, bony fish, are paraphyletic when they include only Actinopterygii (ray-finned fish) and Sarcopterygii (lungfish, etc.), excluding tetrapods; more recently, Osteichthyes is treated as a clade, including the tetrapods. The wasps are paraphyletic, consisting of the narrow-waisted Apocrita without the ants and bees. The sawflies (Symphyta) are similarly paraphyletic, forming all of the Hymenoptera except for the Apocrita, a clade deep within the sawfly tree. Crustaceans are not a clade because the Hexapoda (insects) are excluded. The modern clade that spans all of them is the Tetraconata.
Species have a special status in systematics as being an observable feature of nature itself and as the basic unit of classification. The phylogenetic species concept requires species to be monophyletic, but paraphyletic species are common in nature. Paraphyly is common in speciation, whereby a mother species (a paraspecies) gives rise to a daughter species without itself becoming extinct. Research indicates as many as 20 percent of all animal species and between 20 and 50 percent of plant species are paraphyletic. Accounting for these facts, some taxonomists argue that paraphyly is a trait of nature that should be acknowledged at higher taxonomic levels.
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) has taken place in an environment 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 excludes many of its descendant organisms (the eukaryotes), but it is very useful because it has a clearly defined and significant distinction (absence of a cell nucleus, a plesiomorphy) from its excluded descendants.
Also, paraphyletic groups are involved in evolutionary transitions, the development of the first tetrapods from their ancestors for example. Any name given to these ancestors to distinguish them from tetrapods—"fish", for example—necessarily picks out a paraphyletic group, because the descendant tetrapods are not included.
The term "evolutionary grade" is sometimes used for paraphyletic groups. Moreover, the concepts of monophyly, paraphyly, and polyphyly have been used in deducing key genes for barcoding of diverse group of species.
Viviparity, the production of offspring without the laying of a fertilized egg, developed independently in the lineages that led to humans (Homo sapiens) and southern water skinks (Eulampus tympanum, a kind of lizard). Put another way, at least one of the lineages that led to these species from their last common ancestor contains nonviviparous animals, the pelycosaurs ancestral to mammals; vivipary appeared subsequently in the mammal lineage.
Independently-developed traits like these cannot be used to distinguish paraphyletic groups because paraphyly requires the excluded groups to be monophyletic. Pelycosaurs were descended from the last common ancestor of skinks and humans, so vivipary could be paraphyletic only if the pelycosaurs were part of an excluded monophyletic group. Because this group is monophyletic, it contains all descendants of the pelycosaurs; because it is excluded, it contains no viviparous animals. This does not work, because humans are among these descendants. Vivipary in a group that includes humans and skinks cannot be paraphyletic.
The following list recapitulates a number of paraphyletic groups proposed in the literature, and provides the corresponding monophyletic taxa.
|Paraphyletic taxon||Excluded clades||Corresponding monophyletic taxon||References and notes|
|Protista||Animalia, Plantae, and Fungi||Eukaryota|||
|Worm||Lots of Groups||Nephrozoa|||
|Charophyte||Embryophyte (Land plants)||Streptophyta|||
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.
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.
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Aquiloeurycea is a genus of salamanders in the family Plethodontidae. They are endemic to Mexico. The genus corresponds to the former "Pseudoeurycea cephalica species group", which was established in order to preserve Ixalotriton and Bolitoglossa while avoiding paraphyly of Pseudoeurycea.Chirixalus
Chirixalus is a now-synonymized genus in the moss frog family (Rhacophoridae). It used to include species from southern and eastern Asia. These species are now found mostly in Chiromantis, but also in Kurixalus, Liuixalus, Feihyla, Gracixalus, and Theloderma. The demise of Chirixalus and its absorption into Chiromantis resulted mostly from polyphyly of Chirixalus and paraphyly of Chiromantis.Crane fly
Crane fly is a common name referring to any member of the insect family Tipulidae, of the order Diptera, true flies in the superfamily Tipuloidea. Cylindrotominae, Limoniinae, and Pediciinae have been ranked as subfamilies of Tipulidae by most authors, though occasionally elevated to family rank. In the most recent classifications, only Pediciidae is now ranked as a separate family, due to considerations of paraphyly. In colloquial speech, crane flies are sometimes known as mosquito hawks or daddy longlegs, a term also used to describe opiliones or the family Pholcidae, both of which are arachnids. The larvae of crane flies are known commonly as leatherjackets.Crane flies are found worldwide, though individual species usually have limited ranges. They are most diverse in the tropics, and are also common in northern latitudes and high elevations.The Tipulidae is one of the largest groups of flies, including over 15,000 species and subspecies in 525 genera and subgenera. Most crane flies were described by the entomologist Charles Paul Alexander, a fly specialist, in over 1000 research publications.Evolutionary taxonomy
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.
Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only), in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them), thus permitting paraphyletic taxa.Flea beetle
The flea beetle is a small, jumping beetle of the leaf beetle family (Chrysomelidae), that makes up the tribe Alticini which is part of the subfamily Galerucinae. Historically the flea beetles were classified as their own subfamily.
Though most tribes of the Galerucinae are suspect of rampant paraphyly in the present delimitation, the Alticini seem to form a good clade.Hydroidolina
Hydroidolina is a subclass of hydrozoans in the phylum Cnidaria. It contains the bulk of the paraphyletic "Hydroida" which were one of the main groupings of the class Hydrozoa in older classifications and were placed at order rank. Hydroidolina also includes, however, the highly advanced colonial jellies of Siphonophora, which were not included in the "Hydroida".Lophotrochozoa
Lophotrochozoa (, "crest/wheel animals") is a clade of protostome animals within the Spiralia. The taxon was established as a monophyletic group based on molecular evidence.Monophyly
In cladistics, a monophyletic group, or clade, is a group of organisms that consists of all the descendants of a common ancestor (or more precisely ancestral population). Monophyletic groups are typically characterised by shared derived characteristics (synapomorphies), which distinguish organisms in the clade from other organisms. The arrangement of the members of a monophyletic group is called a monophyly.
Monophyly is contrasted with paraphyly and polyphyly as shown in the second diagram. A paraphyletic group consists of all of the descendants of a common ancestor minus one or more monophyletic groups. A polyphyletic group is characterized by convergent features or habits of scientific interest (for example, night-active primates, fruit trees, aquatic insects). The features by which a polyphyletic group is differentiated from others are not inherited from a common ancestor.
These definitions have taken some time to be accepted. When the cladistics school of thought became mainstream in the 1960s, several alternative definitions were in use. Indeed, taxonomists sometimes used terms without defining them, leading to confusion in the early literature, a confusion which persists.The first diagram shows a phylogenetic tree with two monophyletic groups. The several groups and subgroups are particularly situated as branches of the tree to indicate ordered lineal relationships between all the organisms shown. Further, any group may (or may not) be considered a taxon by modern systematics, depending upon the selection of its members in relation to their common ancestor(s); see second and third diagrams.Osteolepidida
Osteolepidida, also known as osteolepiformes, are a group of prehistoric lobe-finned fishes which appeared first time during the Devonian period. The order contains five families: Canowindridae, Megalichthyidae, Osteolepidae, Thysanolepidae and Tristichopteridae. The superorder is generally considered to be paraphyletic because the characters that define it are mainly attributes of stem tetrapodomorphs.Below is a cladogram showing the paraphyly of Osteolepiformes compiled and modified from Ahlberg and Johanson (1998). See also Swartz 2012. The Osteolepiformes are marked by the green bracket.Polyphyly
A polyphyletic group is a set of organisms, or other evolving elements, that have been grouped together but do not share an immediate common ancestor. The term is often applied to groups that share characteristics that appear to be similar but have not been inherited from common ancestors; these characteristics are known as homoplasies, and the development and phenomenon of homoplasies is known as convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly.
Alternatively, polyphyletic is simply used to describe a group whose members come from multiple ancestral sources, regardless of similarity of characteristics. For example, the biological characteristic of warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds. Other polyphyletic groups are for example algae, C4 photosynthetic plants, and edentates.Many biologists aim to avoid homoplasies in grouping taxa together and therefore it is frequently a goal to eliminate groups that are found to be polyphyletic. This is often the stimulus for major revisions of the classification schemes.
Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group Alternaria, for example, can lead researchers to regard the group as a valid genus while acknowledging its polyphyly.. In recent research, the concepts of monophyly, paraphyly, and polyphyly have been used in deducing key genes for barcoding of diverse group of species.Pompiloidea
Pompiloidea is a superfamily that includes spider wasps and velvet ants, among others. in the order Hymenoptera. There are at least 5 families and 290 described species in Pompiloidea.Proteromonadidae
Proteromonadidae is a paraphyletic family of heterokonts, that resemble Opalinidae.Pseudoeurycea
Pseudoeurycea is a genus of salamander in the family Plethodontidae. The members of this genus are commonly known as the false brook salamanders. They are found in Mexico and Guatemala.In order to preserve Ixalotriton and Bolitoglossa while avoiding paraphyly of Pseudoeurycea, species in the former "Pseudoeurycea bellii species group" have been moved to the genus Isthmura, and those in the former "Pseudoeurycea cephalica species group" to Aquiloeurycea.Sidalcea
Sidalcea is a genus (approx. 25 species) of the botanical family Malvaceae. It contains several species of flowering plants known generally as checkerblooms or checkermallows, or prairie mallows in the United Kingdom. They can be annuals or perennials, some rhizomatous. They are native to West and Central North America.
In mid- to late summer the clumps of toothed basal leaves produce erect flowering stems, with 5-petalled mallow-type flowers in terminal racemes, in shades of pink, white and purple.Sidalcea is generally diploid (2n = 20), but polyploidy (4n, 6n) also occurs.Annuality appears to have evolved multiple times (4+) within this genus, although an ancestral annual state with annual paraphyly is also possible. Further, evolution rates within annual Sidalcea lineages appear to be faster than those of perennial lineages, at least when examining nuclear ribosomal DNA (internal and external transcribed spacer regions).Selected species:
(A = annual, P = perennial)
Sidalcea asprella (P)
Sidalcea calycosa – annual checkerbloom (A)
Sidalcea campestris – meadow checkermallow (P)
Sidalcea candida – white checkerbloom (P)
Sidalcea covillei – Owens Valley sidalcea (P)
Sidalcea cusickii – Cusick's checkermallow (P)
Sidalcea diploscypha – fringed checkerbloom (A)
Sidalcea glaucescens – waxy checkerbloom (P)
Sidalcea gigantea (P)
Sidalcea hartwegii – valley checkerbloom (A)
Sidalcea hendersonii – Henderson's checkermallow (P)
Sidalcea hickmanii – chaparral checkerbloom (P)
Sidalcea hirsuta – hairy checkerbloom (A)
Sidalcea hirtipes - hairy-stemmed checker-mallow (P)
Sidalcea keckii – Keck's checkerbloom (A)
Sidalcea malachroides – mapleleaf checkerbloom (P)
Sidalcea malviflora – dwarf checkerbloom
Sidalcea multifida (P)
Sidalcea nelsoniana – Nelson's checkermallow (threatened)
Sidalcea neomexicana – Salt Spring checkerbloom (P)
Sidalcea oregana – Oregon checkerbloom (miniature hollyhock)
Sidalcea oregana var. calva – Wenatchee Mountains checkermallow
Sidalcea pedata – birdfooted checkerbloom, Big Bear checkerbloom (P)
Sidalcea ranunculacea – marsh checkerbloom
Sidalcea reptans – Sierra checkerbloom
Sidalcea robusta – Butte County checkerbloom (P)
Sidalcea stipularis – Scadden Flat checkerbloom (P)
Sidalcea virgata (P)Garden cultivars are hybrids between S. candida and S. malviflora. The cultivars "Elsie Heugh" and "William Smith" have gained the Royal Horticultural Society's Award of Garden Merit.Syndiniales
The Syndiniales are an order of early branching dinoflagellates (also known as Marine Alveolates, "MALVs"), found as parasites of crustaceans, fish, algae, cnidarians, and protists (ciliates, radiolarians, other dinoflagellates). The trophic form is often multinucleate, and ultimately divides to form motile spores, which have two flagella in typical dinoflagellate arrangement. They lack a theca and chloroplasts, and unlike all other orders, the nucleus is never a dinokaryon. A well-studied example is Amoebophrya, which is a parasite of other dinoflagellates and may play a part in ending red tides. Several MALV groups have been assigned to Syndiniales; recent studies, however, show paraphyly of MALVs suggesting that only those groups that branch as sister to dinokaryotes ('core dinoflagellates') belong to Syndiniales.Taxon in disguise
In bacteriology, a taxon in disguise is a species, genus or higher unit of biological classification whose evolutionary history reveals has evolved from another unit of similar or lower rank, making the parent unit paraphyletic. This happens when rapid evolution makes a new species appear radically different from the ancestral group, so that it is not (initially) recognised as belonging to the parent phylogenetic group, leaving the latter an evolutionary grade.
While the term is from bacteriology, parallel examples are found throughout the tree of life. E.g. four-footed animals have evolved from piscine ancestors, yet are not generally considered fish. The four footed animals can thus be said to be "fish in disguise". In many cases, the paraphyly can be resolved by re-classifying the taxon in question under the parent group, but in bacteriology renaming groups may have serious consequences as it may cause confusion over the identity of pathogens, and is generally avoided for some groups.Thynnidae
Thynnidae (also known as flower wasps) are a family of large solitary wasps whose larvae are almost universally parasitoids of various beetle larvae, especially those in the superfamily Scarabaeoidea. Until recently, the constituents of this family were classified in the family Tiphiidae, but multiple studies have independently confirmed that thynnids are a separate lineage.Most species are small, but they can be up to 30 mm long. The females of some subfamilies (all Diamminae, Methochinae, and Thynninae) are wingless, and hunt ground-dwelling (fossorial) beetle larvae, or (in one species) mole crickets. The prey is paralysed with the female's sting and an egg is laid on it so the wasp larva has a ready supply of food. In species where both sexes are winged, males are similar in size to the females, but are much more slender. The males of species with wingless females, however, are often much larger than the females and have wings, the adults mating in the air, with the female carried by the male's genitalia. Adults feed on nectar and are minor pollinators. As some of the ground-dwelling scarab species attacked by thynnids are pests, some of these wasps are considered beneficial as biological control agents.Tiphioidea
Tiphioidea is a suggested superfamily of stinging wasps in the order Hymenoptera. There are two families in Tiphioidea, Tiphiidae and Sierolomorphidae.
Recent research in molecular phylogenetics has resulted in the reorganization of the infraorder Aculeata, which now contains eight superfamilies: Apoidea, Chrysidoidea, Formicoidea, Pompiloidea, Scolioidea, Tiphioidea, Thynnoidea, and Vespoidea.Victorinini
Victorinini is a tribe of brush-footed butterflies. The four butterfly genera contained in this tribe are Anartia, Metamorpha, Napeocles, and Siproeta.
Those genera were previously included in the Kallimini tribe. In the early 2000s, molecular phylogenetics determined that Kallimini encountered a paraphyly with regard to the Melitaeini. There is also some indication that the genus Siproeta could be paraphyletic with regard to Napeocles.