DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

<p>The 5% confidence intervals for all values are shown.</p

DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

<p>The 5% confidence intervals are shown.</p

Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

<p>MPSS data recorded in five different organs are shown (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 2) (B), ten organs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 4) (C), and five flower tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 6) (D) are given. For MPSS-based experiments (A), tpm are indicated; for experiments based on the Affymetrix platform (B–D), Affymetrix expression values are plotted. The 5% confidence intervals calculated using bootstrap set for all values are shown.</p

Histograms of (A) distance between neighboring markers and (B) gap size in the final data set.

<p>Histograms of (A) distance between neighboring markers and (B) gap size in the final data set.</p

A graphical comparison of two genome scanning strategies.

<p>sliding windows (SW) vs., creeping windows (CW). With SW a chromosome is split into non (or partly) overlapping windows of 40 K and while passing over genomic gaps, it may not perfectly overlie a selective sweep. CW implements an elevated resolution moving windows in steps of only one SNP forward. The approach bridges small (<10 K) gaps while it stops at larger gaps and re-starts at the opposite side. CW always centers a window relative to a sweep position.</p

Distribution patterns of the <i>H_P</i> profile from 862’400 windows creeping over the genome.

<p>Pink and blue densities represent, respectively, the observed and the panel of recorded lowest <i>H_P</i>-values from 10’000 re-sampling runs in real data. Windows with <i>H_P</i>≤0.252 represent significant signals at the empirical error level <i>P</i>≤0.001. As indicated, 1816 windows characterize 82 selected regions with a more extreme local homozygosity than expected under neutrality.</p

Collected panel of genomic regions identified as candidate selective sweeps.

a<p>Positions in normal format represent “distinct sweeps” revealed by the <i>H_P</i> metric. A distinct sweep spans over numerous consecutive significant windows and depicts a typical valley of heterozygosity.</p>b<p>Signals overlapping genes with a previously described association.</p

Summary statistics of the pooled heterozygosity metric for selection signature in candidate genes.

<p>Summary statistics of the pooled heterozygosity metric for selection signature in candidate genes.</p

The negative tail of the <i>ZH_P</i> distribution presented along GGA1 to GGA28.

<p>Each dot represents a CW of 40 Kb and arrows point at the location of candidate genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049525#pone-0049525-t001" target="_blank">Table 1</a>) and genes with reported associations in the literature. The horizontal dashed line indicates the significance threshold at <i>P</i>≤0.001 (Genome-wide <i>ZH_P</i> = −3.7).</p

Distributions of (A) the number of SNPs per window and (B) the size of 862’400 windows creeping along chicken chromosomes GGA1 to GGA28.

<p>Distributions of (A) the number of SNPs per window and (B) the size of 862’400 windows creeping along chicken chromosomes GGA1 to GGA28.</p