increasing distance and with increasing phylogenetic age of the variant. Further, due to the non-uniform recombination rates in the genome and the existence of recombination “hot-spots” (6) the correlation between genotypes, or LD, has a patchy distribution with regions of higher LD separated, often abruptly, by regions of lower LD, a phenomenon that gave rise to the term “islands” of LD (5) (see Figure 2). Regions of high LD are often referred to as haplotype blocks, referring to short haplotype fragments that contain only some of the possible combinations of alleles across their length. These blocks should not be confused with the traditional meaning of the word haplotype, which does not assume any correlation between alleles at the population level, but only their coexistence in the same strand in an individual.
