Paraphyletic in the context of Microbat

Marine protists are defined by their habitat as protists that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life originated as marine single-celled prokaryotes (bacteria and archaea) and later evolved into more complex eukaryotes. Eukaryotes are the more developed life forms known as plants, animals, fungi and protists. Protists are the eukaryotes that cannot be classified as plants, fungi or animals. They are mostly single-celled and microscopic. The term protist came into use historically as a term of convenience for eukaryotes that cannot be strictly classified as plants, animals or fungi. They are not a part of modern cladistics because they are paraphyletic (lacking a common ancestor for all descendants).

Most protists are too small to be seen with the naked eye. They are highly diverse organisms currently organised into 18 phyla, but not easy to classify. Studies have shown high protist diversity exists in oceans, deep sea-vents and river sediments, suggesting large numbers of eukaryotic microbial communities have yet to be discovered. There has been little research on mixotrophic protists, but recent studies in marine environments found mixotrophic protists contribute a significant part of the protist biomass. Since protists are eukaryotes (and not prokaryotes) they possess within their cell at least one nucleus, as well as organelles such as mitochondria and Golgi bodies. Many protist species can switch between asexual reproduction and sexual reproduction involving meiosis and fertilization.

Archaea (/ɑːrˈkiːə/ ar-KEE-ə) is a domain of organisms. Traditionally, Archaea included only its prokaryotic members, but has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even though the domain Archaea cladistically includes eukaryotes, the term archaea (sing. archaeon /ɑːrˈkiːɒn/ ar-KEE-on; from Ancient Greek ἀρχαῖον arkhaîon 'ancient') in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria (/ˌɑːrkibækˈtɪəriə/, in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from Bacteria and Eukaryota, including: cell membranes made of ether-linked lipids; metabolisms such as methanogenesis; and a unique motility structure known as an archaellum. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. It is unknown if they can produce endospores.

Archaea are often similar to bacteria in size and shape, although a few have very different shapes, such as the flat, square cells of Haloquadratum walsbyi. Despite this, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. The salt-tolerant Halobacteria use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores. The first observed archaea were extremophiles, living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.

A fish is an aquatic, anamniotic, gill-bearing vertebrate animal with swimming fins and a hard skull, but lacking limbs with digits. Fish can be grouped into the more basal jawless fish and the more common jawed fish, the latter including all living cartilaginous and bony fish, as well as the extinct placoderms and acanthodians. In a break from the long tradition of grouping all fish into a single class (Pisces), modern phylogenetics views fish as a paraphyletic group which includes all vertebrates except tetrapods. In English, the plural of "fish" is fish when referring to individuals and fishes when referring to species.

Most fish are cold-blooded, their body temperature varying with the surrounding water, though some large, active swimmers like the white shark and tuna can maintain a higher core temperature. Many fish can communicate acoustically with each other, such as during courtship displays. The study of fish is known as ichthyology.

The gymnosperms (/ˈdʒɪmnəˌspɜːrmz, -noʊ-/ nə-spurmz, -⁠noh-; from Ancient Greek γυμνός (gumnós), meaning "naked", and σπέρμα (spérma), meaning "seed", and thus, "naked seed") are a group of woody, perennial seed-producing plants, typically lacking the protective outer covering which surrounds the seeds in flowering plants, that include conifers, cycads, Ginkgo, and gnetophytes, forming the clade Gymnospermae. The name is based on the unenclosed condition of their seeds (called ovules in their unfertilized state). The non-encased condition of their seeds contrasts with the seeds and ovules of flowering plants (angiosperms), which are enclosed within an ovary. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or on their own as in yew, Torreya, and Ginkgo.

The life cycle of a gymnosperm involves alternation of generations, with a dominant diploid sporophyte phase, and a reduced haploid gametophyte phase, which is dependent on the sporophytic phase. The term "gymnosperm" is often used in paleobotany to refer to (the paraphyletic group of) all non-angiosperm seed plants. In that case, to specify the modern monophyletic group of gymnosperms, the term Acrogymnospermae is sometimes used.

Invertebrates are animals that neither develop nor retain a vertebral column (commonly known as a spine or backbone), which evolved from the notochord. It is a paraphyletic grouping including all animals excluding the chordate subphylum Vertebrata, i.e. vertebrates. Well-known phyla of invertebrates include arthropods, molluscs, annelids, echinoderms, flatworms, cnidarians, and sponges.

The majority of animal species are invertebrates; one estimate puts the figure at 97%. Many invertebrate taxa have a greater number and diversity of species than the entire subphylum of Vertebrata. Invertebrates vary widely in size, from 10 μm (0.0004 in) myxozoans to the 9–10 m (30–33 ft) colossal squid.

Amphibians are ectothermic, anamniotic, four-limbed vertebrate animals that constitute the class Amphibia. In its broadest sense, it is a paraphyletic group encompassing all tetrapods, but excluding the amniotes (tetrapods with an amniotic membrane, such as modern reptiles, birds and mammals). All extant (living) amphibians belong to the monophyletic subclass Lissamphibia, with three living orders: Anura (frogs and toads), Urodela (salamanders), and Gymnophiona (caecilians). Evolved to be mostly semiaquatic, amphibians have adapted to inhabit a wide variety of habitats, with most species living in freshwater, wetland or terrestrial ecosystems (such as riparian woodland, fossorial and even arboreal habitats). Their life cycle typically starts out as aquatic larvae with gills known as tadpoles, but some species have developed behavioural adaptations to bypass this.

Young amphibians generally undergo metamorphosis from an aquatic larval form with gills to an air-breathing adult form with lungs. Amphibians use their skin as a secondary respiratory interface, and some small terrestrial salamanders and frogs even lack lungs and rely entirely on their skin. They are superficially similar to reptiles like lizards, but unlike reptiles and other amniotes, require access to water bodies to breed. With their complex reproductive needs and permeable skins, amphibians are often ecological indicators to habitat conditions; in recent decades there has been a dramatic decline in amphibian populations for many species around the globe.

Agnatha (/ˈæɡnəθə, æɡˈneɪθə/; from Ancient Greek ἀ- (a-) 'without' and γνάθος (gnáthos) 'jaws') or jawless fish is a paraphyletic infraphylum of animals in the subphylum Vertebrata of the phylum Chordata, characterized by the lack of jaws. The group consists of both living (cyclostomes such as hagfishes and lampreys) and extinct clades (e.g. conodonts and cephalaspidomorphs, among others). They are sister to vertebrates with jaws known as gnathostomes, who evolved from jawless ancestors during the early Silurian by developing folding articulations in the first pairs of gill arches.

Molecular data, both from rRNA and from mtDNA as well as embryological data, strongly supports the hypothesis that both groups of living agnathans, hagfishes and lampreys, are more closely related to each other than to jawed fish, forming the superclass Cyclostomi.

Acanthodii or acanthodians is an extinct class of gnathostomes (jawed fishes). They are currently considered to represent a paraphyletic grade of various fish lineages basal to extant Chondrichthyes, which includes living sharks, rays, and chimaeras. Acanthodians possess a mosaic of features shared with both osteichthyans (bony fish) and chondrichthyans (cartilaginous fish). In general body shape, they were similar to modern sharks, but their epidermis was covered with tiny rhomboid platelets like the scales of holosteians (gars, bowfins).

The popular name "spiny sharks" is because they were superficially shark-shaped, with a streamlined body, paired fins, a strongly upturned tail, and stout, largely immovable bony spines supporting all the fins except the tail—hence, "spiny sharks". However, acanthodians are not true sharks; their close relation to modern cartilaginous fish can lead them to be considered "stem-sharks". Acanthodians had a cartilaginous skeleton, but their fins had a wide, bony base and were reinforced on their anterior margin with a dentine spine. As a result, fossilized spines and scales are often all that remains of these fishes in ancient sedimentary rocks. The earliest acanthodians were marine, but during the Devonian, freshwater species became predominant.

Bos (from Latin bōs: cow, ox, bull) is a genus of bovines, which includes, among others, wild and domestic cattle.

Bos is often divided into four subgenera: Bos, Bibos, Novibos, and Poephagus, but including these last three divisions within the genus Bos without including Bison is believed to be paraphyletic by many workers on the classification of the genus since the 1980s. The genus as traditionally defined has five extant species, but this rises to eight when the domesticated varieties are counted as separate species, and ten when the closely related Bison is also included. Most but not all modern breeds of domesticated cattle (including taurine cattle and zebu) are believed to have originated from the extinct aurochs. Others like Bali cattle and gayal are thought to have originated from South and Southeast Asian Bos species.

In biological taxonomy, circumscription is the content of a taxon, that is, the delimitation of which subordinate taxa are parts of that taxon. For example, if it is determined that species X, Y, and Z belong in genus A, and species T, U, V, and W belong in genus B, those are the circumscriptions of those two genera. Another systematist might determine that T, U, V, W, X, Y, and Z all belong in genus A. Agreement on circumscriptions is not governed by the codes of zoological or botanical nomenclature, and must be reached by scientific consensus.

A goal of biological taxonomy is to achieve a stable circumscription for every taxon. This goal conflicts, at times, with the goal of achieving a natural classification that reflects the evolutionary history of divergence of groups of organisms. Balancing these two goals is a work in progress, and the circumscriptions of many taxa that had been regarded as stable for decades are in upheaval in the light of rapid developments in molecular phylogenetics. New evidence may suggest that a traditional circumscription should be revised, particularly if the old circumscription is shown to be paraphyletic (a group containing some but not all of the descendants of the common ancestor).

The term Japhetites (sometimes spelled Japhethites; in adjective form Japhetic or Japhethitic) refers to the descendants of Japheth, one of the three sons of Noah in the Book of Genesis. The term was used in ethnological and linguistic writings from the 18th to the 20th centuries as a Biblically derived racial classification for the European peoples, but is now considered obsolete. Medieval ethnographers believed that the world had been divided into three large-scale groupings, corresponding to the three classical continents: the Semitic peoples of Asia, the Hamitic peoples of Africa, and the Japhetic peoples of Europe.

The term has been used in modern times as a designation in physical anthropology, ethnography, and comparative linguistics. In anthropology, it was used in a racial sense for White people (the Caucasian race). In linguistics, it referred to the Indo-European languages. Both of these uses are considered obsolete nowadays. Only the Semitic peoples form a well-defined language family. The Indo-European group is no longer known as "Japhetite", and the Hamitic group is now recognized as paraphyletic within the Afro-Asiatic family.

Bryophytes (/ˈbraɪ.əˌfaɪts/) are a group of land plants (embryophytes), sometimes treated as a taxonomic division referred to as Bryophyta sensu lato, that contains three groups of non-vascular land plants: the liverworts, hornworts, and mosses. In the strict sense, the division Bryophyta consists of the mosses only. Bryophytes are characteristically limited in size and prefer moist habitats although some species can survive in drier environments. The bryophytes consist of about 20,000 plant species. Bryophytes produce enclosed reproductive structures (gametangia and sporangia), but they do not produce flowers or seeds. They reproduce sexually by spores and asexually by fragmentation or the production of gemmae.

Though bryophytes were considered a paraphyletic group in recent years, almost all of the most recent phylogenetic evidence supports the monophyly of this group, as originally classified by Wilhelm Schimper in 1879.

Rabbits or bunnies are small mammals in the family Leporidae (which also includes the hares), which is in the order Lagomorpha (which also includes pikas). They are familiar throughout the world as a small herbivore, a prey animal, a domesticated form of livestock, and a pet, having a widespread effect on ecologies and cultures. The most widespread rabbit genera are Oryctolagus and Sylvilagus. The former, Oryctolagus, includes the European rabbit, Oryctolagus cuniculus, which is the ancestor of the hundreds of breeds of domestic rabbit and has been introduced on every continent except Antarctica. The latter, Sylvilagus, includes over 13 wild rabbit species, among them the cottontails and tapetis. Wild rabbits not included in Oryctolagus and Sylvilagus include several species of limited distribution, including the pygmy rabbit, volcano rabbit, and Sumatran striped rabbit.

Rabbits are a paraphyletic grouping, and do not constitute a clade, as hares (belonging to the genus Lepus) are nested within the Leporidae clade and are not described as rabbits. Although once considered rodents, lagomorphs diverged earlier and have a number of traits rodents lack, including two extra incisors. Similarities between rabbits and rodents were once attributed to convergent evolution, but studies in molecular biology have found a common ancestor between lagomorphs and rodents and place them in the clade Glires.

Artiodactyls are placental mammals belonging to the order Artiodactyla (/ˌɑːrtioʊˈdæktɪlə/ AR-tee-oh-DAK-tih-lə; from Ancient Greek ἄρτιος ártios 'even' and δάκτυλος dáktylos 'finger, toe'). Typically, they are ungulates which bear weight equally on two (an even number) of their five toes (the third and fourth, often in the form of a hoof). The other three toes are either present, absent, vestigial, or pointing posteriorly. By contrast, most perissodactyls bear weight on an odd number of the five toes. Another difference between the two orders is that many artiodactyls (except for Suina) digest plant cellulose in one or more stomach chambers rather than in their intestine (as perissodactyls do). Molecular biology, along with new fossil discoveries, has found that cetaceans (whales, dolphins, and porpoises) fall within this taxonomic branch, being most closely related to hippopotamuses. Some modern taxonomists thus apply the name Cetartiodactyla (/sɪˌtɑːrtioʊˈdæktɪlə/) to this group, while others opt to include cetaceans within the existing name of Artiodactyla. Some researchers use "even-toed ungulates" to exclude cetaceans and only include terrestrial artiodactyls, making the term paraphyletic in nature.

The roughly 270 land-based even-toed ungulate species include pigs, peccaries, hippopotamuses, antelopes, deer, giraffes, camels, llamas, alpacas, sheep, goats and cattle. Many are herbivores, but suids are omnivorous, and cetaceans are entirely carnivorous. Artiodactyls are also known by many extinct groups such as anoplotheres, cainotheriids, merycoidodonts, entelodonts, anthracotheres, basilosaurids, and palaeomerycids. Many artiodactyls are of great dietary, economic, and cultural importance to humans.

The Hemerobiiformia are a suborder of insects in the order Neuroptera that include most of the lacewings, antlions and their allies. The phylogeny of the Neuroptera was explored in 2014 using mitochondrial DNA sequences. The results indicate that the traditional Hemerobiiformia are paraphyletic, meaning that not all the members of the clade are considered to belong to it, in particular since it would include all the Myrmeleontiformia, with which the Hemerobiiformia were traditionally contrasted. The Osmyloidea, usually included in Hemerobiiformia, actually seem to represent a more ancient lineage basal to Hemerobiiformia as well as Myrmeleontiformia. The broken-up group is shown in the cladogram:

Artiodactyls are placental mammals belonging to the order Artiodactyla (/ˌɑːrtioʊˈdæktɪlə/ AR-tee-oh-DAK-tih-lə; from Ancient Greek ἄρτιος ártios 'even' and δάκτυλος dáktylos 'finger, toe'). Typically, they are ungulates which bear weight equally on two (an even number) of their five toes (the third and fourth, often in the form of a hoof). The other three toes are either present, absent, vestigial, or pointing posteriorly. By contrast, most perissodactyls bear weight on an odd number of the five toes. Another difference between the two orders is that many artiodactyls (except for Suina) digest plant cellulose in one or more stomach chambers rather than in their intestine (as perissodactyls do). Molecular biology, along with new fossil discoveries, has found that cetaceans (whales, dolphins, and porpoises) fall within this taxonomic branch, being most closely related to hippopotamuses. Some modern taxonomists thus apply the name Cetartiodactyla (/sɪˌtɑːrtioʊˈdæktɪlə/) to this group, while others opt to include cetaceans within the existing name of Artiodactyla. Some researchers use "even-toed ungulates" to exclude cetaceans and only include terrestrial artiodactyls, making the term paraphyletic in nature, but since cetaceans have 0 toes, and 0 is an even number, they technically fit the label.

The roughly 270 land-based even-toed ungulate species include pigs, peccaries, hippopotamuses, antelopes, deer, giraffes, camels, llamas, alpacas, sheep, goats and cattle. Many are herbivores, but suids are omnivorous, and cetaceans are entirely carnivorous. Artiodactyls are also known by many extinct groups such as anoplotheres, cainotheriids, merycoidodonts, entelodonts, anthracotheres, basilosaurids, and palaeomerycids. Many artiodactyls are of great dietary, economic, and cultural importance to humans.

Adapiformes is a group of early primates. Adapiforms radiated throughout much of the northern continental mass (now Europe, Asia and North America), reaching as far south as northern Africa and tropical Asia. They existed from the Eocene to the Miocene epoch. Some adapiforms resembled living lemurs.

Adapiforms are known from the fossil record only, and it is unclear whether they form a monophyletic or paraphyletic group. When assumed to be a clade, they are usually grouped under the "wet-nosed" taxon Strepsirrhini, which would make them more closely related to the lemurs and less so to the "dry-nosed" Haplorhini taxon that includes monkeys and apes.