Linkage Disequilibrium and Haplotype Structure

Genomes are organized in one or several molecules of DNA each made of a few base pairs to hundreds of megabases. Each of these molecules stores information on possibly several thousands of loci. The association of different alleles on the same DNA molecule creates haplotype structure. Genes do not work independently of each others in a cell, and it is advantageous for an organism to carry in its genome combinations of alleles that "work well together." Because the conditions of life change through time, it is also advantageous to be able to change these combinations. These two seemingly opposite "needs" outline the difficulties in the analysis of recombination and linkage disequilibrium. The idea of linkage between two loci is independent of the idea of their physical positions on chromosomes: if they are sufficiently a distance apart on the same chromosome so that recombinations occur surely between them, then they will appear unlinked when looking at the frequencies of gamete genotypes.