Haplotype evolution and linkage disequilibrium: A simulation study

We simulated the evolution of a three-site haplotype system, two restrictio n fragment length polymorphisms flanking one short tandem repeat polymorphi sm, under five different demographic scenarios, three with constant populat ion size and two with population growth. The simulation was designed to obs erve the effects of population history, recombination fraction, and mutatio n rate on allele and haplotype frequencies, haplotype diversity, frequency of ancestral alleles, and linkage disequilibrium. The known ancestral haplo types were often found at low frequencies and even became extinct after 5,0 00 generations, especially with small effective population sizes. The origi nal linkage disequilibrium was eroded and even reversed. Copyright (C) 2000 S. Karger AG, Basel.