Physical linkage

Linkage is the physical association of loci on a chromosome that causes alleles at the loci to be inherited in their original combinations. This association of alleles at loci on the same chromosome is broken down by crossing over and recombination. The probability that a recombination event occurs between two loci is a function of the distance along the chromosome between two loci. Loci that are very far apart (or on separate chromosomes) have recombination rates approaching 50% and are said to be unlinked. Loci located very near each other on the same chromosome might have recombination rates of 5 or 1% and would be described as tightly linked. Therefore, the degree of physical linkage of loci dictates the recombination rate and thereby the decay of gametic disequilibrium.

Linkage-like effects can be seen in some chromosomes and genomes where gametic disequilibrium is expected to persist over longer time scales due to exceptional inheritance or recombination patterns. Organisms such as birds and mammals have chromosomal sex determination, as with the well-known X and Y sex chromosome system in humans. Loci located on X chromosomes experience recombination normally whereas those on Y chromosomes experience no recombination. This is caused by the Y chromosome lacking a homologous chromosome to pair with at meiosis since YY genotypes do not exist. In addition, we would expect that the rate of decay of gametic disequilibrium for X chromosomes is about half that of autosomes with comparable recombination rates, since X recombination takes place only in females (XX) at meiosis, and not at all in males (XY). Organelle genomes found in mitochondria and chloroplasts are a case where gametic disequilibrium persists indefinitely since these genomes are unipar-entally inherited and do not experience observable levels of recombination.

Natural selection

Natural selection is a process that can continuously counteract the randomizing effects of recombination. Imagine a case where genotypes have different rates of survival or different fitnesses. In such a case natural selection will reduce the frequency of lower

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