The effects of the values of the nuisance parameters <i>r</i>_min and <i>n</i>₁ on the number of chromosomes that show significant values for the test statistics <i>p_D</i>^max and <i>n</i>_P at the nominal <i>p</i><0.05 level (without a Bonferroni correction).

<p>The effects of the values of the nuisance parameters <i>r</i>_min and <i>n</i>₁ on the number of chromosomes that show significant values for the test statistics <i>p_D</i>^max and <i>n</i>_P at the nominal <i>p</i><0.05 level (without a Bonferroni correction).</p

Patches of LRLD on Chromosome 1.

<p><i>Left:</i> The circle plot represents patches by lines that connect the chromosome blocks involved. The most extreme value of <i>p_D</i> in each patch is represented by the color of the segment. The line segments on the outside of the circle show regions identified in Akey's <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080754#pone.0080754-Akey1" target="_blank">[36]</a> catalogue of genomic targets of positive selection. <i>Right:</i> The triangle plot shows the patches as circles whose size is scaled to the value of the most extreme value of <i>p_D</i> in that patch.</p

Schematic of the structure of long range linkage disequilibria.

<p><i>Right:</i> Sites <i>A</i> and <i>B</i> are the target of selection or other force that generates disequilibria between them (red arrow). Site <i>A</i> is in disequilibrium with site <i>A′</i> nearby as the result of shared ancestry of that small segment of chromosome; likewise <i>B</i> and <i>B</i>′ also show short range disequilibrium (blue arrows). <i>Right:</i> A triangle plot of LD. Disequilibria between nearby sites appear as the band along the diagonal. The dash line encloses a “patch” consisting of pairs of widely-separated SNPs that are in LD.</p

Scatter plot of the maximum value of −ln(p_D) in every patch across all chromosomes vs the distance r between the patches.

<p>Recombination is expected to make this correlation negative.</p

Patches of LRLD on Chromosome 12.

<p>Patches of LRLD on Chromosome 12.</p

The number of patches that appear in the Akey's [36] catalogue of putative targets of selection.

<p><i>p</i> values give the significance for individual chromosomes tested individually. Values significant at the 0.05 level are in bold; none is significant after a Bonferroni correction for tests of multiple chromosomes. Akey 1 gives the number of patches in which one of the two participating sites is in the Akey catalogue; Akey 2 is the number in which both sites do. The </p

Patches of LRLD on Chromosome 12 to 22.

<p>Patches of LRLD on Chromosome 12 to 22.</p

Sved's [17] measure for the correlation of heterozygosity between blocks of 50 SNPs as a function of the recombination rate between the blocks.

<p>The squares show the genome-wide average for the Yoruba population (calculated by Sved). The circles pertain to the 10 cM region of Chromosome 8 that has the highest density of LRLD patches identified by our method. The difference is highly significant (<i>p</i><10⁻³).</p

Schematic of the randomization method used to construct null distributions for patterns of LRLD.

<p>For each randomization, the identity numbers of the haplotypes are permuted randomly (left hand column). The disequilibrium between sites <i>A</i> and <i>B</i> is calculated using the allele at site <i>A</i> from one chromosome and the allele at site <i>B</i> from the following chromosome.</p

Spearman rank correlations between −ln(<i>p_D</i>) and distance, and between patch density and distance.

<p><i>p</i> values in bold are less than 0.05; values with asterisks are significant after a Bonferroni correction. Recombination is expected to make −ln(<i>p_D</i>) decline with distance, giving a negative correlation. The </p