A phenotype (from Greek phainein, meaning 'to show', and typos, meaning 'type') is the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). A phenotype results from the expression of an organism's genetic code, its genotype, as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black and brown.
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. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). The genotype-phenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, which is a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse.
Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that bird nests and other built structures such as caddis fly larvae cases and beaver dams can be considered as "extended phenotypes".
Difficulties in definition
Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by Western blotting) and are thus part of the phenotype; human blood groups are an example. It may seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes traits or characteristics that can be made visible by some technical procedure. A notable extension to this idea is the presence of "organic molecules" or metabolites that are generated by organisms from chemical reactions of enzymes.
Another extension adds behavior to the phenotype, since behaviors are also observable characteristics. Behavioral phenotypes include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders or syndromes.
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 (G) + environment (E) → phenotype (P)
A more nuanced version of the relationship is:
- genotype (G) + environment (E) + genotype & environment interactions (GE) → phenotype (P)
Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions (see ecophenotypic variation). The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows.
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.
The concept of phenotype can be extended to variations below the level of the gene that affect 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.
The extended phenotype
The term extended phenotype refers to the idea that a phenotype is not restricted to biological processes but also defines all effects that a gene has on its surroundings. The concept generalized by Richard Dawkins explains that phenotype includes all the influence a gene has on the environment and other organisms. One can begin to understand the concept of extended phenotype through the central theorem of the extended phenotype: "An animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." 
There are three types of extended phenotypes. The first describes an organism using architectural constructions to modify their environment for living. The most common example given by Dawkins is the beaver. For instance, a beaver dam might be considered a phenotype of beaver genes, the same way a beaver's powerful incisor teeth are phenotypic expressions of its genes. A beaver uses these incisors to modify its environment. This influence of a gene on the environment is an example of an extended phenotype.
Dawkins also cites the effect of an organism on the behavior of another organism (such as the devoted nurturing of a cuckoo by a parent of a different species) as an example of the extended phenotype as well as parasites living inside the body of a host. The first example he used was sporocysts of flukes of the genus Leucochloridium that invade the tentacles of snails where they can be seen conspicuously pulsating through the snail's skin. This change in both color and behavior (infected snails move upwards on vegetation) is suggested to increase predation on the snail by birds and therefore to assist the parasite enter its final host, a bird.
The third example of the extended phenotype is "Action at a Distance". This is where genes in one organism affect the behavior of another organism. The examples Dawkins used were genes in orchids affecting orchid bee behavior (to increase pollination), genes in rattlesnakes causing avoidance behavior in other animals, and genes in male peacocks affecting copulatory decisions of peahens.
The smallest unit of replicators is the gene. Replicators cannot be directly selected upon, but they are selected on by their phenotypic effects. These effects are packaged together in organisms. We should think of the replicator as having extended phenotypic effects. These are all of the ways it affects the world, not just the effects the replicators have on the body in which they reside.
Phenome and phenomics
Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics. Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness. Phenomics is also a large part of the Human Genome Project
Phenomics has widespread applications in the agricultural industry. With an exponentially growing population and inconsistent weather patterns due to global warming, it has become increasingly difficult to cultivate enough crops to support the world’s population. Advantageous genomic variations, like drought and heat resistance, can be identified through the use of phenomics to create more durable GMOs.
Phenomics is also a crucial step stone towards personalized medicine, particularly drug therapy. This application of phenomics has the greatest potential to avoid testing drug therapies that will prove to be ineffective or unsafe. Once the phenomic database has acquired more data, patient phenomic information can be used to select specific drugs tailored to the patient. As the regulation of phenomics develops there is a potential that new knowledge bases will help achieve the promise of personalized medicine and treatment of neuropsychiatric syndromes.
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