Abstract
Long-range linkage disequilibria (LRLD) between sites that are widely separated on chromosomes may suggest that population admixture, epistatic selection, or other evolutionary forces are at work. We quantified patterns of LRLD on a chromosome-wide level in the YRI population of the HapMap dataset of single nucleotide polymorphisms (SNPs). We calculated the disequilibrium between all pairs of SNPs on each chromosome (a total of >2×1011 values) and evaluated significance of overall disequilibrium using randomization. The results show an excess of associations between pairs of distant sites (separated by >0.25 cM) on all of the 22 autosomes. We discuss possible explanations for this observation.
Highlights
Linkage disequilibrium (LD) is a key feature of genetic variation in human and other populations [1]
These results suggest there is long-range linkage disequilibrium in the YRI population
Linkage disequilibrium is classically viewed as an association between pairs of sites or loci
Summary
Linkage disequilibrium (LD) is a key feature of genetic variation in human and other populations [1]. Disequilibria between closely-linked sites result largely from random genetic drift or (equivalently) the common ancestry of unrecombined chromosome blocks. These short range disequilibria are of great practical interest. Blocks of unrecombined chromosome can be exploited to identify recent and ongoing selective sweeps [3,4]. While these ‘‘long range haplotypes’’ can extend over a few hundred kb in unrelated humans [5], they still span only a very small fraction of an entire chromosome
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