Paraphyly in the context of Coniferales

A protist (/ˈproʊtɪst/ PROH-tist) or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a paraphyletic grouping of all descendants of the last eukaryotic common ancestor excluding land plants, animals, and fungi.

Protists were historically regarded as a separate taxonomic kingdom known as Protista or Protoctista. With the advent of phylogenetic analysis and electron microscopy studies, the use of Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread across several eukaryotic clades called supergroups, such as Archaeplastida (photoautotrophs that includes land plants), SAR, Obazoa (which includes fungi and animals), Amoebozoa and "Excavata".

Cladistics (/kləˈdɪstɪks/ klə-DIST-iks; from Ancient Greek κλάδος kládos 'branch') 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.

As a hypothesis, a clade can be rejected only if some groupings were explicitly excluded. It may then be found that the excluded group did actually descend from the last common ancestor of the group, and thus emerged within the group. ("Evolved from" is misleading, because in cladistics all descendants stay in the ancestral group). To keep only valid clades, upon finding that the group is paraphyletic this way, either such excluded groups should be granted to the clade, or the group should be abolished.

In biology, a clade (//kleɪd//) (from Ancient Greek κλάδος (kládos) 'branch'), also known as a monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields.

The common ancestor may be an individual, a population, or a species (extinct or extant). Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed monophyletic (Greek: "one clan") groups.

Monkey is a common name that may refer to most mammals of the infraorder Simiiformes, also known as simians. Traditionally, all animals in the group now known as simians are counted as monkeys except the apes. Thus monkeys, in that sense, constitute an incomplete paraphyletic grouping; alternatively, if apes (Hominoidea) are included, monkeys and simians are synonyms.

In 1812, Étienne Geoffroy grouped the apes and the Cercopithecidae group of monkeys together and established the name Catarrhini, "Old World monkeys" ("singes de l'Ancien Monde" in French). The extant sister of the Catarrhini in the monkey ("singes") group is the Platyrrhini (New World monkeys). Some nine million years before the divergence between the Cercopithecidae and the apes, the Platyrrhini emerged within "monkeys" by migration to South America likely by ocean. Apes are thus deep in the tree of extant and extinct monkeys, and any of the apes is distinctly closer related to the Cercopithecidae than the Platyrrhini are.

Reptiles, as commonly defined, are a group of tetrapods with an ectothermic metabolism and amniotic development. Living traditional reptiles comprise four orders: Testudines, Crocodilia, Squamata, and Rhynchocephalia. About 12,000 living species of reptiles are listed in the Reptile Database. The study of the traditional reptile orders, customarily in combination with the study of modern amphibians, is called herpetology.

Reptiles have been subject to several conflicting taxonomic definitions. In evolutionary taxonomy, reptiles are gathered together under the class Reptilia (/rɛpˈtɪliə/ rep-TIL-ee-ə), which corresponds to common usage. Modern cladistic taxonomy regards that group as paraphyletic, since genetic and paleontological evidence has determined that crocodilians are more closely related to birds (class Aves), members of Dinosauria, than to other living reptiles, and thus birds are nested among reptiles from a phylogenetic perspective. Many cladistic systems therefore redefine Reptilia as a clade (monophyletic group) including birds, though the precise definition of this clade varies between authors. A similar concept is clade Sauropsida, which refers to all amniotes more closely related to modern reptiles than to mammals.

Viridiplantae (lit. 'green plants'; kingdom Plantae sensu stricto) is a clade of around 450,000–500,000 species of eukaryotic organisms, most of which obtain their energy by photosynthesis. The green plants are chloroplast-bearing autotrophs that play important primary production roles in both terrestrial and aquatic ecosystems. They include green algae, which are primarily aquatic, and the land plants (embryophytes, Plantae sensu strictissimo), which emerged within freshwater green algae. Green algae traditionally excludes the land plants, rendering them a paraphyletic group, however it is cladistically accurate to think of land plants as a special clade of green algae that evolved to thrive on dry land. Since the realization that the embryophytes emerged from within the green algae, some authors are starting to include them.

Viridiplantae species all have cells with cellulose in their cell walls, and primary chloroplasts derived from endosymbiosis with cyanobacteria that contain chlorophylls a and b and lack phycobilins. Corroborating this, a basal phagotroph Archaeplastida group has been found in the Rhodelphidia. In some classification systems, the group has been treated as a kingdom, under various names, e.g. Viridiplantae, Chlorobionta, or simply Plantae, the latter expanding the traditional plant kingdom of embryophytes to include the green algae. Adl et al., who produced a classification for all eukaryotes in 2005, introduced the name Chloroplastida for this group, reflecting the group having primary chloroplasts. They rejected the name Viridiplantae on the grounds that some of the species are not plants as understood traditionally. Together with Rhodophyta, glaucophytes and other basal groups, Viridiplantae belong to a larger clade called Archaeplastida which in itself is sometimes described as Plantae sensu lato.

Charophyta (UK: /kəˈrɒfɪtə, ˌkærəˈfaɪtə/) is a paraphyletic group of freshwater green algae, called charophytes (/ˈkærəˌfaɪts/), sometimes treated as a division, yet also as a superdivision. The terrestrial plants, the Embryophyta emerged deep within Charophyta, possibly from terrestrial unicellular charophytes, with the class Zygnematophyceae as a sister group.

With the Embryophyta now cladistically placed in the Charophyta, it is a synonym of Streptophyta. The sister group of the charophytes are the Chlorophyta. In some charophyte groups, such as the Zygnematophyceae or conjugating green algae, flagella are absent and sexual reproduction does not involve free-swimming flagellate sperm. Flagellate sperm, however, are found in stoneworts (Charales) and Coleochaetales, orders of parenchymatous charophytes that are the closest relatives of the land plants, where flagellate sperm are also present in all except the conifers and flowering plants. Fossil stoneworts of early Devonian age that are similar to those of the present day have been described from the Rhynie chert of Scotland. Somewhat different charophytes have also been collected from the Late Devonian (Famennian) Waterloo Farm lagerstätte of South Africa. These include two species each of Octochara and Hexachara, which are the oldest fossils of Charophyte axes bearing in situ oogonia.

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 /ˈpɒlɪˌfaɪli/. It is contrasted with monophyly and paraphyly.

For example, the biological characteristic of warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds; "warm-blooded animals" is therefore a polyphyletic grouping. Other examples of polyphyletic groups are algae, C4 photosynthetic plants, and edentates.

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

1. the grouping contains its own most recent common ancestor (or more precisely an ancestral population), i.e. excludes non-descendants of that common ancestor
2. the grouping contains all the descendants of that common ancestor, without exception

Monophyly is contrasted with paraphyly and polyphyly as shown in the second diagram. A paraphyletic grouping meets 1. but not 2., thus consisting of the descendants of a common ancestor, excepting one or more monophyletic subgroups. A polyphyletic grouping meets neither criterion, and instead serves to characterize convergent relationships of biological features rather than genetic relationships – for example, night-active primates, fruit trees, or aquatic insects. As such, these characteristic features of a polyphyletic grouping are not inherited from a common ancestor, but evolved independently.

The anamniotes are an informal group of vertebrates comprising all fish and amphibians, which lay their eggs in aquatic environments. They are distinguished from the amniotes (reptiles, birds and mammals), which can reproduce on dry land either by laying shelled eggs or by carrying fertilized eggs within the female. Older sources, particularly before the 20th century, may refer to anamniotes as "lower vertebrates" and amniotes as "higher vertebrates", based on the antiquated idea of the evolutionary great chain of being.

The name "anamniote" is a back-formation word created by adding the prefix an- to the word amniote, which in turn refers to the amnion, an extraembryonic membrane present during the amniotes' embryonic development which serves as a biochemical barrier that shields the embryo from environmental fluctuations by regulating the oxygen, carbon dioxide and metabolic waste exchanges and secreting a cushioning fluid. As the name suggests, anamniote embryos lack an amnion during embryonic development, and therefore rely on the presence of external water to provide oxygen and help dilute and excrete waste products (particularly ammonia) via diffusion in order for the embryo to complete development without being intoxicated by their own metabolites. This means anamniotes are almost always dependent on an aqueous (or at least very moist) environment for reproduction and are thus restricted to spawning in or near water bodies. They are also highly sensitive to chemical and temperature variation in the surrounding water, and are also more vulnerable to egg predation and parasitism.

Excavata is an obsolete, extensive and diverse paraphyletic group of unicellular Eukaryota. The group was first suggested by Simpson and Patterson in 1999 and the name latinized and assigned a rank by Thomas Cavalier-Smith in 2002. It contains a variety of free-living and symbiotic protists, and includes some important parasites of humans such as Giardia and Trichomonas. Excavates were formerly considered to be included in the now- obsolete Protista kingdom. They were distinguished from other lineages based on electron-microscopic information about how the cells are arranged (they have a distinctive ultrastructural identity). They are considered to be a basal flagellate lineage.

On the basis of phylogenomic analyses, the group was shown to contain three widely separated eukaryote groups, the discobids, metamonads, and malawimonads. A current view of the composition of the excavates is given below, indicating that the group is paraphyletic. Except for some Euglenozoa, all are non-photosynthetic.

Pteropoda (common name pteropods, from the Greek meaning "wing-foot") are specialized free-swimming pelagic sea snails and sea slugs, marine opisthobranch gastropods. Most live in the top 10 m of the ocean and are less than 1 cm long. The monophyly of Pteropoda is the subject of a lengthy debate; they have even been considered as paraphyletic with respect to cephalopods. Current consensus, guided by molecular studies, leans towards interpreting the group as monophyletic.

Pteropoda encompasses the two clades Thecosomata, the sea butterflies, and Gymnosomata, the sea angels. The Thecosomata (lit. "case-body") have a shell, while the Gymnosomata ("naked body") do not. The two clades may or may not be sister taxa; if not, their similarity (in that they are both pelagic, small, and transparent, and both groups swim using wing-like flaps (parapodia) which protrude from their bodies) may reflect convergent adaptation to their particular lifestyle.

Phasianidae is a family of heavy, ground-living birds, which includes pheasants, grouse, partridges, junglefowl, chickens, turkeys, Old World quail, and peafowl. The family includes many of the most popular gamebirds. The family includes 185 species divided into 54 genera. It was formerly broken up into two subfamilies, the Phasianinae and the Perdicinae. However, this treatment is now known to be paraphyletic and polyphyletic, respectively, and more recent evidence supports breaking it up into two subfamilies: Rollulinae and Phasianinae, with the latter containing multiple tribes within two clades. The New World quail (Odontophoridae) and guineafowl (Numididae) were formerly sometimes included in this family, but are now typically placed in families of their own; conversely, grouse and turkeys, formerly often treated as distinct families (Tetraonidae and Meleagrididae, respectively), are now known to be deeply nested within Phasianidae, so they are now included in the present family.

Eagle is the common name for certain large birds of prey within the family of the Accipitridae. While on a genetic level, only the subfamily Aquilinae comprises "true eagles", many other species are commonly referred to as eagles, such as the bald eagle, and the term generally carries no taxonomic weight. Most of the 68 species of eagles are from Eurasia and Africa. Outside this area, just 14 species can be found—two in North America, nine in Central and South America, and three in Australia.

Eagles are not a natural group but denote essentially any kind of bird of prey large enough to hunt sizeable (about 50 cm long or more overall) vertebrates.