in biology, the general appearance of an organism as determined by the quality and quantity of light that is reflected or emitted from its surfaces. Coloration depends upon several factors: the colour and distribution of the organism's biochromes (pigments), particularly the relative location of differently coloured areas; the shape, posture, position, and movement of the organism; and the quality and quantity of light striking the organism. The perceived coloration depends also on the visual capabilities of the viewer. Coloration is a dynamic and complex characteristic and must be clearly distinguished from the concept of “colour,” which refers only to the spectral qualities of emitted or reflected light.

Many evolutionary functions have been suggested for the effects of coloration on optical signaling. An organism with conspicuous coloration draws attention to itself, with some sort of adaptive interaction the frequent result. Such “advertising” coloration may serve to repel or attract other animals. While conspicuous coloration emphasizes optical signals and thereby enhances communication, coloration may, conversely, suppress optical signals or create incorrect signals and thereby reduce communication. This “deceptive” coloration serves to lessen detrimental or maladaptive interactions with other organisms.

Coloration may also affect an organism in ways other than its interaction with other organisms. Such nonoptical functions of coloration include physiological roles that depend on the molecular properties (e.g., strength and type of chemical bonds) of the chemicals that create colour. For example, dark hair is mechanically stronger than light hair, and dark feathers resist abrasion better than light feathers. Coloration may also play a part in the organism's energy budget, because biochromes create colour by the differential reflection and absorption of solar engery. Energy absorbed as a result of coloration may be used in biochemical reactions, such as photosynthesis, or it may contribute to the thermal equilibrium of the organism. Nonoptical functions of coloration also include visual functions in which coloration or its pattern affects an animal's own vision. Surfaces near the eye may be darkly coloured, for instance, to reduce reflectance that interferes with vision.

Emitted light, the product of bioluminescence, forms a portion of the coloration of some organisms. Bioluminescence may reveal an organism to nearby animals, but it may also serve as a light source in nocturnal species or in deepwater marine animals such as the pinecone fishes (pinecone fish) (Monocentris). These fishes feed at night and have bright photophores, or bioluminescent organs, at the tips of their lower jaws; they appear to use these organs much like tiny searchlights as they feed on planktonic (minute floating) organisms.

Because many pigments are formed as the natural or only slightly modified by-products of metabolic processes, some coloration may be without adaptive function. Nonfunctional coloration can, for example, be an incidental effect of a pleiotropic gene (a gene that has multiple effects), or it can result from pharmacological reaction (as when the skin of a Caucasian person turns blue in cold water) or from pure chance. It seems unlikely, however, that any apparently fortuitous coloration could long escape the process of natural selection and thus remain totally without function.

Regardless of its adaptive advantages, a particular coloration or pattern of coloration cannot evolve unless it is within the species' natural pool of genetic variability. Thus a species may lack a seemingly adaptive coloration because genetic variability has not included that coloration or pattern in its hereditary repertoire.

Because humans are highly visual animals, we are naturally interested in and attentive to biological coloration. Human attention to coloration ranges from the purely aesthetic to the rigidly pragmatic. Soft, pastel colorations aid in increasing work efficiency and contribute to tranquil moods; bright, strongly contrasting colours seem to contribute to excitement and enthusiasm. These phenomena may be extensions of the basic human response to the soft blue, green, and brown backgrounds of the environment as opposed to sharply contrasting warning colorations found on many dangerous organisms. It is possible that much of the aesthetic value humans attach to coloration is closely related to its broad biological functions.

Human interest in coloration has led to biological studies. The classical work by the Moravian abbot Gregor Mendel on inherited characteristics, based largely on plant coloration, formed the foundation for modern genetics. Coloration also aids in the identification of organisms. It is an easily perceived, described, and compared characteristic. Related species living in different habitats, however, frequently have strikingly different colorations. Since coloration is susceptible to alteration in various functional contexts, it usually lacks value as a conservative characteristic for determining systematic relationships between all but the most closely related species.

Related articles of interest include animal behaviour; mimicry.

Organisms produce colour physically, by submicroscopic structures that fractionate incident light into its component colours (schemochromes); or chemically, by natural pigments (biochromes) that reflect or transmit (or both) portions of the solar spectrum. Pigmentary colours, being of molecular origin, may be expressed independently of structural colour and are not altered by crushing, grinding, or compression. Structural colours are often reinforced by the presence of biochromes and are altered or destroyed by crushing, grinding, or compression.

The physical principles of total reflection, spectral interference, scattering, and, to some extent, polychromatic diffraction, all familiar in reference to inanimate objects, are also encountered among tissues of living forms, most commonly in animals. In plants these physical principles are exemplified only by the total reflection of white light by some fungi and bacteria and by the petals of some flowers and barks, and by some spectral interference in certain sea plants.

Total reflection of light—which imparts whiteness to flowers, birds' feathers (feather), mammalian hair, and the wings of certain butterflies—often results from the separation of finely divided materials by minute air spaces. Secretions or deposits in tissues may also contribute to the whiteness; for example, the fat and protein in mammalian milk and the calcium carbonate in the shells of mollusks, crustaceans, certain echinoderms, corals, and protozoans.

Brilliant interference colours may display variety or be predominantly of one kind, depending upon the relative thicknesses of layers and interlaminar spaces giving rise to the colours. Such colours also are changeable with the angle of vision of the viewer.

Purely prismatic refraction of light (sometimes confused with interference iridescence) is probably rare in animals and is limited to instances in which direct beams of light impinge upon certain microcrystalline deposits. Polychromatic diffraction—e.g., by natural, fine gratings or regular fine striations—may be observed among certain insects, but, like prismatic refraction, it is conspicuous only when a direct beam of light strikes such structures and they are viewed at an angle.

Two types of coloration may act in combination; in some instances, for example, structurally coloured and pigmented layers may be superimposed. Most of the greens found in the skin of fishes, amphibians, reptiles, and birds do not arise from the presence of green pigments (although exceptions occur); rather, they result from the emergence of scattered blue light through an overlying layer of yellow pigment. Extraction of the yellow pigment from the overlying cuticle of a green feather or of a reptilian skin leaves the object blue.

Plants and animals commonly possess characteristic pigments. They range in plants from those that impart the brilliant hues of many fungi, through those that give rise to the various browns, reds, and greens of species that can synthesize their food from inorganic substances (autotrophs), to the colourful pigments found in the flowers of seed plants. The pigments of animals are located in nonliving skin derivatives such as hair in mammals, feathers in birds, scales in turtles and tortoises, and cuticles and shells in many invertebrates. Pigments also occur within living cells of the skin. The outermost skin cells may be pigmented, as in humans, or special pigment-containing cells, chromatophores (chromatophore), may occur in the deeper layers of the skin. Depending on the colour of their pigment, chromatophores are termed melanophores (black), erythrophores (red), xanthophores (yellow), or leucophores (white).

The colour of a chemical compound depends on the selective absorption of light by molecules whose size or vibrational wavelengths or both lie between 3000 and 7000 angstroms (one angstrom equals 10^-7 millimetre). Selective absorption of visible light results from retardation in the relative speed or vibrational frequency of the many rapidly vibrating electron pairs found in a compound. Sufficient modification in the frequency of vibration imparts to the whole molecule a special motion, or chemical resonance, that absorbs entering light rays of matching frequency with the evolution of heat; the residual, unabsorbed light is transmitted to the eye.

If the molecular resonance involves short, rapid waves, the shorter visible light waves are absorbed (i.e., violet and blue) and the compound appears yellow or orange; red-appearing substances, having slightly longer resonance values, absorb light from the blue and green regions; and blue and green compounds result from cancellation of light in the red or orange realms. Black substances absorb all light equally and completely; white compounds absorb no light in the visible spectrum. The colour reflected by a pigment usually includes all the wavelengths of visible light except the absorbed fraction; the observed colour of a compound thus depends upon the dominant wavelength reflected or transmitted.

The more important natural pigments may be grouped into (1) classes whose molecules lack nitrogen and (2) those that contain nitrogen. Of the nonnitrogenous pigments, by far the most important, conspicuous, and widely distributed in both plants and animals are the carotenoids. Naphthoquinones, anthraquinones, and flavonoids are other nitrogen-free pigments that occur in animals, all being synthesized originally in plants, as are the carotenoids. But unlike the carotenoids, the others have a limited distribution in animals, and little is known of their physiological attributes in either kingdom.

Prominent among the nitrogenous biochromes are the tetrapyrroles, including both the porphyrins (i.e., the red or green heme compounds present in the blood of many animals and the green chlorophylls of many plants) and the bile pigments, which occur in many secretions and excretory products of animals and in plant cells. Equally prominent are the melanins, which are dark biochromes found in skin, hair, feathers, scales, and some internal membranes; they represent end products from the breakdown of tyrosine and related amino acids.

Below are outlined the basic colours, sources, and metabolic features of some representative biological pigments.

The carotenoids constitute a group of yellow, orange, or red pigments of almost universal distribution in living things. Carotenoids generally are insoluble in water but dissolve readily in fat solvents such as alcohol, ether, and chloroform. They are readily bleached by light and by exposure to atmospheric oxygen and are also unstable in acids such as sulfuric acid.

Carotenoids occur as two major types: the hydrocarbon class, or carotenes (carotene), and the oxygenated (alcoholic) class, or xanthophylls. Some animals exhibit a high degree of selectivity for the assimilation of members of one or the other class. The horse (Equus caballus), for instance, absorbs through its intestine only the carotenes, even though its green food contains mostly xanthophylls; the domestic hen (Gallus domesticus (chicken)), on the other hand, stores only members of the xanthophyll class, as do many fishes and invertebrates. Other animals, including certain frogs, Octopus species, and humans, assimilate and store both classes in the liver and in fat deposits.

The quinones include the benzoquinones (benzoquinone), naphthoquinones, anthraquinones, and polycyclic quinones.

Benzoquinones occur in certain fungi and in roots, berries, or galls (abnormal growths) of higher plants, from which they can be recovered as yellow, orange, red, violet, or darker coloured crystals or solids. Small quantities of pale-yellow crystals of coenzyme Q, often called ubiquinones (ubiquinone), are almost universally distributed in plants and animals. The ubiquinones impart no recognizable coloration to an organism because of their very small concentrations; they play an important role, however, as respiratory enzymes in catalyzing cellular oxidations.

Naphthoquinones are encountered in some bacteria and in the leaves, seeds, and woody parts of higher plants. They can be recovered as yellow, orange, red, or purple crystals. They are soluble in organic solvents and have been used extensively as dyes (dye) for fabrics. Among the naphthoquinones of biochemical and physiological importance are the K vitamins (vitamin K). Another series within the naphthoquinone class manifests conspicuous red, purple, or sometimes green colours in a few animal types. These are the echinochromes and spinochromes, so named because they are conspicuous in tissues and in the calcareous tests (shells) of echinoids, or sea urchins.

The anthraquinones occur widely in plants but in only a few animals. These brilliantly coloured compounds have found wide application as dyes and as chemical indicators of acidity or alkalinity.

The polycyclic quinones occur in some bacteria, fungi, and parts of higher plants. One of the more interesting representatives is the aphin group, so called because of their initial recovery from the hemolymph (circulating fluid) of several coloured species of aphids; aphids parasitize plants, as do the other quinone-assimilating insects.

The biochromes in the class of flavonoids, another instance of compounds lacking nitrogen, are extensively represented in plants but are of relatively minor and limited occurrence in animals, which rely on plants as sources of these pigments. Flavonoids consist of a 15-carbon skeleton compound called flavone (2-phenylbenzopyrone), in which one or more hydrogen atoms (H) is replaced either by hydroxyl groups (-OH) or by methoxyl groups (-OCH₃). Flavonoids occur in living tissue mainly in combination with sugar molecules, forming glycosides. Many members of this group, notably the anthoxanthins, impart yellow colours, often to flower petals; the class also includes the anthocyanins, which are water-soluble plant pigments exhibiting orange-reds, crimson, blue, or other colours.

The variety of anthoxanthins is greater than that of anthocyanins, and new anthoxanthins are continuously being discovered. A prominent flavonoid is the pale-yellow flavonal quercitin, first isolated from an oak (Quercus) but widely distributed in nature. A weak acid, it combines with strong acids to form orange salts, which are not very stable and readily dissociate in water. Quercitin is a strong dyestuff; it yields more than one colour, depending on the mordant used. A yellow pigment isolated from the wings of the butterfly Melanargia galatea possesses chemical properties closely allied to those of quercitin. Other well-known anthoxanthins include chrysin, found in the leaf buds of the poplar (Populus), and apigenin, found in the leaves, stem, and seeds of parsley (Petroselinum) and the flowers of the camomile (Anthemis).

The anthocyanins are largely responsible for the red colouring of buds and young shoots and the purple and purple-red colours of autumn leaves. The red colour becomes apparent when the green chlorophyll decomposes with the approach of winter. Intense light and low temperatures favour the development of anthocyanin pigments. Some leaves and flowers lose anthocyanins on reaching maturity; others gain in pigment content during development. Often an excess of sugars (sugar) exists in leaves when anthocyanins are abundant. Injury to individual leaves may be instrumental in causing the sugar excess in such cases. Anthocyanins also occur in blossoms, fruits, and even roots (e.g., beets) and occasionally in larval and adult flies and in true bugs (Heteroptera).

A typical anthocyanin is red in acid, violet in neutral, and blue in alkaline solution. Thus, the blue cornflower, the bordeaux-red cornflower, the deep-red dahlia, and the red rose contain the same anthocyanin, the variation in colour resulting from the different degrees of acidity and alkalinity of the cell sap. More than one anthocyanin may be present in a flower or blossom, and the colours of many flowers are caused by the presence of both anthocyanins and plastid pigments in the tissues. Moreover, small genetic changes in varieties or species may be associated with the development of different anthocyanins.

No physiological functions seem to have been definitely established for the flavonoids in animals and plants. It has been pointed out, however, that flower colour is valuable in attracting bees, butterflies, and other pollen-transporting visitors that implement fertilization in plants; brightly coloured fruits have improved seed dispersal by animals attracted to them as food.

A biologically important class of water-soluble, nitrogenous 16-membered ring, or cyclic, compounds is referred to as porphyrins. The elementary structural unit of all porphyrins (porphyrin) is a large ring itself composed of four pyrrole rings, or cyclic tetrapyrroles. This basic compound is known as porphin.

Porphyrins combine with metals (metalloporphyrins) and protein. They are represented by the green, photosynthetic chlorophylls of higher plants and by the hemoglobins in the blood of many animals.

Hemoglobins are present in the red blood cells of all vertebrate animals and in the circulatory fluids of many invertebrates, notably annelid worms, some arthropods, echinoderms, and a few mollusks. The hemoglobin molecule consists of a heme fraction and a globin fraction; the former consists of four pyrrole moieties (porphin) with a ferrous iron (Fe²⁺) atom in the centre. The globin fraction is a protein that may constitute more than 90 percent of the total molecular weight of hemoglobin. Hemoglobins have the capacity to combine with atmospheric oxygen in lungs, gills, or other respiratory surfaces of the body and to release oxygen to tissues. They are responsible for the pink to red colours observed in combs and wattles of birds and in the skin of humans and other primates. Particularly prominent are portions of the face, buttocks, and genital areas of baboons.

Chlorophyll is one of the most important pigments in nature. Through the process of photosynthesis, it is capable of channeling the radiant energy of sunlight into the chemical energy of organic carbon compounds in the cell. For a detailed account of this process, see photosynthesis. A pigment very much like chlorophyll was probably the first step in the evolution of self-sustaining life. Chlorophyll exists in several forms. Chlorophylls a and b are the chief forms in higher plants and green algae; bacteriochlorophyll is found in certain photosynthetic bacteria.

The chlorophylls are magnesium porphyrin compounds in which a cyclic tetrapyrrole is attached to a single central magnesium atom. They contain two more hydrogen atoms than do other porphyrins. The various forms differ in minor modifications of side groups attached to the pyrrole groups. In higher plants, chlorophyll is bound to proteins and lipids aschloroplastin in definite and specific laminations in bodies called chloroplasts. The combination of chlorophyll with protein in chloroplastin is of special significance, because only as a result of the combination is chlorophyll able to remain resistant to light.

Among the metabolic products of certain porphyrins, including the heme portion of hemoglobin, is a series of yellow, green, red, or brown nonmetallic compounds arranged as linear, or chain, structures rather than in the cyclic configuration of porphyrins. These are the so-called bilins (bilin), or bilichromes. Small quantities of the red waste compound, bilirubin (C₃₃H₃₆O₆N₄); a green product formed from it by the removal of two hydrogen atoms, biliverdin (C₃₃H₃₄O₆N₄); and various other chemically similar compounds occur in normal tissues and may be conspicuous in excretory or secretory materials under normal circumstances and certain pathological conditions. The bile pigments, although first identified in mammalian tissues or products (e.g., in the bile of the gall bladder), are by no means confined thereto. Various members of the bilichrome series are encountered in invertebrates, lower vertebrates, and in red algae and green plants.

Although the bile pigments of animals arise in all probability from the catabolism of heme precursors, there is evidence that bilirubin, accompanied by iron salts, promotes the synthesis of new hemoglobin when injected into humans, dogs, or rabbits suffering from secondary anemia.

In addition to the chlorophylls, plants also contain linear bilichromes, which have especially important roles in green plants. Among them are the blue phycocyanins and the red phycoerythrins, which serve, in red algae, as accessory pigments in photosynthesis. Another example is phytochrome, a bilichrome pigment of blue colour, which, although present in very minute quantities in green plants, is indispensable in various photoperiodic processes.

Phytochrome exists in two alternative forms: P₆₆₀ and P₇₃₀. Of these, P₇₃₀ triggers the germination and respiration of seeds (and of spores of ferns and mosses), the flowering of long-day plants (or inhibition of flowering in short-day plants), etiolation (growth in darkness), cuticle coloration, anthocyanin synthesis (e.g., in apples, red cabbage, and turnips), and several structural and physiological responses. P₆₆₀ is capable of reversing many physiological reactions initiated by P₇₃₀. Even very brief exposures to light absorbed by P₆₆₀ delays flowering in some short-day plants otherwise geared to flower by previous exposure to light of such wavelength that only the P₇₃₀ phytochrome is involved. Much yet remains to be learned about the biochemistry of phytochromes and the reactions catalyzed or otherwise regulated by them.

These pigments produce buff, red-brown, brown, and black colours. Melanins occur widely in the feathers of birds; in hair, eyes, and skin of mammals, including humans; in skin or scales or both of many fishes, amphibians, and reptiles; in the ink of cephalopods (octopus, squid); and in various tissues of many invertebrates.

Melanins are polymers (compounds consisting of repeating units) of variable mass and complexity. They are synthesized from the amino acid tyrosine by progressive oxidation, a process catalyzed by the copper-containing enzyme tyrosinase. Extractable in very dilute alkali, melanins are also soluble when fresh and undried in very dilute acid solutions; they are bleached by hydrogen peroxide, which is sometimes applied to growing hair to create a blond effect, and by chlorine, chromate, and permanganate.

Pale-yellow, tawny, buff, reddish, brown, and black colours of hair and some feathers can arise from the presence of melanins in various phases of formation or subdivision in granules. The dark, light-absorbing sublayers of melanin that intensify reflected structural (Tyndall) blues or iridescent displays in feathers were mentioned above. Black melanins and brown melanoproteins occur in many invertebrate animals. Certain worms and many crustaceans and mollusks exhibit melanism in the skin.

The degree of natural melanization depends upon relative concentrations of copper and of the copper-containing enzyme tyrosinase. Dark hairs (hair) contain higher traces of copper than pale hairs do; should the intake of copper fall substantially below a fraction of a milligram per day, new fur emerges successively less dark. This trend is reversed by restoring sufficient copper to the diet.

All human skin except that of albinos contains greater or lesser amounts of melanin. In fair-skinned persons the epidermis, or outermost layer of the skin, contains little of the pigment; in the dark-skinned races epidermal deposits of melanin are heavy. On exposure to sunlight, human epidermis undergoes gradual tanning with increases in the melanin content, which helps to protect underlying tissues from injurious sun rays.

Like melanins, the indigo compounds are excretory metabolic breakdown products in certain animals. But, in contrast to the melanins, their distribution as conspicuous pigmentary compounds is very limited, and they are not dark but red, green, blue, or purple.

One of the most common members of this group is indigo, or indigotin, which occurs as a glucoside (i.e., chemically combined with glucose) in many plants of Asia, the East Indies, Africa, and South America. It has long been used as a blue dye.

Once confused with melanins, biochromes such as phenoxazones and sclerotins show a similar colour series (yellow, ruddy, brown, or black). Genetic research, notably with reference to eye pigments of the fruitfly, Drosophila melanogaster, has resulted in the description of a class of so-called ommochromes (ommochrome), which are phenoxazones. The ommochromes not only are conspicuous in the eyes of insects and crustaceans but have also been detected in the eggs of the echiurid (spoonworm) worm Urechis caupo and in the changeable chromatophores in the skin of cephalopods. In addition to being responsible for the brown, vermilion, cinnabar, and other colours of insect eyes, ommochromes are also sometimes present in the molting fluid and integument. They are distinguished from the melanins by solubility in formic acid and in dilute mineral acids, by manifestation of violet colours in concentrated sulfuric acid, and by showing reversible colour changes with oxidizing and reducing agents. The ommochromes, which are derived from breakdown of the amino acid tryptophan, include ommatins and ommins. The ommatins, although complex in chemical structure, are relatively small molecules. The ommins are large molecules, in which the chromogenic moiety is seemingly condensed with longer chains, such as peptides (amino acids linked together).

Sclerotins (sclerotin) arise as a result of an enzyme-catalyzed tanning of protein. Certain roaches secrete a phenolase enzyme, the glucoside of a dihydroxyphenol, and a glycosidase. Mixing of these substances results in the release of the phenolic compound from glucose and its combination, via a reaction catalyzed by the phenolase, with protein; the products are pink, ruddy, and ultimately dark-brown polymers that are incorporated into the insect's body cuticle and egg cases. Similar reactions take place in the carapace (the shell covering the body) of certain crustaceans.

The white, silvery, or iridescent chromatophores, both stationary iridocytes and changeable leucophores, of some fishes, amphibians, lizards, and cephalopods contain microcrystalline aggregates of the purine guanine; (guanine) a layer of white skin on the underside of many fishes, called the stratum arginatum, is particularly rich in guanine.

Closely related to the purines and formerly classed among them are the pterins, so named from their notable appearance in and first chemical isolation from the wings of certain butterflies. Both purines and pterins contain a six-atom pyrimidine ring; in purines this ring is chemically condensed with an imidazole ring; pterins contain the pyrazine ring. Pterins occur as white, yellow, orange, or red granules in association with insect wing material.

Flavins constitute a class of pale-yellow, greenly fluorescent, water-soluble biochromes widely distributed in small quantities in plant and animal tissues. The most prevalent member of the class is riboflavin (vitamin B₂).

Flavins are synthesized by bacteria, yeasts, and green plants; riboflavin is not manufactured by animals, which therefore are dependent upon plant sources. Riboflavin is a component of an enzyme capable of combining with molecular oxygen; the product, which is yellow, releases the oxygen in the cell with simultaneous loss of colour.

The chemical constitution of many pigments remains imperfectly known. Only a few of the more conspicuous examples are mentioned below.

Copper-containing proteins called hemocyanins occur notably in the blood of larger crustaceans and of gastropod and cephalopod mollusks. Hemocyanins are colourless in the reduced, or deoxygenated, state and blue when exposed to air or to oxygen dissolved in the blood. Hemocyanins serve as respiratory pigments in many animals, although it has not been established that they perform this function wherever they occur.

Iron-containing, proteinaceous pigments, hemerythrins are present in the blood of certain bottom-dwelling marine worms (notably burrowing sipunculids) and of the brachiopod Lingula; the pigments serve as oxygen-carriers.

Pale-green pigment, hemovanadin, is found within the blood cells (vanadocytes) of sea squirts (sea squirt) (Tunicata) belonging to the families Ascidiidae and Perophoridae. The biochemical function of hemovanadin, a strong reducing agent, is unknown.

A relatively rare pigment, actiniochrome occurs in red or violet tentacle tips and in the stomodeum (oral region) of various sea anemones. The pigment plays no recognized physiological role.

Adenochrome is a nonproteinaceous pigment that occurs as garnet-red inclusions at high concentrations in the glandular, branchial heart tissues of Octopus bimaculatus. The compound contains small amounts of ferric iron and some nitrogen and gives a positive reaction for pyrroles. It is believed to be an excretory product.

Coloration is in large measure determined genetically. As mentioned earlier, the inheritance of colour in garden peas provided part of the basis for the pioneering studies of heredity by Mendel (Mendel, Gregor). These studies led Mendel to postulate the existence of discrete units of heredity that segregate independently of one another during the formation of reproductive cells. The studies also led to his discovery of the phenomenon of dominance. The basic units of heredity are now known as genes, and the variant forms of a given gene are termed alleles (allele). Among species that reproduce sexually, an individual normally possesses a pair of alleles for any gene—one inherited from the female parent and one from the male parent. These two alleles are situated at corresponding loci on the paired chromosomes found in diploid cells—i.e., cells containing two similar sets of complementary chromosomes. Segregation of the alleles occurs during formation of reproductive cells, with the result that only one of the pairs enters each cell, which is called a haploid cell.

In his experiments Mendel crossed purple-flowered peas with white-flowered ones. The plants he used in these crosses were true-breeding for flower colour, meaning that the purple-flowered plants were descended for generations from only other purple-flowered plants, and that the white-flowered plants were likewise descended for generations from only other white-flowered plants. Because of these true-breeding characteristics, Mendel postulated that the original plants were homozygous for the trait of flower colour—in other words, that each plant carried a pair of identical heredity units (i.e., alleles) for this trait. When he crossed purple-flowered peas with white-flowered ones, he obtained a first filial (F₁) generation in which all the offspring had purple flowers. He therefore deduced that the unit for purple (usually designated R) was dominant over the unit for white (r). Thus in the parental generation the purple-flowered plants can be designated RR (indicating that they are homozygous for the dominant allele), and the white-flowered plants can be symbolized as rr. The F₁ plants were heterozygous for flower colour (Rr), but they expressed purple colour because of the complete dominance of the allele R over r.

Dominance may be incomplete, however; a crossing between homozygous red Japanese four-o'clocks (four-o'clock) (Mirabilis) and homozygous white ones yields heterozygous Rr offspring, which are all pink. A cross of the heterozygous pink generation of four-o'clocks with each other yields a second generation with the colour ratio of 25 percent red (RR), 50 percent pink (Rr), and 25 percent white (rr). This is because each of the parent (F₁) plants produces equal numbers of R- and r-containing reproductive cells through segregation, and there is a random chance of either type of male haploid cell (gamete) fertilizing either of the two female types. For peas, on the other hand, the ratio resulting from a cross of parent (F₁) plants is three purple (one RR and two Rr) to one white (rr) because of the dominance of R.

Although the principle of inheritance of colour and coloration patterns in all organisms is like that for the two plants described above, it is usually far more complex. Within the species population, a particular gene may have multiple alleles instead of two; thus numerous combinations within any individual may be possible; in addition, the coloration may depend upon genes at several sites. In this case either all pairs may segregate simultaneously and more or less independently into the gametes, or the genes may be linked in their inheritance by location on the same chromosome. Such possibilities, together with different degrees of dominance, result in tremendously complex hereditary bases for the genetic control of colour and colour patterns within many species. For a fuller treatment of these principles, see Genetics And Heredity, The Principles Of: Mendelian genetics (heredity).

The development of coloration often depends upon regulatory substances (hormones (hormone)) secreted by endocrine glands. In birds (bird) the level of the hormone thyroxine determines the coloration of feathers and bill, although specific seasonal biochromes are often laid down under the influence of sex hormones, as in the beak of the starling, which turns from black to yellow in early spring. The variability in control among bird species is so great, however, that generalizations are impossible. Hormonally controlled colour changes also occur in mammals; for example, swellings in the genital areas that become pink due to vascularization during the reproductive season. The species specificity of coloration patterns, however, always depends on a genetically determined responsiveness of various target tissues to certain hormones.

Chromatophores (chromatophore) occur in cephalopods, crustaceans, insects, fishes, amphibians, and lizards and are responsible for the most rapid colour changes. They allow conspicuous display of a biochrome by dispersing it in the chromatophore-bearing surface, or they conceal the biochrome by concentrating it into small areas. Chromatophores are of three kinds. The chromatophoric organs of cephalopods (cephalopod) consist of an elastic sac filled with biochrome and controlled by a ring of radiating muscle fibres. These fibres contract in response to neural stimulation, thereby stretching the sac into a broad, thin disk. Chromatophoric syncytia occur in crustaceans (crustacean), the movement of biochrome being due to the ebb and flow of cytoplasm through fixed tubular spaces that collapse when the cell is contracted and fill when the cell expands. Chromatophoric syncytia are hormonally controlled. Cellular chromatophores, the third kind, are found in vertebrates. In these cells melanic granules flow in stable cellular processes that maintain a fixed position, unlike the contracting and expanding processes of the syncytia. Control among vertebrates is varied: chromatophores of bony fishes are controlled by the autonomic nervous system; those of elasmobranch fishes (sharks and rays) and lizards are controlled by hormones and nerves; those of amphibians are regulated by hormones alone.

One animal may contain biochromes of several colours, commonly red, yellow, black, and reflecting white; prawns also have a blue biochrome. By appropriate migrations of biochromes, an animal can achieve substantial alterations in colour or shade for varying periods of time. In prawns, dispersion of blue and yellow yields green; unequal dispersion of biochromes over parts of the body produces patterns of coloration.

Rapid physiological colour changes are supplemented by morphological ones, the animal either gradually synthesizing or destroying biochromes, usually in an adaptive manner (see the section Coloration changes (coloration)).

Coloration and the pattern of coloration play a central role in the lives of plants and animals—even those species in which vision is lacking or not the dominant sense. For example, cryptic coloration often goes hand in hand with cryptic behaviour; nonreflective colours occur on the faces of birds that forage in bright sunlight; and abrasion-resistant coloration occurs more often among species that inhabit abrasive habitats than among species that inhabit nonabrasive habitats. The functions of biological coloration fall into three broad categories: (1) optical functions, in which coloration affects the animal's or plant's visibility to other animals; (2) visual functions, in which coloration affects the animal's own vision; and (3) physiological functions, in which the molecular properties of biochromes play a role unrelated to either optical signaling or vision.

Deceptive coloration depends on four factors: the coloured organism, hereafter referred to as the organism; its model, which may be the background against which it is concealed; the spectral quality of the illumination; and the visual sensitivity and behaviour of the animal or animals that the organism is deceiving. To some extent the following discussion considers the relationships among the four factors separately; but in reality the deceptive, optical effect results from the interaction of all four factors. There are two basic types of deceptive coloration: (1) concealing coloration, or camouflage, in which the organism blends into its surroundings; and (2) mimicry, in which the organism is not hidden but rather presents a false identity by its resemblance to another species.

The simplest examples of background matching are provided by the fish eggs and planktonic (free-floating) larval fishes that exist in the uniformly blue environment of the open sea—i.e., those that are pelagic. They usually possess minimal pigmentation and are transparent.

In other organisms and environments the behaviour and form of the organism become more important as adjuncts to coloration. Evidence of the importance of the choice of a proper background is provided by three differently coloured species of lizards (lizard) of the genus Anolis (anole), which form mixed hunting groups over the same background. Many of the individuals are easily perceived on this background, but, when disturbed, they conceal themselves by segregating according to species over the appropriately coloured backgrounds. Camouflage may also be accomplished through a change in coloration. Many flatfishes (pleuronectiform), for example, show a remarkable ability to match the pattern of the surface on which they are resting. Some nudibranchs (nudibranch), a group of marine gastropods, such as Phestilla melanobrachia, manage to establish and maintain their resemblance to the background by ingesting portions of their model, which is the living coral on which they live. The pigments in the coral polyps are deposited in diverticula (branches) of the gut and occasionally in the epidermis and show through as nearly perfect camouflage. The slow-moving nudibranchs are very difficult to see on their coral host, and when they move to differently coloured coral, their coloration changes as their food source changes.

Some of the parasites that live on marine fishes conceal themselves in a similar manner. Flukes (fluke), or monogenean trematodes, gorge themselves on their hosts' tissues and biochromes and appear to remain within areas on the host that have similar pigmentation. The adaptive significance of the coloration is known to lie in escape from predation by the third party, cleaning organisms such as the fish Labroides, which feeds on the external parasites of other fishes. Several decorator crabs (crab) use portions of the model for concealment by picking up algae and sponges and placing them on the carapace (upper shell) to cover their own coloration; the algae and sponges continue to live as if in their normal habitat.

Some forms of disruptive coloration also function to conceal movement. Forward movement in concentrically banded snakes, for example, is difficult to perceive when the animal moves between reeds or long blades of grass.

The light-producing organs, or photophores (photophore), of many deepwater fishes provide a unique form of countershading. Photophores occur in bands along the lower parts of the sides and are directed downward. Deepwater fishes live in the twilight zone of the sea, in which the illumination is too weak to allow little more than a silhouette of prospective prey sighted by a predator from below. The downward-projecting photophores may provide countershading by obliterating the silhouette when it is viewed by a predator from below.

The shape of an organism is important in determining the total configuration for protection. Both concealment and mimicry may depend strongly on imitation of both the shape and coloration of the model. Deep-bodied schooling fishes frequently show vertical banding, and elongated forms usually bear horizontal stripes. This dichotomy may be partially related to different swimming patterns: deep-bodied fishes perform frequent lateral turns; elongated forms show frequent horizontal movement and change of position.

As mentioned above, deception may be accomplished by providing false information through mimicry. aggressive mimicry occurs when a predator resembles its prey or a harmless third party. For example, the American zone-tailed hawk (Buteo albonotatus) is nearly black and has long narrow wings, and it glides in the company of similarly coloured and shaped vultures. The vultures do not prey on small animals and therefore do not cause fright reactions among them. The zone-tailed hawk exploits this lack of fear by suddenly diving on its prey from among the group of circling vultures.

Some organisms provide false information as to their identity by mimicking dangerous or inedible species. When a third party, such as a predator, fails to distinguish between the mimic and its inedible model, the relationship is termed Batesian mimicry (see mimicry). Batesian mimicry can be contrasted to those forms of camouflage in which organisms show an “imitative resemblance” to inanimate objects in their environment, such as the leaves or twigs of a tree. Imitative resemblance is a true concealing coloration in that it usually disguises the organism sufficiently so it is not perceived as distinct from its background. The form and coloration of a Batesian mimic, on the other hand, usually ensures that the organism will be perceived by animals, including predators, but that it will be identified with the harmful or distasteful model species. Batesian mimicry is thus both a deceptive and an advertising coloration, and it is effective only because the model species itself has a warning coloration (see below).

Whereas concealing coloration reduces visual information, advertising coloration provides easily perceived information as to an organism's location, identity, and movement.

In gregarious animals, coloration, morphology, and general behaviour may identify an individual to others of its species and can aid in the formation of species aggregations throughout the year. This is seen in schooling fishes (fish), in which the portion of the body moved by swimming motions frequently contrasts with the coloration of the rest of the body, apparently providing an attracting stimulus within the school.

During the reproductive season, many animals defend a particular area or territory that includes their nest or spawning site. Many other animals defend territories throughout the year. In either case, coloration is frequently important. In species in which the task of territorial defense is accomplished largely by one sex, strong sexual dimorphism usually exists, the more brightly coloured sex being the one that holds the territory. Both male- and female-territorial species are found within the diverse fish family Cichlidae. Species in which the male holds a territory are marked by large and colourful males, the females being smaller and camouflaged; in those species in which the female defends the territory the reverse is found. In still other species the fish pair and share the territory, and there is little sexual dimorphism.

Coloration frequently releases agonistic (flight or attack) behaviour in territorial animals and intimidates intruders. The flashing coloration displays of a dominant octopus are an excellent example of a visual battle in which the victor may be determined with little or no bodily contact.

Although similar advertising colorations may contribute to the spacing out of territorial animals (animal development), dissimilarity in coloration between members of a species may allow closer spacing. Many brightly coloured reef fishes, for example, defend territories or personal spaces. In many of these species the young and subadults, with radically different coloration from the adult, live within the territory of an adult but remain free from attack; after they assume adult coloration, however, they are driven away. The territories frequently function to ensure a food supply; because the juveniles utilize different food, they pose no threat to the adult's supply. As the juveniles age, their feeding habits overlap those of the adult, and spacing is necessary.

As discussed above, Batesian mimicry is the imitation of aposematic coloration by benign organisms, which thereby enjoy at least a portion of the protection of the model species. While Batesian mimicry involves deceptive coloration, resemblance in warning coloration need not provide false information. Müllerian mimicry refers to instances in which several noxious species display the same warning coloration, thus enabling potential predators to learn and generalize the signal easily. The black-and-yellow coloration of bees and wasps is a typical example.

Most animals need both concealment and advertisement. An animal may need to conceal itself from predators and to advertise its presence to symbionts or to members of its own species for reproductive purposes.

Many birds that conceal courtship coloration when their feathers are held close to the body present a brilliant display upon erecting their feathers. Similar mechanisms are common in many animals, such as Anolis (anole) lizards, which have brightly coloured throat fans that are visible only when erected during courtship or threat behaviour.

Many bower birds (Ptilonorhynchidae (bowerbird)) have bright courtship colorations, although some males of Amblyornis species do not. Instead, they decorate an elaborate bower with leaves, flower petals, and other brightly coloured objects, which attract females but provide no clue to predators as to the exact location of the male.

Some predators deceive with advertising coloration. The frogfishes (frogfish), or shallow-water anglerfishes (anglerfish), are extremely difficult to detect against their background. They have intricate and obvious lures that are waved near the mouth on a long stalk; prey fishes attracted to the lure are eaten.

Coloration change is another obvious mechanism that can restrict advertisement to times when it is needed for purposes of communication. Many animals change from cryptic to noncryptic colorations as they change from their normal resting coloration to a display coloration during social interactions. These changes are particularly common in fishes and cephalopods, which have efficient neural mechanisms of coloration change.

Of obvious importance in the evolution of coloration is the third party, which is the actual selective (natural selection) agent involved in the relationship between the organism and its background. Identification of the third party and the sensory and nervous system components used by it are important in order to understand thoroughly the adaptive nature of deceptive or advertising coloration.

In analyzing concealing coloration, the actual identification of the third party may have a profound influence on the interpretation of the coloration and behaviour. For example, the early stages of the green Scotch pine caterpillar (Bupalus piniarius and others) are found at the tips of pine needles, well camouflaged in this position. As they grow larger, they move into the bases of the needles and onto the branch. One explanation for the movement is that the older caterpillars (caterpillar) are much larger than the background needle, thus rendering the camouflage less effective. Another factor appears to be a shift in the third party as the caterpillar ages; young caterpillars are preyed upon by spiders found on the twigs; larger caterpillars, by birds such as titmice (Parus).

After the initial identification of the third party, its visual (vision) capabilities must be investigated. The spectral sensitivity of its eyes must be determined, as must the way in which it perceives combinations of biochromes and their arrangements. The visual stimulus is subject to encoding and integrating steps as it passes from the eye to the cerebral cortex of the brain. Contrast and movement are amplified by some cells, while other properties, such as shape and intensity, are ignored. In humans, for example, contrast is greatly enhanced at the junction between a red and a blue stripe, producing the optical illusion that the two stripes never meet and are on different planes. Such phenomena may be of importance in disruptive coloration.

In social signals, the visual system of a species is frequently maximally responsive to its own range of colorations. Butterflies of the genus Dardanus, for example, are maximally responsive to their own blue courtship coloration. The visual system and coloration are coadapted to provide an efficient signal mechanism.

Most optical signals depend on sunlight reflected from the animal or plant. Therefore, the receiver's perception of the signal depends on the characteristics of the ambient illumination, which, in turn, depends on such variables as time of year, time of day, amount of cloud cover, amount of vegetation between the light source and the optical signal, and spectral reflectance of the habitat. Clear-sky sunlight with the Sun overhead is essentially white, but with the Sun low in the sky the light has a yellow or orange spectral emphasis. Light in broadleaf forests has a yellow-green emphasis, whereas light in conifer forests has a slight bluish emphasis. These small but consistent differences may affect the evolution of optical coloration.

Biological coloration can play a variety of roles in an animal's visual system. For example, facial coloration can help determine the amount of light that is reflected into the eyes. Among animals living in brightly lit habitats, too much reflected light could have undesirable effects on vision. It could, for example, produce blinding glare or dazzle; it might result in high luminance in parts of the visual field, thereby diminishing contrast in other parts of the field; or it could cause adaptation to a higher illuminance level than is appropriate for the remainder of the visual field. Birds that forage in sunlight for aerial insects—a visually demanding task—have bills that are black. Apparently the black coloration reduces reflectance that interferes with their vision.

Vision itself depends on a biochrome that consists of a protein, opsin, attached to a chromophore. The chromophore may be either retinal ( vitamin A₁), in which case the molecule is called rhodopsin; (rhodopsin) or 3-dehydroretinal (vitamin A₂), in which case the molecule is called porphyropsin. When light enters the eye and strikes the visual biochrome, the molecule undergoes a chemical change that stimulates the receptor nerve and thereby produces a visual stimulus.

In addition to the visual pigments, the eyes of many invertebrates contain biochromes that affect the spectrum of light that reaches the photoreceptors. Similarly, oil droplets in the retina and epithelium of vertebrate eyes contain carotenoids that may affect colour perception. More importantly, the epithelium contains melanin, which absorbs stray light that penetrates the retina without being absorbed by the visual pigments. In insect eyes a similar function is performed by ommochromes in secondary pigment cells surrounding the photoreceptors.

Among many nocturnal vertebrates the white compound guanine is found in the epithelium or retina of the eye. This provides a mirrorlike surface, the tapetum lucidum, which reflects light outward and thereby allows a second chance for its absorption by visual pigments at very low light intensities. Tapeta lucida produce the familiar eyeshine of nocturnal animals.

The discussion of biochromes earlier in this article touched upon the many important physiological roles of biological pigments, including that of the chlorophylls in photosynthesis and of the hemoglobins in oxygen transport. This section provides examples of other physiological effects of biological coloration.

Hair and feathers that contain melanin are more durable than those that lack this biochrome. Increased durability probably accounts for the dark, melanic wing tips of most birds. It may also be a contributing factor to the high proportion of black among birds that live in deserts, which are exceptionally abrasive habitats.

The absorption of solar energy by dark skin, scales, feathers, or hair is often associated with increased heat gain and reduced metabolic rates. Because birds lose a large amount of body heat through their uninsulated legs, dark leg coloration may help to warm the legs by absorbing solar energy, thereby reducing heat loss. Such reduced heat loss may explain why dark-legged North American woodwarblers (Parulidae) arrive in their northern breeding areas earlier than light-legged woodwarblers. Dark feathers (feather), however, may actually reduce the amount of solar energy that penetrates to and is absorbed by a bird's skin. With fully erect plumage in moderate winds, a dark bird in full sunlight absorbs less heat into its body than a light bird does. This may also be a factor contributing to the high proportion of black among desert-dwelling birds.

Photoactivation of 7-dehydrocholesterol into vitamin D occurs throughout the epidermis of humans in the presence of ultraviolet light. The melanization (melanin) of human skin may be an adaptation to optimize synthesis of vitamin D by permitting more or less ultraviolet radiation to penetrate the epidermis.

A widespread response to increased light levels is the addition of melanin, or darkening of the body—for example, tanning in humans. Such melanic shielding protects the tissues of the organism from potentially dangerous levels of ultraviolet radiation. Since the ultraviolet shield need protect only easily damaged cells in the nervous and reproductive systems, it does not necessarily have to lie in the skin but can instead be located internally, immediately around sensitive organs. When the ultraviolet shield is internal, external coloration may conform to other selection pressures.

Water is conserved by reducing evaporative loss and by reducing excretory water loss. Insects reduce evaporative water loss by adding melanin to the cuticle, melanin being more waterproof than other biochromes. The black-coloured beetle Onymacris laeviceps loses significantly less water than does the white-coloured beetle O. brincki when both species are kept without food under identical conditions. Quinones also darken insect exoskeletons, and in Drosophila quinones contribute to the low permeability of the exoskeleton. Some insects avoid excretory water loss by depositing nitrogenous wastes in the exoskeleton, which is shed periodically. In these species external coloration is a consequence of nitrogen excretion.

Some arthropods produce offensive odours as a means of defense against predators. These odours derive from p-benzoquinones in the exoskeleton and are correlated with the chromatic properties of the molecules. Consequently, coloration in these species may be a consequence of selection for chemical defense.

Changes in colour that extend over periods of several months may involve the synthesis or destruction of chromatophores or biochromes. The quantities of deposited guanine in some fishes vary in proportion to the relative lightness in colour of the background upon which they are living. Greenfish, or opaleye (Girella nigricans), kept in white-walled aquariums became very pale during a four-month period, storing about four times the quantity of integumentary guanine as was recoverable from the skins of individuals living in black-walled aquariums but receiving the same kind and amounts of food and the same overhead illumination.

Some chromatophores respond directly to relevant environmental stimuli, independent of the nervous system. Such response occurs in the young of some fish and of the clawed frog (Xenopus); but in older individuals the nervous system, which is by this time fully developed, controls responsiveness. More typically the chromatophore response is mediated by the sensorimotor system from the start. The eye plays a major role in cephalopods and most vertebrates, particularly in animals capable of matching complex backgrounds, but the pineal organ (a light-sensitive organ on top of the brain) and a generalized dermal light sense may also mediate the chromatophore response.

Colour changes during the life of an individual are common. Graying hair is a familiar badge of the elderly, both in humans and, to varying degrees, in other mammals. Among primate groups, particularly gorillas and chimpanzees, silver hairs indicate both age (aging) and dominance. Young birds of many species have a juvenile plumage that gives way to either an adult plumage in short-lived birds or a series of immature plumages in longer-lived species. Most gulls, for example, are deep gray or brown during their first year and become increasingly white thereafter. Changes of colour are also associated with age and size in many fish; for example, the blue parrot fish changes from a vertically barred pattern to all blue in association with increasing age and size.

Coloration changes occur not only in individuals but in populations as well. These latter result from evolutionary pressures—i.e., agents of natural selection—that act upon the natural variations in colour types (morphs) found among the population. As a result of such pressures, certain colour morphs have increased odds of surviving and passing on their coloration pattern. Depending on the nature of the selection pressures, the population may come to include substantial numbers of individuals of different colour morphs; or one morph may become dominant, largely supplanting an earlier dominant colour form.

When individual colour variation is discontinuous within a species, that species is said to be polychromatic. The white-throated sparrow (Zonotrichia albicollis) of North America, for example, has individuals with white-and-black head stripes and other individuals with tan-and-brown head stripes. The different colorations are not associated with age, sex, or geographic region. Polychromatism may evolve in response to predation. A predator that successfully takes one prey type may then concentrate its search on others of this type and hence may overlook differently coloured prey of the same species. The phenomenon—known as a perceptual set or a search image—is exemplified by the predator of the European snail Cepaea. Predators encounter one morph and form a search image; they continue to hunt for that one form until its increasing rarity causes the predator to hunt randomly, encounter a different morph, and form a new search image. In this way, oscillating selection pressures maintain several contemporaneous colour morphs among the snail population.

Evolutionary colour changes dictated by shifting selection are suggested by many populations that show geographical or temporal clines (graded series of morphological characters). For example, the common flicker (Colaptes auratus) has yellow markings in eastern North America and red markings in western North America, suggesting a change in selection pressure as one moves from east to west. The best documented temporal shift in selection is the industrial melanism of noctuid and geometrid moths (moth) in England and Europe. The proportion of melanic, or darkly coloured, individuals in about 70 species of moths has increased dramatically since the 1850s. This increase correlates with the Industrial Revolution and the associated pollution of the countryside. Prior to that time, tree trunks, the normal daytime resting place of these nocturnal moths, had been covered by scattered whitish lichens. The trunks have turned dark in areas of industrial development because the lichens have been killed by pollutants and the trunks have been dirtied by soot. Blotched gray moths, previously protected from predation by birds, are now vulnerable, while the dark moths are less conspicuous. The shift to melanic populations in the United States lagged behind that in England and Europe, as did the industrialization process; but in Michigan by the early 1970s darkly coloured individuals formed up to 97 percent of some populations in regions where melanism was unknown before 1927. Since the 1970s in England there has been a reversal in the number of melanic individuals of some species, a sign that efforts to curb air pollution are having far-reaching effects.

The many diverse functions discussed above lead to the inevitable conclusion that no single function can explain the coloration of living things. While biologists are far from a comprehensive theory that predicts the hues and patterns of coloration of plants and animals, such a theory will have to integrate the optical, visual, and physiological functions of biological coloration.