Chordates are animals which at some point in their development bear a notochord, a flexible rod-like structure running down the length of the body. Collectively, these animals belong to the taxon Chordata, which includes Urochordata (tunicates), Cephalochordata (lancelets), Hyperotreta (hagfishes), and Vertebrata (vertebrates). In vertebrates, the notochord has evolved into the vertebral column, which encases and protects the spinal cord. Vertebrate animals include fishes, amphibians, reptiles, birds, and mammals.
Modern biological classification began in 1758 with the work of Carolus Linnaeus, the founder of the Linnaean classification system. The Linnaean system was modified over time to comprise the "ranks" of kingdom, phylum, class, order, family, genus (plural: genera), and species, with ever-increasing numbers of intermediate ranks formed by adding prefixes such as "super-" and "sub-" to the basic ranks. The genus and species together are called the scientific name and are always italicized; for example, our scientific name (genus and species, respectively) is Homo sapiens. In recent years, all of the ranks in the Linnaean system above the level of species have been recognized as artificial constructs, representing nothing more than an arbitrary grouping of related animals. However, many of these ranks are still used informally, and in the case of families and genera, as the basis of new system of taxonomic nomenclature governed by the ICZN (International Commission on Zoological Nomenclature).
Taxonomy and Systematics
In a biological context, taxonomy refers to the identification, description, nomenclature, and classification of organisms, while systematics refers to the study of how organisms are related to each other. While taxonomy involves classification of organisms, it does not necessarily rely on how closely related the organisms are. For instance, the taxon Pachydermata Cuvier 1795 groups together rhinoceroses, hippopotami, and elephants because they are large mammals with thick skin. However, rhinos are more closely related to horses than to the other two, hippos are closer to whales, and elephants are closer to manatees. Systematics involves the classification of organisms into groups that reflect relatedness and ancestry.
A taxon (plural: taxa) is a group of organisms which may or may not be related to each other. A clade is a specific type of taxon which is monophyletic, meaning it includes an ancestor and all descendants of that ancestor. Other taxa, such as Pachydermata, are non-monophyletic (pseudophyletic, as termed here) and represent artificial groupings. There are two types of pseudophyletic taxa: paraphyletic taxa (including an ancestor and some, but not all, of its descendants; e.g., dinosaurs without including birds) and polyphyletic taxa (including two or more organisms but not their most recent common ancestor and all of its descendants; e.g., Pachydermata). The ICZN governs the nomenclature of animal family-group taxa, which are named after genera and are derived from the Linnaean rank of "family." Family-group taxa include (in order from most to least inclusive): "superfamily" (taxa ending in -oidea), "family" (-idae), "subfamily" (-inae), "tribe" (-ini), and "subtribe" (-ina).
An antiquated systematic method called phenetics has been used to determine relationships between organisms, but assesses similarities based upon the analysis of a random aggregate of characteristics. This system is not used in modern systematics, as it cannot sort out symplesiomorphies (shared ancestral characteristics) from synapomorphies (shared derived characteristics). Modern systematics makes use of phylogenetics, which focuses on synapomorphies as a means of determining how closely related organisms are. In this manner, one can see that, for example, crocodiles are closer to birds (both have four-chambered hearts) than to lizards. The most recent common ancestor of crocodylians and birds had a four-chambered heart (a synapomorphy they share), something lacking in both lizards and the most recent common ancestor of lizards and crocodiles. The scaly skin and low metabolism shared by lizards and crocodiles are symplesiomorphies which their most recent common ancestor possessed and which belie the closer relationship between crocodiles and birds, the latter of which later evolved feathers and higher metabolisms.
Phylogenetic relationships are frequently represented in diagram form, typically by a branching, tree-like structure. This is how life evolves, with new lineages branching off as time passes, so the branching pattern of a tree is an apt symbol of this process. The phylogeny (evolutionary history) of a clade can be pictorially represented as a phylogenetic tree or a cladogram. Phylogenetic trees take into account time since the divergence of each lineage, while cladograms omit temporal information and simply depict the relationships between each organism. Cladistics, which makes use of cladograms, is a subfield of phylogenetics that de-emphasizes the time element.
Phylogenetic definitions describe exactly what a taxon consists of (and does not consist of). A taxon is defined in terms of particular species which are either expressly included within or excluded from the taxon. Defining taxa is extremely useful and is becoming more and more common in the literature. It allows systematists to use a taxon in a consistent context and to circumscribe the same group of organisms. There are two basic types of phylogenetic definitions: node-based and stem-based.
A taxon with a node-based definition (a node taxon) includes the most recent common ancestor of two or more species and all of its descendants. A node taxon can also be described as "the least inclusive clade containing [Species A] and [Species B (C, D, E, etc.)]." Here, all of these species are internal specifiers. A node-based definition can be modified by adding one or more external qualifiers which must be excluded from the taxon for it to remain monophyletic. In this case, appended to the end of the definition in quotes above would be "but excluding [Species Q (R, S, T, etc.)]."
A taxon with a stem-based definition (a stem taxon) includes all species more closely related to one particular species than to one or more other species. A stem taxon can also be described as "the most inclusive clade containing [Species A] but not [Species B (C, D, E, etc.)]." Here, Species A is the internal specifier and the other species are external specifiers. A stem-based definition can be modified by adding one or more internal qualifiers which must be included in the taxon for it to remain monophyletic. In this case, appended to the end of the definition in quotes above would be "and including [Species Q (R, S, T, etc.)]."
Phylogenetic definitions can be written in shorthand form (usually enclosed in parentheses) using the following symbols:
< = "the least inclusive clade containing"
Node Taxon 1 = The least inclusive clade containing Species A and Species B, Species C but excluding Species D.
Stem Taxon 2 = The most inclusive clade containing Species A but not Species B, Species C and including Species D.
N.B. A listing of phylogenetic definitions presented on this site can be found here. All phylogenetic definitions on this site are presented in the style of Sereno (2005), on his TaxonSearch website. The PhyloCode provides an alternate form of phylogenetic definition and includes other types of definitions, such as "apomorphy-based" definitions and definitions that describe "crown groups" and "total groups." Unfortunately, this style of definition is quite impractical and needlessly complicated and so is not employed on this site.
* To be updated *
A node-stem triplet (NST) is term coined by Sereno (1997) to collectively describe a node taxon and the two sister taxa stemming directly from it. Below is a list of all named NSTs presented on this site.
† Indicates a taxon is extinct. If the node taxon in a NST is extinct, so are both the stem taxa.
Disclaimer: All unsourced taxonomic opinions presented on this site are solely that of the author. Said author has a bachelor's degree in biology, a life-long interest in biology (esp. dinosaurs) and systematics, and is currently assisting Dr. Paul Sereno in compiling data for his TaxonSearch website. Please note that the author of this site has considerable informal, but minimal formal, education in chordate systematics. Consequently, the information presented on this site is reliable, but the author most certainly does not claim the final word on anything. Suggestions, comments, and constructive criticism are welcome (contact info below).