A phenotype is an observable characteristic of an organism, arising from its genotype, environment and other influences. Seed shape is a phenotype; is a genotype. The distinction prevents appearance from being mistaken for a complete inherited description. See NHGRI: phenotype.
For a specified binary phenotype , let its penetrance in genotype be . The law of total probability gives . Thus the ideal example has : the familiar follows only when these penetrances are . A pedigree likelihood keeps inheritance and the conditional phenotype model as separate factors.
Dependence of the phenotype expressed by a genotype on the environment. An immediate response can be beneficial or harmful; evolutionary change additionally requires a change in inherited properties across generations.
Environment-dependent variation in developmental trajectories within a genotype. Plasticity need not be adaptive, and an environmentally induced developmental change need not be reversible.
Fitness costs associated with maintaining or using a responsive system, distinct from poor performance of a particular expressed phenotype. Comparisons should match the expressed outcome while varying the capacity for response.
Environment- or experience-dependent change in animal behaviour expressed by an individual. A change within a lifetime must be distinguished from an evolutionary change in its reaction norm.
Costs of acquiring information, maintaining responsiveness or switching action. They must be distinguished from a maladaptive action caused by an unreliable cue.
Reduction of phenotypic or fitness effects of environmental variation through plastic responses. It can reduce immediate selection on other inherited traits.
A distinguishable measurable characteristic of an organism. Trait definitions matter: several correlated measurements need not represent independent dimensions of a phenotype.
A systematic difference in phenotypic traits between sexes within a species, such as body proportions or coloration. It can make specimen-based species delimitation difficult if sexes are mistaken for separate species. The degree of dimorphism can also supply an empirical proxy for reproductive investment in particular fossil groups.
The relationship between the phenotype of a heterozygote and those of the two corresponding homozygotes at a genetic locus. Under complete dominance, one allele gives the same phenotype in the heterozygote as in its homozygote; the term describes expression rather than the frequency or evolutionary advantage of the allele.
For a specified characteristic, complete dominance means that the heterozygote has the same phenotype as one of the two homozygotes. It does not mean that the dominant allele is more common, more advantageous, or transmitted more often. Penetrance specifies the conditional probability of an expressed phenotype given a genotype and is a separate modeling assumption.
Penetrance is the probability of an expressed phenotype conditional on a specified genotype. It can depend on age, sex and environment. A fully penetrant recessive model assigns disease probability one to the recessive homozygote and zero to other genotypes; incomplete penetrance or phenocopies replace these indicators by intermediate probabilities.
For a binary disease trait with genotype , the genetic variance of penetrance is the between-genotype term in the law of total variance. The averaged within-genotype term is . Under multiplicative diallelic penetrance, the genetic term is . This decomposition attributes variance to the modeled locus, not automatically to all hereditary causes.
With Hardy-Weinberg equilibrium, let count copies of the risk allele. The penetrance must lie in for every possible genotype. Writing and gives and .
