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

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

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

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

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

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

A graphical representation of simulation results from two genetic models.

<p>Neut and SP abbreviate genetic models with neutral and selective sweep along with Neut.per and SP.per representing corresponding distribution of permutation. <i>H_P</i> profiles estimated from 23’265 and 22’955 creeping windows are plotted across a chromosome of 10 Mb in Neutral (a) and Sweep (b) models, respectively. A distinct valley of homozygosity at the middle of chromosome represents the simulated sweep. (c) Density distributions of <i>H_P</i> profiles form both models are depicted along with 1000 resamples.</p

The negative end of the <i>ZH_P</i> distribution from the creeping windows (CW) versus the sliding windows (SW) strategy is presented along GGA5.

<p>The horizontal dashed line stands for the significance level at <i>P</i>≤0.001 (<i>ZH_P</i> = −3.70, genome-wide) and vertical gridlines help to compare similar signals between plots. Capital letters highlight positions where (A) CW produces more pronounced signals than SW; (B) SW misses signals found by CW; (C) SW produces spurious signals not confirmed by CW; and (D) CW finds classic long-range sweeps with typical patterns. A strong signal is found at the position of the <i>TSHR</i> gene already described by Rubin et al. (2010).</p

Parameters for the MSMS simulations.

<p>Parameters for the MSMS simulations.</p