UCMP Glossary: Phylogenetics
basal group -- The earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals.
binomial nomenclature -- n. A method of identifying and naming organisms using two names. The first name is the genus name, and the second is the species name. Names are usually Latin or Greek in origin.
character -- Heritable trait possessed by an organism; characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.
clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.
cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.
derived -- adj. Refers to a character or feature found within a single lineage of a larger group; it is not shared with all organisms in the larger group. Derived characters are used to infer evolutionary relationships, as derived characters evolved after primitive characters. In comparing humans and apes, it can be said that an upright stance in humans is a derived character.
endosymbiosis -- When one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis.
evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.
gradualism -- A model of evolution that assumes slow, steady rates of change. Charles Darwin's original concept of evolution by natural selection assumed gradualism. Contrast with punctuated equilibrium.
homology -- Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent.
monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade. More?
outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.
paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor. More?
parataxonomy -- n. The grouping of organisms based on common morphology; does not imply evolutionary relationships. For example, fossil eggs can be assigned to parataxons without any knowledge of which specific organism produced them.
phylogenetics -- Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern.More?
polarity of characters -- The states of characters used in a cladistic analysis, either original or derived.Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.
polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group. More?
primitive -- adj. Refers to a character or feature in a group of organisms that is inherited from a common ancestor. Teeth are a primitive characteristic of birds since birds inherited them from their dinosaur ancestors.
pseudoextinction -- The apparent disappearance of a taxon. In cases of pseudoextinction, this disappearance is not due to the death of all members, but the evolution of novel features in one or more lineages, so that the new clades are not recognized as belonging to the paraphyletic ancestral group, whose members have ceased to exist. The Dinosauria, if defined so as to exclude the birds, is an example of a group that has undergone pseudoextinction.
reticulation -- Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.
selection -- Process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproductionthose with the favored feature produce more offspring than those with the other feature, such that they become a greater percentage of the population in the next generation.
taxon -- n. A named group of organisms, not necessarily a clade, but linked by shared physical or genetic characteristics. A taxon may be designated by a Latin name or by a letter, number, or any other symbol; taxa- pl.