Cladistic in the context of Biological species

A species (pl. species) is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. It can be defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour, or ecological niche. In addition, palaeontologists use the concept of the chronospecies since fossil reproduction cannot be examined. The most recent rigorous estimate for the total number of species of eukaryotes is between 8 and 8.7 million. About 14% of these had been described by 2011. All species (except viruses) are given a two-part name, a "binomen". The first part of a binomen is the name of a genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes in zoological nomenclature). For example, Boa constrictor is one of the species of the genus Boa, with constrictor being the specific name.

While the definitions given above may seem adequate at first glance, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clonal lineage is potentially a microspecies. Although none of these are entirely satisfactory definitions, and while the concept of species may not be a perfect model of life, it is still a useful tool to scientists and conservationists for studying life on Earth, regardless of the theoretical difficulties. If species were fixed and distinct from one another, there would be no problem, but evolutionary processes cause species to change. This obliges taxonomists to decide, for example, when enough change has occurred to declare that a fossil lineage should be divided into multiple chronospecies, or when populations have diverged to have enough distinct character states to be described as cladistic species.

Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.

The opposite of convergent evolution is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evolution, which occurs when two independent species evolve in the same direction and thus independently acquire similar characteristics; for instance, gliding frogs have evolved in parallel from multiple types of tree frog.

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.

Satureja is a genus of aromatic plants of the family Lamiaceae, related to rosemary and thyme. It is native to southern and southeastern Europe, North Africa, the Middle East, and Central Asia. Historically, Satureja was defined broadly and many species of the subtribe Menthinae from throughout the world were included in it. In the modern cladistic era of botany, Satureja was redefined to a narrower monophyletic genus whose species are all native to Eurasia. Several species are cultivated as culinary herbs called savory, and they have become established in the wild in a few places.

Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.

The opposite of convergent evolution is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evolution, which occurs when two independent species evolve in the same direction and thus independently acquire similar characteristics; for instance, gliding frogs have evolved in parallel from multiple types of tree frog.

Puffballs are a type of fungus featuring a ball-shaped fruiting body that, when mature, bursts on contact or impact, releasing a cloud of dust-like spores into the surrounding area. Puffballs belong to the division Basidiomycota and encompass several genera, including Calvatia, Calbovista and Lycoperdon. The puffballs were previously treated as a taxonomic group called the Gasteromycetes or Gasteromycetidae, but they are now known to be a polyphyletic assemblage.

The distinguishing feature of all puffballs is that they do not have an open cap with spore-bearing gills. Instead, spores are produced internally, in a spheroidal fruit body called a gasterothecium (gasteroid 'stomach-like' basidiocarp). As the spores mature, they form a mass called a gleba in the centre of the fruitbody that is often of a distinctive color and texture. The basidiocarp remains closed until after the spores have been released from the basidia. Eventually, it develops an aperture, or dries, becomes brittle, and splits, and the spores escape. The spores of puffballs are statismospores rather than ballistospores, meaning they are not forcibly extruded from the basidium. Puffballs and similar forms are thought to have evolved convergently (that is, in numerous independent events) from Hymenomycetes by gasteromycetation, through secotioid stages. Thus, 'Gasteromycetes' and 'Gasteromycetidae' are now considered to be descriptive, morphological terms (more properly gasteroid or gasteromycetes, to avoid taxonomic implications) but not valid cladistic terms.

Amphibious fish are fish that are able to leave water for extended periods of time. About 11 distantly related genera of fish are considered amphibious. This suggests that many fish genera independently evolved amphibious traits, a process known as convergent evolution. These fish use a range of methods for land movement, such as lateral undulation, tripod-like walking (using paired fins and tail), and jumping. Many of these methods of locomotion incorporate multiple combinations of pectoral-, pelvic-, and tail-fin movement.

Many ancient fish had lung-like organs, and a few, such as the lungfish and bichir, still do. Some of these ancient "lunged" fish were the ancestors of tetrapods. In most recent fish species, though, these organs evolved into the swim bladders, which help control buoyancy. Having no lung-like organs, modern amphibious fish and many fish in oxygen-poor water use other methods, such as their gills or their skin to breathe air. Amphibious fish may also have eyes adapted to allow them to see clearly in air, despite the refractive index differences between air and water.

Synapsida is a diverse group of tetrapod vertebrates that includes all mammals and their extinct relatives. It is one of the two major clades of the group Amniota, the other being the more diverse group Sauropsida (which includes all extant reptiles and, therefore, birds). Unlike other amniotes, synapsids have a single temporal fenestra, an opening low in the skull roof behind each eye socket, leaving a bony arch beneath each; this accounts for the name "synapsid". The distinctive temporal fenestra developed about 318 million years ago during the Late Carboniferous period, when synapsids and sauropsids diverged, but was subsequently merged with the orbit in early mammals.

The basal amniotes (reptiliomorphs) from which synapsids evolved were historically simply called "reptiles". Therefore, stem group synapsids were then described as mammal-like reptiles in classical systematics, and non-therapsid synapsids were also referred to as pelycosaurs or pelycosaur-grade synapsids. These paraphyletic terms have now fallen out of favor and are only used informally (if at all) in modern literature, as it is now known that all extant reptiles are more closely related to each other and birds than to synapsids, so the word "reptile" has been re-defined to mean only members of Sauropsida or even just an under-clade thereof. In a cladistic sense, synapsids are in fact a monophyletic sister taxon of sauropsids, rather than a part of the sauropsid lineage. Therefore, calling synapsids "mammal-like reptiles" is incorrect under the new definition of "reptile", so they are now referred to as stem mammals, proto-mammals, paramammals or pan-mammals. Most lineages of pelycosaur-grade synapsids were replaced by the more advanced therapsids, which evolved from sphenacodontoid pelycosaurs, at the end of the Early Permian during the so-called Olson's Extinction.

Agaricomycotina is one of three subdivisions of the Basidiomycota (fungi bearing spores on basidia), and represents many fungi which form macroscopic fruiting bodies. Agaricomycotina contains over 30,000 species, divided into three classes: Tremellomycetes, Dacrymycetes, and Agaricomycetes. Around 98% of the species are in the class Agaricomycetes, including all the agarics (gilled mushrooms), bracket fungi, clavarioid fungi, corticioid fungi, and gasteroid fungi. Tremellomycetes contains many basidiomycete yeasts and some conspicuous jelly fungi. Dacrymycetes contains a further group of jelly fungi. These taxa are founded on molecular research, based on cladistic analysis of DNA sequences, and supersede earlier morphology-based classifications. Agaricomycotina contains nearly one third of all described species of fungi.

The class Bartheletiomycetes contains a single anomalous species of basidiomycete which grows on fallen leaves of Ginkgo biloba. Some researchers suggest that this class should be included in Agaricomycotina.

The Yinpterochiroptera (or Pteropodiformes) is a suborder of the Chiroptera, which includes taxa formerly known as megabats and five of the microbat families: Rhinopomatidae, Rhinolophidae, Hipposideridae, Craseonycteridae, and Megadermatidae. This suborder is primarily based on molecular genetics data. This proposal challenged the traditional view that megabats and microbats form monophyletic groups of bats. Further studies are being conducted, using both molecular and morphological cladistic methodology, to assess its merit.

The term Yinpterochiroptera is constructed from the words Pteropodidae (the family of megabats) and Yinochiroptera (a term proposed in 1984 by Karl F. Koopman to refer to certain families of microbats).Recent studies using transcriptome data have found strong support for the Yinpterochiroptera-Yangochiroptera classification system.Researchers have created a relaxed molecular clock that estimates the divergence between Yinpterochiroptera and Yangochiroptera around 63 million years ago. The most recent common ancestor of Yinpterochiroptera, corresponding to the split between Rhinolophoidea and Pteropodidae (Old World Fruit bats), is estimated to have occurred 60 million years ago.

Yangochiroptera, or Vespertilioniformes, is a suborder of Chiroptera that includes most of the microbat families, except the Rhinopomatidae, Rhinolophidae, Hipposideridae, Craseonycteridae and Megadermatidae. These other families, plus the megabats, are seen as part of another suborder, the Yinpterochiroptera. All bats in Yangochiroptera use laryngeal echolocation (LE), which involves the use of high-frequency sounds to detect prey and avoid obstacles.

The rationale for the Yangochiroptera taxon is primarily based on molecular genetics data. The Yangochiroptera/ Yinpterochiroptera classification remains a relatively recent proposal, which challenges the traditional view that megabats and microbats form monophyletic groups by claiming that the superfamily Rhinolophoidea is more closely related to Old World fruit bats than other microbats. Further studies are being conducted, using both molecular and morphological cladistic methodology, to assess the merit of this alternative view of bat evolution.

Chondrostei is a subclass of non-neopterygian ray-finned fish. While the term originally referred to the paraphyletic grouping of all non-neopterygian ray-finned fish, it was redefined by Patterson in 1982 to be a clade comprising the Acipenseriformes (which includes sturgeon and paddlefish) and their extinct relatives.

Taxa commonly suggested to represent relatives of the Acipenseriformes include the Triassic marine fish Birgeria and the Saurichthyiformes, but their relationship with the Acipenseriformes has been strongly challenged on cladistic grounds. Coccolepididae, a group of small weakly ossified Jurassic and Cretaceous fish found in both marine and freshwater environments, have also been suggested to be close relatives of the Acipenseriformes. However, this has never been subject to cladistic analysis. Near & Thacker (2024) also recovered the ptycholepiform Boreosomus as a stem-acipenseriform.

Wastebasket taxon (also called a waste-bin taxon, dustbin taxon or catch-all taxon) is a term used by some taxonomists to refer to a taxon that has the purpose of classifying organisms that do not fit anywhere else. They are typically defined by either their designated members' often superficial similarity to each other, or their lack of one or more distinct character states or by their not belonging to one or more other taxa. Wastebasket taxa are by definition either paraphyletic or polyphyletic, and are therefore not considered valid taxa under strict cladistic rules of taxonomy. The name of a wastebasket taxon may in some cases be retained as the designation of an evolutionary grade, however.