Supergene

A supergene is a group of neighbouring genes on a chromosome which are inherited together because of close genetic linkage and are functionally related in an evolutionary sense, although they are rarely co-regulated genetically.

Supergenes have cis-effects due to multiple loci (which may be within a gene, or within a single gene's regulatory region), and tight linkage. They are classically polymorphic, and different elements code for different fitness effects which combine to form a coherent or epistatic whole. The two classic supergenes are (1) the Primula heterostyly locus, which controls "pin" and "thrum" types, and (2) the locus controlling Batesian mimetic polymorphism in Papilio memnon butterflies. For example, pin and thrum morphs of Primula have effects on genetic compatibility (pin style x thrum pollen, or thrum style x pin pollen matings are successful, while pin x pin, and thrum x thrum matings are rarely successful due to pollen-style incompatibility), and have different style length, anther height in the corolla tube, pollen size, and papilla size on the stigma. Each of these effects is controlled by a different locus in the same supergene, but recombinants are occasionally found with traits combining those of "pin" and "thrum" morphs.

Gene complexes, in contrast, are simply tightly linked groups of genes, often created via gene duplication (sometimes called segmental duplication if the duplicates remain side-by-side). Here, each gene has similar though slightly diverged function. For example, the human major histocompatibility complex (MHC) region is a complex of tightly linked genes all acting in the immune system, but has no claim to be a supergene, even though the component genes very likely have epistatic effects and are in strong disequilibrium due in part to selection.

No supergene has yet been characterized to the functional DNA level, but work is proceeding in a number of species.

The earliest use of the term "supergene" may be in an article by A. Ernst (1936) in the journal Archiv der Julzus Klaus-stiftung fur Vererbungsforschung, Sozialanthropologie und Rassenhygiene.

Origin of supergenes
Classically, supergenes were hypothesized to have evolved from less tightly-linked genes coming together via chromosomal rearrangement or reduced crossing over, due to selection for particular multilocus phenotypes. For instance, in Batesian mimicry supergenes in species such as Papilio memnon, genes are required to affect hind-wing, fore-wing, and body colour, and also the presence or absence of long projections (the "tails" of swallowtail butterflies).

However, most scientists today disbelieve in the gradual evolution of linkage in supergenes, because some linkage disequilibrium is initially needed to select for tighter linkage, and linkage disequilibrium requires both the previous existence of polymorphisms via some other process, like natural selection favouring gene combinations (Charlesworth & Charlesworth 1982). If genes are weakly linked, it is probable that the rarer advantageous haplotype dies out, leading to the loss of polymorphism at the other locus.

Most people following Turner (1984) therefore argue that supergenes arose in situ due to selection for correlated and epistatic traits, which just happened to have been possible to select via the existence of suitable loci closely linked to the original variant. Turner calls this a "sieve" explanation, and the Turner explanation might be called the "Turner sieve" hypothesis.