Solution (source code)

= Solution

Across a human <chromosome>, neighboring <single-nucleotide polymorphisms> often show substantial <linkage disequilibrium>, while average <allelic correlation> tends to decline with increasing genetic distance. A new <mutation> starts on one ancestral <haplotype>; repeated <genetic recombination> separates it from progressively more distant markers. In an ideal randomly mating two-locus population without further <mutation>, migration or selection, gamete formation gives $p'_{11}=(1-c)p_{11}+cp_Ap_B$, where $c$ is the <recombination fraction>. The marginal <allele> frequencies remain fixed, so
$$
D'=(1-c)D,\qquad D_t=(1-c)^tD_0.
$$
Here the prime means the next-generation value, not a separately standardized LD statistic. This simple decay explains the distance trend, rather than asserting an exact deterministic law for real finite populations.

The local pattern is heterogeneous. Many regions have <haplotype blocks> with strong LD and a small number of common <haplotypes>, separated by intervals showing more historical recombination, often <recombination hotspots>. A hotspot can therefore cause a rapid drop in LD between markers that are close in physical distance. Block lengths and boundaries are not uniform, perfectly sharp or independent of the population and the statistical block definition. These empirical features are documented in https://www.genome.gov/Pages/Research/DER/HapMap.pdf[the HapMap data].

Population history also matters. <Population bottlenecks> can reduce the number of ancestral <haplotypes> and increase the extent of LD; <population stratification> or admixture can create longer-range associations, including between distant loci. Different populations can consequently have different <haplotype> frequencies and LD patterns at the same genomic interval. Raw $D$ also varies with <allele> frequency, so comparing LD across markers requires attention to the chosen measure. \b[The typical pattern is locally strong, block-like and highly variable LD, with a broad decline over genetic distance rather than a uniform chromosome-wide decay.]