Fortunately, the first studies that performed high throughput genotyping showed that determining the genotypes of all common SNPs is not necessary to survey all common variation (3–5). This is a result of the phenomenon of linkage disequilibrium (LD), an old genetic concept that came to enjoy renewed popularity. As shown in Figure 1, when a mutation arises in the population it generates a new variable location. The newly generated allele resides on a preexisting haplotype – a DNA strand that carries a specific sequence of alleles on the other variable positions. The new allele will then be transmitted to the next generations always on this haplotype except where the haplotype continuity is broken by recombination. As a result, the genotype of every variant in the genome is correlated with the genotypes of neighboring variants, and this correlation is reduced with 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
