Cladistics in the context of Basal (evolution)

Birds are a group of warm-blooded theropod dinosaurs constituting the class Aves, characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweight skeleton. Birds live worldwide and range in size from the 5.5 cm (2.2 in) bee hummingbird to the 2.8 m (9 ft 2 in) common ostrich. There are over 11,000 living species and they are split into 44 orders. More than half are passerine or "perching" birds. Birds have wings whose development varies according to species; the only known groups without wings are the extinct moa and elephant birds. Wings, which are modified forelimbs, gave birds the ability to fly, although further evolution has led to the loss of flight in some birds, including ratites, penguins, and diverse endemic island species. The digestive and respiratory systems of birds are also uniquely adapted for flight. Some bird species of aquatic environments, particularly seabirds and some waterbirds, have further evolved for swimming. The study of birds is called ornithology.

Birds evolved from earlier theropods, and thus constitute the only known living dinosaurs. Likewise, birds are considered reptiles in the modern cladistic sense of the term, and their closest living relatives are the crocodilians. Birds are descendants of the primitive avialans (whose members include Archaeopteryx) which first appeared during the Late Jurassic. According to some estimates, modern birds (Neornithes) evolved in the Late Cretaceous or between the Early and Late Cretaceous (100 Ma) and diversified dramatically around the time of the Cretaceous–Paleogene extinction event 66 million years ago, which killed off the pterosaurs and all non-ornithuran dinosaurs.

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.

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.

Linnaean taxonomy can mean either of two related concepts:

1. The particular form of biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his Systema Naturae (1735) and subsequent works. In the taxonomy of Linnaeus there are three kingdoms, divided into classes, and the classes divided into lower ranks in a hierarchical order.
2. A term for rank-based classification of organisms, in general. That is, taxonomy in the traditional sense of the word: rank-based scientific classification. This term is especially used as opposed to cladistic systematics, which groups organisms into clades. It is attributed to Linnaeus, although he neither invented the concept of ranked classification (it goes back to Plato and Aristotle) nor gave it its present form. In fact, it does not have an exact present form, as "Linnaean taxonomy" as such does not really exist: it is a collective (abstracting) term for what actually are several separate fields, which use similar approaches.

Linnaean name also has two meanings, depending on the context: it may either refer to a formal name given by Linnaeus (personally), such as Giraffa camelopardalis Linnaeus, 1758; or a formal name in the accepted nomenclature (as opposed to a modernistic clade name).

Archosauria (lit. 'ruling reptiles') or archosaurs (/ˈɑːrkəˌsɔːr/) is a clade of diapsid sauropsid tetrapods, with birds and crocodilians being the only known extant representatives. Although broadly classified as reptiles, which traditionally exclude birds, the cladistic sense of the term includes all living and extinct relatives of birds and crocodilians such as non-avian dinosaurs, pterosaurs, phytosaurs, aetosaurs and rauisuchians as well as many Mesozoic marine reptiles. Modern paleontologists define Archosauria as a crown group that includes the most recent common ancestor of living birds and crocodilians, and all of its descendants.

The base of Archosauria splits into two clades: Pseudosuchia, which includes crocodilians and their extinct relatives; and Avemetatarsalia, which includes birds and their extinct relatives (such as non-avian dinosaurs and pterosaurs). Older definitions of the group Archosauria rely on shared morphological characteristics, such as an antorbital fenestra in the skull, serrated teeth, and an upright stance. Some extinct reptiles, such as proterosuchids and euparkeriids, also possessed these features yet originated prior to the split between the crocodilian and bird lineages. The older morphological definition of Archosauria nowadays roughly corresponds to Archosauriformes, a group named to encompass crown-group archosaurs and their close relatives.

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.

A cladogram (from Greek κλάδος klados "branch" and γραμμα gramma "character") is a diagram used in cladistics to show evolutionary relations (common descent) between groups of organisms. Cladograms are a type (subset) of phylogenetic trees that do not normally show evolutionary time but are required to meet specific criteria defined by cladistics. Like other evolutionary trees, cladograms can be used show actual, hypothesized, or even hypothetical descent. Modern cladograms are most often generated algorithmically through computational phylogenetics using genetic data, typically from DNA sequencing, as part of a molecular systematics approach.

A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors.

Whales are a widely distributed and diverse group of fully aquatic placental marine mammals. As an informal and colloquial grouping, they correspond to large members of the infraorder Cetacea, i.e. all cetaceans apart from dolphins and porpoises. Dolphins and porpoises may be considered whales from a formal, cladistic perspective. Whales, dolphins and porpoises belong to the order Cetartiodactyla, which consists of even-toed ungulates. Their closest non-cetacean living relatives are the hippopotamuses, from which they and other cetaceans diverged about 54 million years ago. The two parvorders of whales, baleen whales (Mysticeti) and toothed whales (Odontoceti), are thought to have had their last common ancestor around 34 million years ago. Mysticetes include four extant (living) families: Balaenopteridae (the rorquals), Balaenidae (right whales), Cetotheriidae (the pygmy right whale), and Eschrichtiidae (the grey whale). Odontocetes include the Monodontidae (belugas and narwhals), Physeteridae (the sperm whale), Kogiidae (the dwarf and pygmy sperm whale), and Ziphiidae (the beaked whales), as well as the six families of dolphins and porpoises which are not considered whales in the informal sense.

Whales are fully aquatic, open-ocean animals: they can feed, mate, give birth, suckle and raise their young at sea. Whales range in size from the 2.6 metres (8.5 ft) and 135 kilograms (298 lb) dwarf sperm whale to the 29.9 metres (98 ft) and 190 tonnes (210 short tons) blue whale, which is the largest known animal that has ever lived. The sperm whale is the largest toothed predator on Earth. Several whale species exhibit sexual dimorphism, in that the females are larger than males.

In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. The term may be more strictly applied only to nodes adjacent to the root, or more loosely applied to nodes regarded as being close to the root. Note that extant taxa that lie on branches connecting directly to the root are not more closely related to the root than any other extant taxa.

While there must always be two or more equally "basal" clades sprouting from the root of every cladogram, those clades may differ widely in taxonomic rank, species diversity, or both. If C is a basal clade within D that has the lowest rank of all basal clades within D, C may be described as the basal taxon of that rank within D. The concept of a 'key innovation' implies some degree of correlation between evolutionary innovation and diversification. However, such a correlation does not make a given case predicable, so ancestral characters should not be imputed to the members of a less species-rich basal clade without additional evidence.

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 annelids (/ˈænəlɪdz/), also known as the segmented worms, are animals that comprise the phylum Annelida (/əˈnɛlɪdə/; from Latin anellus 'little ring'). The phylum contains over 22,000 extant species, including ragworms, earthworms, and leeches. The species exist in and have adapted to various ecologies – some in marine environments as distinct as tidal zones and hydrothermal vents, others in fresh water, and yet others in moist terrestrial environments.

The annelids are bilaterally symmetrical, triploblastic, coelomate, invertebrate organisms. They also have parapodia for locomotion. Most textbooks still use the traditional division into Polychaetes (almost all marine), Oligochaetes (which include earthworms) and Hirudinea (leech-like species). Cladistic research since 1997 has radically changed this scheme, viewing leeches as a sub-group of oligochaetes and oligochaetes as a sub-group of polychaetes. In addition, the Pogonophora, Echiura and Sipuncula, previously regarded as separate phyla, are now regarded as sub-groups of polychaetes. Annelids are considered members of the Lophotrochozoa, a "super-phylum" of protostomes that also includes molluscs, brachiopods, and nemerteans.

An earthworm is a soil-dwelling terrestrial invertebrate that belongs to the phylum Annelida. The term is the common name for the largest members of the class (or subclass, depending on the author) Oligochaeta. In classical systems, they were in the order of Opisthopora since the male pores opened posterior to the female pores, although the internal male segments are anterior to the female. Theoretical cladistic studies have placed them in the suborder Lumbricina of the order Haplotaxida, but this may change. Other slang names for earthworms include "dew-worm", "rainworm", "nightcrawler", and "angleworm" (from its use as angling hookbait). Larger terrestrial earthworms are also called megadriles (which translates to "big worms") as opposed to the microdriles ("small worms") in the semiaquatic families Tubificidae, Lumbricidae and Enchytraeidae. The megadriles are characterized by a distinct clitellum (more extensive than that of microdriles) and a vascular system with true capillaries.

Earthworms are commonly found in moist, compost-rich soil, eating a wide variety of organic matters, which include detritus, living protozoa, rotifers, nematodes, bacteria, fungi and other microorganisms. An earthworm's digestive system runs the length of its body. They are one of nature's most important detritivores and coprophages, and also serve as food for many low-level consumers within the ecosystems.

In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). 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.