Linkage disequilibrium

Equilibrium numbers of the individual genotypes corresponding to the numbers of the individual alleles will become balanced even if a genetic linkage exists between the studied loci; however, equilibrium will not be established immediately in this case, but rather gradually, where the rate of establishment of equilibrium is inversely proportionate to the strength of the genetic linkage. The population can be inthe linkage disequilibrium, i.e. the numbers of the individual genotypes need not correspond to their theoretical frequencies calculated on the basis of the relative numbers of the individual alleles, for several reasons. The degree of disequilibrium is most frequently expressed as the coefficient of linkage disequilibrium D which, for genes located in two different alleles, is calculated from the equation D= ¦n¦n- ¦r¦r, where ¦nand ¦nare the frequencies of the individual genotypes containing the unrecombined halotypes and ¦rand ¦rare the frequencies of individuals with genotypes containing recombined halotypes. Disequilibrium can, first of all, be caused by the fact that some genotypes are not viable and are continuously eliminated from the population by natural selection. In this case, zygotes with the individual genotypes are formed with the expected theoretical frequency, but some genotypes are frequently eliminated already during embryogenesis, prior to the birth of the individual. The second reason for the existence of linkage disequilibrium could be the existence of genetic linkage between the loci of interest. Each population has a unique history; at some point in the past, it was formed by splitting off from some other population or other populations. If a population was formed from more than one original population, the frequencies of the individual genotypes in the founding population will not apparently correspond to equilibrium values calculated on the basis of the frequencies of the individual alleles. Because of the existence of genetic linkage, the equilibrium frequencies of the individual genotypes will be established only gradually over a large number of generations

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