Figure 1. The relationship between the local recombination rate and patterns of genetic diversity. Shown at the top of the figure is the estimated local recombination rate over a 30-kb region of human chromosomes 20. Shown below are the haplotypes (rows) of a 100 chromosomes assayed at 40 biallelic single nucleotide polymorphisms (SNPs, columns). Four SNPs are labelled a–d (see text). Data taken from www.hapmap.org The International HapMap Consortium (2005).

Figure 2. The average similarity of haplotypes carrying the same new (derived) mutation in relation to its frequency in the population and the local recombination rate. A haplotype is defined by the nearest 10 SNPs. Light colours indicate a 50% chance that two haplotypes, carrying the same derived allele, are identical at the neighbouring 10 SNPs, when sampled at random. Red (below light colours) indicates greater than half chance and blue (above light colours) indicates that haplotypes are rarely similar in the alleles present at nearby loci. Computed from data published in Spencer et al. (2006).

Figure 3. Recombination and haplotype structure over a 3-Mb region of human chromosome 20. Along the bottom of the plot is a scaled version of the local recombination landscape, showing peaks of recombination (hotspots). Superimposed above is the length of haplotypes (ordered arbitrarily from top to bottom), defined to have limited pairwise diversity. Note that although haplotypes often terminate at hotspots of recombination, others do not. Data taken from Spencer et al. (2006).

Figure 4. The effect of natural selection on haplotype diversity in a recombining region. Shown on the right is a set of haplotypes (rows) typed at SNPs (columns) at which strong positive selection has favoured the red allele at the left-hand most SNP. The genealogical relationship (time runs backwards right to left) between the chromosomes at the locus under selection is shown on the left of the figure, with the beneficial mutation coloured red. Simulated using SelSim Spencer and Coop (2004).

Figure 5. Clustering of the sequence motif CCTCCCT within inferred recombination hotspots. The stacked bar graph gives counts of the motif when found within a THE1B transposable element (+ve) and in unique DNA (–ve). Adapted from supplementary material of The International HapMap Consortium (2005).