Where does genotype collide?

The inherited constitution of an individual organism: the specific combination of gene variants it carries, at one locus or across many, as opposed to the visible traits those variants help produce. Johannsen's 1911 The genotype conception of heredity used the word to separate what an organism transmits, its hereditary makeup, from what it displays, which he named the phenotype. The referent here is an individual's own set of alleles, written as symbols like Aa or as a list of variants, and it is not a named category of virus strain nor a coded string that a program mutates.[1]

Unit

One organism's set of alleles, at a locus or genome-wide

Recovery means

Not applicable

Measured by

Read by genetic markers, sequencing, or breeding crosses that infer which alleles an individual carries

A discrete class of a virus or microbe, defined by how far its genome sequence diverges from others and given a fixed label such as genotype 1 through 7. Simmonds and colleagues' 2005 Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes set agreed thresholds and names so that a clinical isolate can be sorted into one of a small set of numbered types, a classification that guides treatment choice and predicts response. The referent is a taxonomic bin for a population of strains, counted and named, not the private allele makeup of one organism nor an encoded candidate solution in software.[2]

Unit

A numbered strain class, one bin in a fixed classification

Recovery means

Not applicable

Measured by

Assigned by sequencing part or all of the viral genome and placing it on a reference phylogeny against divergence thresholds

The internal, encoded representation that a genetic algorithm stores and manipulates, typically a fixed string of bits or symbols, which a decoding step maps to a candidate solution and its measured quality. Whitley's 1994 A genetic algorithm tutorial describes how the search operates on these encoded strings, recombining and mutating them, while fitness is judged on what they decode to. The referent is a data structure inside a program, chosen by the designer of the encoding, and it is neither an organism's inherited alleles nor a named category of virus, however deliberately the biological words were borrowed.[3]

Unit

One encoded string in a population the algorithm evolves

Recovery means

Not applicable

Measured by

Inspected directly as the stored bits or symbols, and evaluated through the solution and fitness score it decodes to