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Individuals in the mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes.

A phenotype describes any observed quality of an organism, such as its morphology, development, or behaviour, as opposed to its genotype - the inherited instructions it carries, which may or may not be expressed. This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces.^[1][2] The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). A more modern version is Francis Crick's Central dogma of molecular biology.

Despite its seemingly straightforward definition, the concept of the phenotype has some hidden subtleties. In the first place, most of the molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet are part of the phenotype. Human blood groups are an example. Therefore, by extension, the term phenotype must include characteristics that can be made visible by some technical procedure. A further, and more radical, extension would add inherited behaviour to the phenotype.

Biston betularia morpha typica, the standard light-coloured Peppered Moth.

Biston betularia morpha carbonaria, the melanic Peppered Moth, illustrating discontinuous variation.

Second, the phenotype is not simply a product of the genotype, but is influenced by the environment to a greater or lesser extent (see also phenotypic plasticity). And, further, if the genotype is defined narrowly, then it must be remembered that not all heredity is carried by the nucleus. Mitochondria, for example, divide in unison with the nucleus, but transmit their own DNA directly, not via the nucleus.

The phenotype is composed of traits or characteristics ^[3]. Some phenotypes are controlled entirely by the individual's genes. Others are controlled by genes but are significantly affected by extragenetic or environmental factors. Almost all humans inherit the capacity to speak and understand language, but which language they learn is entirely an environmental matter.

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.

The interaction between genotype and phenotype has often been conceptualized by the following relationship:

genotype + environment → phenotype

A slightly more nuanced version of the relationships is:

genotype + environment + random-variation → phenotype

An example of random variation in Drosophila flies is the number of ommatidia, which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.

A phenotype is any detectable characteristic of an organism (i.e., structural, biochemical, physiological, and behavioral) determined by an interaction between its genotype and environment (of this distinction).

According to the autopoietic notion of living systems by Humberto Maturana, the phenotype is epigenetically being constructed throughout ontogeny, and we as observers make the distinctions that define any particular trait at any particular state of the organism's life cycle.

The idea of the phenotype has been generalized by Richard Dawkins in The Extended Phenotype to mean all the effects a gene has on the outside world that may influence its chances of being replicated. These can be effects on the organism in which the gene resides, the environment, or other organisms. For instance, a beaver dam might be considered a phenotype of beaver genes, the same way beaver's powerful incisor teeth are phenotype expressions of their genes.

The concept of phenotype can be extended to variations below the level of the gene that effect an organism's fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine base pairs (GC content). These base pairs have a higher thermal stability (melting point, see also DNA-DNA hybridization) than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.

1. ^ Churchill F.B. 1974. William Johannsen and the genotype concept. J History of Biology 7, 5-30.
2. ^ Johannsen W. 1911. The genotype conception of heredity. American Naturalist 45, 129-159
3. ^ Sydney Brenner and Jeffrey H. Miller. 2002. Encyclopedia of Genetics San Diego: Academic Press.

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