How genetic markers are simulated?
Samples from natural populations show non-independence between alleles and genotypes at different genetic loci measured by “linkage disequilibrium”, LD (Crow, Kimura, 1970). This non-independence is a consequence of various evolutionary forces, including genetic drift, mutation process, migration, and selection. A large population at equilibrium approaches independence (lack of LD). Recombination process facilitates this process, therefore loci in physical proximity of each other tend to show larger LD. The extent of LD varies across human populations. There is usually substantial LD at distances over tens of kilobases. LD in this data set was modeled by a Markov process that results in LD decay detectable over distances of one to three markers. Marginally, population allele frequencies in this simulation follow U(0,1) distribution with LD between neighbouring markers reaching 0.5 to 1 of its maximum possible value. First, population frequencies have been created. Actual samples were o
