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.
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. 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.
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) 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.
Independently evolved traits
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.
- Amphibious fish are polyphyletic, not paraphyletic. Although they appear similar, several different groups of amphibious fishes such as mudskippers and lungfishes evolved independently in a process of convergent evolution in distant relatives faced with similar ecological circumstances.
- Flightless birds are polyphyletic because they independently (in parallel) lost the ability to fly.
- Animals with a dorsal fin are not paraphyletic, even though their last common ancestor may have had such a fin, because the Mesozoic ancestors of porpoises did not have such a fin, whereas pre-Mesozoic fish did have one.
- Quadrupedal archosaurs are not a paraphyletic group. Bipedal dinosaurs like Eoraptor, ancestral to quadrupedal ones, were descendants of the last common ancestor of quadrupedal dinosaurs and other quadrupedal archosaurs like the crocodilians.
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.
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