Linkage disequilibrium, recombination and haplotype structure
McVean G., Kelleher J.
Every chromosome carries a unique sequence of DNA, or haplotype. However, certain combinations of variants are shared between individuals. The extent of this sharing, or haplotype structure, is referred to as linkage disequilibrium, and its distribution in natural populations can be informative about diverse processes, from the rate of recombination to the influence of adaptive evolution. This chapter aims to provide a foundation for understanding haplotype structure and linkage disequilibrium, discussing how it can be measured, how it relates to the underlying genealogical process and how it can be informative about underlying molecular, historical and evolutionary processes. These ideas play an important role in modern statistical and computational genomics, influencing diverse applications from human migration to genome compression.