GLOSSARY

Accommodation Adjusting the focal length of the eyes.

Actinopterygian From the Greek for "ray winged." Ray-finned fish, a taxonomic group comprising most of the animals today referred to as "fish." See: Tree of Life, Actinopterygii section.

Apomorphic The derived state of a character in an evolutionary analysis. For instance, bipedal walking is apomorphic in humans relative to the quadrupedal locomotion of our ancestors. See plesiomorphic.

Apomorphy A derived character (see Apomorphic).

Catalyst A molecule that facilitates a chemical reaction without actually being modified by that reaction. Most physiological reactions proceed toward equilibrium. However, the rates of these reactions may be greatly increased by the action of catalysts produced by the organism. See enzyme and phototransduction.

Chromophore From the Greek for "color bringer", a chromophore is generally a molecule that acts as a pigment that gives an object color by selectively absorbing light at particular wavelengths. In the context of this article, a chromophore is a retinal (vitamin A) derivative that forms part of a photopigment. See opsin, photopigment, retinal and retinol.

Clade A monophyletic group of organisms.

Cladistics A method of inferring evolutionary ancestry by methodically comparing possible evolutionary relationships between organisms and selecting as most likely the relationships which require, for instance, the fewest number of evolutionary transformations between character states.

Cone A vertebrate photoreceptor that is primarily sensitive to lights with high intensity (e.g., daylight).

Cornea The transparent covering on the front surface of the eye. The cornea and sclera together form the outer surface of the entire eyeball. See sclera.

Dichromatic From the Greek for "two colored." Strictly speaking, an animal for which only two independent lights are required in order to represent all colors visible to the animal. Independence here means that it is not possible to adjust the intensity of one of the lights in such a way as to make it appear like the other light (provided that the lights are intense enough to be visible to the animal and not so intense as to saturate its photoreceptors). Loosely speaking an animal that has only two photopigments operating at a given time is considered to be dichromatic. See monochromatic, trichromatic, and tetrachromatic.

Double Cone A pair of cones that are directly apposed to each other over the length of their inner segments.

Enzyme A protein that catalyzes a chemical reaction. See protein and catalyst.

Eutheria From the Greek for "true beast." In phylogenetic taxonomy it has been defined as placental mammals and all animals more closely related to them than to marsupials. See: Tree of Life, Eutheria section.

Fossorial A reference to an underground lifestyle such as that lead by moles.

Homologous Derived from the same ancestral structure.

Inner Segment One of the constituent regions of a photoreceptor. In all vertebrates the inner segment contains the ellipsoid, a volume filled with mitochondria that serve not only as the site of oxidative phosphorylation but also as a region of high refractive index. The latter property causes the inner segment to act as a waveguide that channels light to the outer segment. Some inner segments contain oil droplets and/or paraboloids. The latter is made up of carbohydrates that are believed to fuel the photoreceptor; the former apparently function as filters of the light impinging upon the photoreceptor.

Isomerization A change in the organization of the atoms in a molecule with no change in the constituency of the molecule. In the context of vision, isomerization usually refers to the rotation around a particular carbon (the 11^th carbon in the traditional numbering system) of the chromophore. Because this isomerization is caused by light, it is frequently referred to as photoisomerization.

Light Radiation with wavelengths which can be perceived by the eyes of animals. For humans this wavelength range is generally considered to be 400 to 700 nm. Absorption by the human lens provides a fairly sharp cutoff at 400 nm, but radiation with wavelengths as long as 1000 nm can be perceived as light if the intensity is high enough relative to the background at shorter wavelengths. Many animals can perceive light with wavelengths both longer and shorter than that perceivable by humans, so a more general definition might include as light electromagnetic radiation with wavelengths ranging from 300 nm to 800 nm (natural sources which would allow for the visual detection of longer wavelengths by any animal are essentially nonexistent).

Metatheria From the Greek for "later beast." A stem clade of mammals represented today by marsupials (e.g., kangaroo and opossum).

Monochromatic From the Greek for "one colored." (1) For an animal, the state of having only one functional photopigment at a particular time. See dichromatic, trichromatic, and tetrachromatic.

(2) For radiation, the state of having all energy concentrated around a narrow range of wavelengths (generally, a monochromatic light is one for which a plot of energy or quantal flux vs. wavelength will have one sharp peak, and the difference in the wavelengths at which the intensity is one-half the value of the maximum on either side of the peak is 10 nm or less).

Monophyletic Pertaining to a set of organisms consisting of one species and all of that species' descendants.

Oil Droplet A structure found in the inner segments of some photoreceptors. Oil droplets generally have a high refractive index, and thus may play some role in sculpting the quantity and polarization of the light passing through them to the light-sensitive part of the photoreceptor. They also frequently contain pigments such as carotenoids, which absorb light, particularly light having relatively short wavelengths.

Opsin A protein that when combined with a chromophore to form a photopigment is converted into an active enzyme by the absorption of light. Photoreceptors contain large numbers of (generally only) one type of opsin. The rate of photon absorption by photopigments within a cell sets the rate at which the chemical reaction catalyzed by the opsin occurs. This reaction is the first link in a cascade of reactions that ultimately leads to the regulation of neurotransmitter release from the photoreceptor to other neurons in the retina; hence modulation in the rate of photon absorption is causally linked to modulations in the rate of neurotransmitter release. See photopigment and phototransduction.

Orthologous Similar to the term homologous, but applied only to molecules (i.e., genes and proteins). The term is also more restrictive than homologous in that it entails a similarity in function. See Figure 17 and paralogous.

Outer Segment One of the constituent regions of a photoreceptor. Specifically, it is the last part of the photoreceptor that light passes through on its first pass (i.e., prior to any reflections) through the retina. Outer segments are composed of stacked disks flattened in planes perpendicular to the path of the light. The photopigments are bound to the membranes of the outer segment disks.

Paralogous A term describing the relationship between two genes that arose via duplication within a single phyletic lineage. See Figure 17 and orthologous.

Photon A quantum of light; the smallest (nonzero) amount of energy which can be transferred via radiation at a given wavelength.

Photoreceptor A cell that is specialized for converting the rate at which it absorbs photons to the magnitude of a signal, which can be relayed to and interpreted by the organism's central nervous system.

Photopigment The combination of a chromophore and an opsin. Photons are absorbed by the chromophore with a probability that depends upon the chemical structure of both the chromophore and the opsin as well as the wavelength of the photon. Vertebrate photopigments use almost exclusively one of two particular chromophores, so most of the differences in spectral sensitivity between photopigments are established by the amino acid compositions of the opsins.

Phototransduction The process of converting the intensity of light to a neural signal. It is a series of chemical steps that begins with the absorption of light by a chromophore and ends with a change in the rate of neurotransmitter release by the cell that absorbed the light. When a chromophore absorbs a photon, the chromophore may isomerize and in turn cause an isomerization of the opsin. The opsin then behaves as an enzyme catalyzing the conversion of another protein, transducin, to its enzymatic form. In vertebrates, activated transducin catalyzes the activation of a phosphodiesterase. The phosphodiesterase catalyzes the conversion of cyclic guanosine monophosphate (cGMP) to 3'-5' GMP, thus reducing the amount of cGMP inside the photoreceptor. Cyclic GMP binds to an ion channel in the cell membrane, and when bound it holds the channel in an open state. As the phosphodiesterase decreases the cell's concentration of cGMP, cGMP molecules bound to ion channels become unbound causing those channels to close. The resultant change in permeability of the cell membrane causes the cell's electrical potential to become more inwardly negative. This change in the voltage across the cell membrane results in a decrease in the rate at which neurotransmitter molecules are released at the base of the cell. Since the absorption of one photon can cause the opsin to convert many transducin molecules to their active form, and each activated transducin molecule can convert the activation of many phosphodiesterase molecules, and each phosphodiesterase molecule can isomerize many cGMP molecules, photon absorption is said to be amplified by the phototransduction process. For additional information about phototransduction and other aspects of retinal function, see the Webvision page, particularly the section on phototransduction.

Phylogenetic Taxonomy A system of naming only monophyletic groups of organisms. The hierarchical structure of the names devised by such a system, in principle, accurately reflects the evolutionary relationships of all the named groups of organisms.

Plesiomorphic The ancestral state of a character in an evolutionary analysis. Plesiomorphic is the antonym of apomorphic.

Plesiomorphy An ancestral character. See plesiomorphic.

Protein A molecule made up of amino acids (also called peptides and hence proteins may be called polypeptides), members of a class of compounds that contain both a carboxylic acid and an amine group in a particular combination. There are 20 amino acids used in the construction of most proteins, which may be composed of thousands of amino acids strung together in a single chain. The chains are folded into a variety of shapes, which allow the proteins to act as catalysts (enzymes) or as structural components of cells and their surrounding media.

Prototheria From the Greek for "first beast." A stem clade of mammals whose only living descendants are the monotremes (platypus and echidna).

Quantal flux The rate at which quanta (plural of quantum) pass through a given region of space.

Quantum The smallest physically realizable unit of something. A quantum of light has the special name of photon.

Radiation (1) A propagating disturbance in the electromagnetic field; see light. (2) The evolutionary diversification of a group of organisms from a smaller number of closely related ancestral organisms.

Reptiles Animals whose ancestry can be traced back (at least in principle) to the most recent common ancestor of snakes and crocodiles. Note that this definition includes birds. See Tree of Life,  Reptilia in the Amniota section.

Retinal (adj). Pertaining to the retina, the thin sheet of cells lining the inside of the eye. (n.) The aldehyde form of vitamin A, which is synthesized in animals from carotenoids extracted from ingested plants. Also called retinaldehyde, retinal is one of the molecules primarily responsible for light sensitivity. See phototransduction.

Retinol The alcohol form of vitamin A. See retinal.

Rod A vertebrate photoreceptor that is primarily sensitive to light at low levels of intensity. Electrophysiology and human psychophysical experiments indicate that rods can reliably respond to the absorption of a single photon. Rods predominate in the retinas of nocturnal animals.

Sarcopterygian From the Greek for "flesh-wing." Lobe-finned fishes and tetrapods. See tetrapod and Terrestrial vertebrates, Stegocephalians: Tetrapods section of the Tree of Life pages, particularly the note about the node T. 

Scleral Ossicles A ring of bones embedded in the sclera and surrounding the irises of the eyes of many animals particularly reptiles.

Sclera The fibrous covering on the posterior part of the vertebrate eye. See cornea.

Spectrum (1) A range of wavelengths (as in, "the visible region of the electromagnetic spectrum"). (2) The variation of some function over a range of wavelengths. Examples of such functions might be power or number of photons passing through an area per unit time, or percentage of light reflected or absorbed by an object or substance.

Tetrachromatic From the Greek for "four colored." Strictly speaking, a tetrachromatic animal is one for which four independent light sources are required for the simulation of all visible colors. Independence here means that no combination of intensities of a subset of the lights can be made to appear identical to any combination of intensities of the remaining lights in the set. More loosely tetrachromatic is taken to mean that an animal has four different photopigments functioning in its retina all at the same time since an animal that is so endowed may possibly meet the stricter definition. See monochromatic, dichromatic, and trichromatic.

Tetrapod From the Greek for "four foot." In phylogenetic taxonomy, tetrapod has been defined as all of the descendants of the most recent common ancestor of amphibians and amniotes. Note that this definition includes many animals (e.g., snakes) that do not have four feet. See: the Tree of Life, Classification of Terrestrial Vertebrates.

Trichromatic From the Greek for "three colored." Strictly speaking, an animal for which any visible color can be simulated with the linear combination of intensities from three independent light sources. Independent here means that no combination of intensities of two of the lights can be made to appear the same as the third light at any intensity. Light-adapted humans with "normal" color vision are trichromatic over much of their visual field, which is why television sets and computer monitors require only three phosphors to do a reasonably good job of representing colors for humans. Loosely speaking trichromacy is the state of having three photopigments operative at the same time. See monochromatic, dichromatic, and tetrachromatic.