Paraphyly

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In this phylogenetic tree, the green group is paraphyletic; it is composed of a common ancestor (the lowest green vertical stem) and some of its descendants, but it excludes the blue group (a monophyletic group) which diverged from the green group. Clade-grade II.svg
In this phylogenetic tree, the green group is paraphyletic; it is composed of a common ancestor (the lowest green vertical stem) and some of its descendants, but it excludes the blue group (a monophyletic group) which diverged from the green group.

Paraphyly is a taxonomic term describing a grouping that consists of the grouping's last common ancestor and some but not all of its descendant lineages. The grouping is said to be paraphyletic with respect to the excluded subgroups. In contrast, a monophyletic grouping (a clade) includes a common ancestor and all of its descendants.

Contents

The terms are commonly used in phylogenetics (a subfield of biology) and in the tree model of historical linguistics. Paraphyletic groups are identified by a combination of synapomorphies and symplesiomorphies. If many subgroups are missing from the named group, it is said to be polyparaphyletic.

The term received currency during the debates of the 1960s and 1970s accompanying the rise of cladistics, having been coined by zoologist Willi Hennig to apply to well-known taxa like Reptilia (reptiles), which is paraphyletic with respect to birds. Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor except for birds. Other commonly recognized paraphyletic groups include fish, monkeys, and lizards. [1] [ page needed ]

Etymology

The term paraphyly, or paraphyletic, derives from the two Ancient Greek words παρά (pará), meaning "beside, near", and φῦλον (phûlon), meaning "genus, species", [2] [3] 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", [2] [3] 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", [2] [3] and refers to the fact that a polyphyletic group includes organisms arising from multiple ancestral sources.

Phylogenetics

Cladogram 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). Monophyly, paraphyly, polyphyly.svg
Cladogram 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).

In 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. [4] 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. [5]

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 ]

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. [6] [7] 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. [8]

Examples

Wasps 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. Wasps are Paraphyletic.svg
Wasps 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 [9] 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). [10]

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. [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. [11]

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. [12] 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". [13]

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. [14] [15]

The "wasps" are paraphyletic, consisting of the narrow-waisted Apocrita without the ants and bees. [16] The sawflies (Symphyta) are similarly paraphyletic, forming all of the Hymenoptera except for the Apocrita, a clade deep within the sawfly tree. [14] Crustaceans are not a clade because the Hexapoda (insects) are excluded. The modern clade that spans all of them is the Tetraconata. [17] [18]

One of the goals of modern taxonomy over the past fifty years has been to eliminate paraphyletic "groups", such as the examples given here, from formal classifications. [19] [20]

Paraphyly in species

Species have a special status in systematics as being an observable feature of nature itself and as the basic unit of classification. [21] 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. [22] Research indicates as many as 20 percent of all animal species and between 20 and 50 percent of plant species are paraphyletic. [23] [24] Accounting for these facts, some taxonomists argue that paraphyly is a trait of nature that should be acknowledged at higher taxonomic levels. [25] [26]

Cladists advocate a phylogenetic species concept [27] that does not consider species to exhibit the properties of monophyly or paraphyly, concepts under that perspective which apply only to groups of species. [28] They consider Zander's extension of the "paraphyletic species" argument to higher taxa to represent a category error [29]

Uses for 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 ]

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. [30] Other systematists consider reification of paraphyletic groups to obscure inferred patterns of evolutionary history. [31]

The term "evolutionary grade" is sometimes used for paraphyletic groups. [32] Moreover, the concepts of monophyly, paraphyly, and polyphyly have been used in deducing key genes for barcoding of diverse group of species. [33]

Independently evolved traits

Current phylogenetic hypotheses of tetrapod relationships imply that viviparity, the production of offspring without the external 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, viviparity is a synapomorphy for Theria within mammals, and an autapomorphy for Eulamprus tympanum (or perhaps a synapomorphy, if other Eulamprus species are also viviparous).[ citation needed ]

Groupings based on independently-developed traits such as these examples of viviparity represent examples of polyphyly, not paraphyly.[ citation needed ]

Not paraphyly

Non-exhaustive list of paraphyletic groups

The following list recapitulates a number of paraphyletic groups proposed in the literature, and provides the corresponding monophyletic taxa.

Paraphyletic taxonExcluded cladesCorresponding monophyletic taxonReferences and notes
Prokaryotes Eukaryota Cellular organisms [36]
Protista Animalia, Plantae, and Fungi Eukaryota [37]
Invertebrates Vertebrata Animalia [38]
Worm Multiple groups Nephrozoa [39] [40]
Radiata Bilateria Eumetazoa [41]
Platyzoa Lophotrochozoa, Mesozoa Spiralia [42]
Fish Tetrapoda Vertebrate [43]
Reptiles Birds Sauropsida [44]
Nonavian Dinosaur Birds Dinosauria
Lizard Snakes, Amphisbaenia Squamates [45]
Plagiaulacidans Cimolodonta, Arginbaataridae Multituberculata [46]
Pelycosaurs Therapsida Synapsida [47]
Even-toed ungulates Cetacea Cetartiodactyla [12] [48]
Archaeoceti Neoceti Cetacea [49]
Prosimians Simiiformes Primates [50]
Crustaceans Hexapoda Tetraconata [17] [18]
Wasps Ants, Bees Apocrita [16]
Sawfly Apocrita Hymenoptera [14]
Vespoidea Apoidea, Ants Euaculeata [16]
Parasitica Aculeata Apocrita [51]
Nautiloidea Ammonoidea, Coleoidea Cephalopoda [52]
Charophyte Embryophyte (Land plants) Streptophyta [53]
Dicotyledon Monocotyledon Angiosperm [11]
Moth Butterfly Lepidoptera [54]
Coral Medusozoa, Myxozoa Cnidaria [55] [56]
Jellyfish Hydroidolina Medusozoa [57] [58] [59]
Cycloneuralia Panarthropoda Ecdysozoa [60] [61]
Rotifera Acanthocephala Syndermata [62] [63]
Mecoptera Siphonaptera Mecopteroidea
Anthoathecata Leptothecata, Siphonophorae Hydroidolina
Monkey Hominoidea Simiiformes [64] [65]
Antelope Bovini, Caprinae Bovidae [66]

Linguistics

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. [67]

See also

Explanatory notes

  1. ↑ The history of flowering plant classification can be found under History of the classification of flowering plants.

Related Research Articles

<span class="mw-page-title-main">Chordate</span> Phylum of animals having a dorsal nerve cord

A chordate is a deuterostomic animal belonging to the phylum Chordata. All chordates possess, at some point during their larval or adult stages, five distinctive physical characteristics (synapomorphies) that distinguish them from other taxa. These five synapomorphies are a notochord, a hollow dorsal nerve cord, an endostyle or thyroid, pharyngeal slits, and a post-anal tail. The name "chordate" comes from the first of these synapomorphies, the notochord, which plays a significant role in chordate body plan structuring and movements. Chordates are also bilaterally symmetric, have a coelom, possess a closed circulatory system, and exhibit metameric segmentation.

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.

<span class="mw-page-title-main">Clade</span> Group of a common ancestor and all descendants

In biological phylogenetics, a clade, also known as a monophyletic group or natural group, is a grouping of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. In the taxonomical literature, sometimes the Latin form cladus is used rather than the English form. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields.

<span class="mw-page-title-main">Monophyly</span> Property of a group of including all taxa descendant from a common ancestral species

In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of taxa which meets these criteria:

  1. the grouping contains its own most recent common ancestor, i.e. excludes non-descendants of that common ancestor
  2. the grouping contains all the descendants of that common ancestor, without exception

In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

<span class="mw-page-title-main">Polyphyly</span> Property of a group not united by common ancestry

A polyphyletic group is an assemblage that includes organisms with mixed evolutionary origin but does not include their most recent common ancestor. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly. It is contrasted with monophyly and paraphyly.

<span class="mw-page-title-main">Euteleostomi</span> Clade including most vertebrates

Euteleostomi is a successful clade that includes more than 90% of the living species of vertebrates. Both its major subgroups are successful today: Actinopterygii includes most extant bony fish species, and Sarcopterygii includes the tetrapods.

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, 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.

<span class="mw-page-title-main">Lophotrochozoa</span> Superphylum of animals

Lophotrochozoa is a clade of protostome animals within the Spiralia. The taxon was established as a monophyletic group based on molecular evidence. The clade includes animals like annelids, molluscs, bryozoans, and brachiopods.

<span class="mw-page-title-main">Apomorphy and synapomorphy</span> Two concepts on heritable traits

In phylogenetics, an apomorphy is a novel character or character state that has evolved from its ancestral form. A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.

<span class="mw-page-title-main">Crown group</span> Monophyletic closure of a set of living species

In phylogenetics, the crown group or crown assemblage is a collection of species composed of the living representatives of the collection, the most recent common ancestor of the collection, and all descendants of the most recent common ancestor. It is thus a way of defining a clade, a group consisting of a species and all its extant or extinct descendants. For example, Neornithes (birds) can be defined as a crown group, which includes the most recent common ancestor of all modern birds, and all of its extant or extinct descendants.

<span class="mw-page-title-main">Labyrinthodontia</span> Paraphyletic group of tetrapodomorphs

"Labyrinthodontia" is an informal grouping of extinct predatory amphibians which were major components of ecosystems in the late Paleozoic and early Mesozoic eras. Traditionally considered a subclass of the class Amphibia, modern classification systems recognize that labyrinthodonts are not a formal natural group (clade) exclusive of other tetrapods. Instead, they consistute an evolutionary grade, ancestral to living tetrapods such as lissamphibians and amniotes. "Labyrinthodont"-grade vertebrates evolved from lobe-finned fishes in the Devonian, though a formal boundary between fish and amphibian is difficult to define at this point in time.

<span class="mw-page-title-main">Rauisuchia</span> Informal group of Triassic archosaurs with pillar-erect posture

"Rauisuchia" is a paraphyletic group of mostly large and carnivorous Triassic archosaurs. Rauisuchians are a category of archosaurs within a larger group called Pseudosuchia, which encompasses all archosaurs more closely related to crocodilians than to birds and other dinosaurs. First named in the 1940s, Rauisuchia was a name exclusive to Triassic archosaurs which were generally large, carnivorous, and quadrupedal with a pillar-erect hip posture, though exceptions exist for all of these traits. Rauisuchians, as a traditional taxonomic group, were considered distinct from other Triassic archosaur groups such as early dinosaurs, phytosaurs, aetosaurs, and crocodylomorphs.

<span class="mw-page-title-main">Lepospondyli</span> Polyphyletic group of tetrapodomorphs

Lepospondyli is a diverse taxon of early tetrapods. With the exception of one late-surviving lepospondyl from the Late Permian of Morocco, lepospondyls lived from the Early Carboniferous (Mississippian) to the Early Permian and were geographically restricted to what is now Europe and North America. Five major groups of lepospondyls are known: Adelospondyli; Aïstopoda; Lysorophia; Microsauria; and Nectridea. Lepospondyls have a diverse range of body forms and include species with newt-like, eel- or snake-like, and lizard-like forms. Various species were aquatic, semiaquatic, or terrestrial. None were large, and they are assumed to have lived in specialized ecological niches not taken by the more numerous temnospondyl amphibians that coexisted with them in the Paleozoic. Lepospondyli was named in 1888 by Karl Alfred von Zittel, who coined the name to include some tetrapods from the Paleozoic that shared some specific characteristics in the notochord and teeth. Lepospondyls have sometimes been considered to be either related or ancestral to modern amphibians or to Amniota. It has been suggested that the grouping is polyphyletic, with aïstopods being primitive stem-tetrapods, while recumbirostran microsaurs are primitive reptiles.

<span class="mw-page-title-main">Evolutionary grade</span> Non-monophyletic grouping of organisms united by morphological or physiological characteristics

A grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

<span class="mw-page-title-main">Autapomorphy</span> Distinctive feature, known as a derived trait, that is unique to a given taxon

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon. It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, autos "self"; ἀπό, apo "away from"; and μορφή, morphḗ = "shape".

Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional method, by which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).

<span class="mw-page-title-main">Orchideae</span> Tribe of orchids

Orchideae is a tribe of orchids in the subfamily Orchidoideae. Historically, it was divided into 2 subtribes, Orchidinae and Habenariinae. The subtribe Orchidinae alone contains about 1,800 species. However, although some phylogenetic studies have established the monophyly of the subtribes, the generic boundaries are unclear, with many genera as traditionally circumscribed being paraphyletic or even polyphyletic. Species of genera such as Habenaria and Platanthera have been placed into both subtribes. A 2017 molecular phylogenetic study found that both subtribes did form clades, but did not formally recognize Habenariinae, because of missing genera and uncertainty over generic boundaries. The Asian species of Orchideae, in particular, have been subject to repeated changes of generic placement from 2012 onwards.

References

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  2. 1 2 3 Bailly, Anatole (1 January 1981). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN   978-2-01-003528-9. OCLC   461974285.
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  6. ↑ Schilhab, Theresa; Stjernfelt, Frederik; Deacon, Terrence (2012). The Symbolic Species Evolved. Springer. ISBN   978-94-007-2335-1.
  7. ↑ Villmoare, Brian (2018). "Early Homo and the role of the genus in paleoanthropology". American Journal of Physical Anthropology. 165: 72–89. doi: 10.1002/ajpa.23387 . PMID   29380889.
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  11. 1 2 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 ...."
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  15. ↑ Betancur-R, Ricardo; et al. (2013). "The Tree of Life and a New Classification of Bony Fishes". PLOS Currents Tree of Life. 5 (Edition 1). doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 . hdl:2027.42/150563. PMC   3644299 . PMID   23653398. Archived from the original on 13 October 2013.
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