UCMP Glossary: Phylogenetics

| Phylogenetics | Geology | Biochemistry | Cell biology | Ecology | Life history | Zoology | Botany | Paleogeography |

adaptation -- Change in a organism resulting from natural selection; a structure which is the result of such selection.

anagensis -- Evolutionary change along an unbranching lineage; change without speciation.

ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction.

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.

cladogenesis -- The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.

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.

convergence -- Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology.

crown group -- All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

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.

diversity -- Term used to describe numbers of taxa, or variation in morphology.

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.

evolution -- Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.

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.

extinction -- When all the members of a clade or taxon die, the group is said to be extinct.

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.

hierarchy -- A series in which each element is categorized into successive ranks or grades with each level subordinate to the one above.

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.

hypothesis -- A concept or idea that can be falsified by various scientific methods.

ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.

lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.

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?

morphotype -- n. An individual or set of organisms within a population distinguished by having a distinct physical structure.

ontogeny -- n. The growth of an organism through all its developmental stages (embryonic stage through death).

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.

parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

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?

phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

plesiomorphy -- A primitive character state for the taxa under consideration.

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.

punctuated equilibrium -- A model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis.

radiation -- Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.

rank -- In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.

relatedness -- Two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade.

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 reproduction—those 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.

sister group -- The two clades resulting from the splitting of a single lineage.

stasis -- A period of little or no discernible change in a lineage.

stem group -- All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group.

synapomorphy -- A character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry.

systematics -- Field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy.

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.

taxonomy -- The science of naming and classifying organisms.

vicariance -- Speciation which occurs as a result of the separation and subsequent isolation of portions of an orginal population.

Last updated:2009-11-12