A phenotype (from polymorph.
The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
This 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.
Difficulties in definition
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 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 beavers' powerful incisor teeth are phenotype expressions of their genes. Dawkins also cites the effect of an organism on the behaviour 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.
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.
- Churchill, F.B. (1974). "William Johannsen and the genotype concept".
- Johannsen, W. (1911). "The genotype conception of heredity".
- O'Brien, Gregory; Yule, William, eds. (1995). Behavioural Phenotypes. Clinics in Developmental Medicine No.138. London: Mac Keith Press.
- O'Brien, Gregory, ed. (2002). Behavioural Phenotypes in Clinical Practice. London: Mac Keith Press.
- "Botany online: Evolution: The Modern Synthesis - Phenotypic and Genetic Variation; Ecotypes". Retrieved 2009-12-29.
- Dawkins, Richard (1982). The Extended Phenotype. Oxford University. p. 4.
- Mahner, M. & Kary, M. (1997). "What exactly are genomes, genotypes and phenotypes? And what about phenomes?".
- Varki, A; Wills, C; Perlmutter, D; Woodruff, D; Gage, F; Moore, J; Semendeferi, K; Bernirschke, K; Katzman, R et al. (1998). "Great Ape Phenome Project?".
- Mouse Phenome Database
- Human Phenotype Ontology
- Europhenome: Access to raw and annotated mouse phenotype data
- "Wilhelm Johannsen's Genotype-Phenotype Distinction" by E. Peirson at the Embryo Project Encyclopedia