Common selection signals.

<p>The number of breeds that showed divergent selection is shown as a function of genomic position (A). Selection peaks were defined as regions with smoothed <i>F</i>_ST in excess of one standard deviation either above (positive selection; blue line) or below the genome-wide average (balancing selection; green line). Four regions were identified with shared positive selection peaks in 30 or more breeds (the chromosomal number is given above each peak). Similarly, five peaks were identified where 20 or more populations shared balancing selection, including the MHC region on OAR 20. One signal was common to each of three separate populations of Texel (B). Pairwise <i>F</i>_ST was calculated between Texel and all other animals, which revealed a strong selection on sheep Chromosome 2 above the <i>GDF8</i> gene, which underpins a breed defining phenotype.</p

Geographic origin of breed development and diversity.

<p>Breeds were genotyped from the Americas, Africa, Asia, and the domestication centre in present-day Iran and Turkey (referred to throughout as South-West Asia). The majority of breeds genotyped were developed in Europe (given in detail at right). Breed names and their abbreviations are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001258#pbio.1001258.s012" target="_blank">Table S1</a>. Marker heterozygosity within each breed compared against increasing physical distance from the domestication centre. Breeds used during SNP discovery are shown using filled circles. Haplotype sharing at 25–50 Kb between Merinos and other breeds (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001258#pbio.1001258.s008" target="_blank">Figure S8</a>) was plotted against heterozygosity to reveal a major influence of Merino admixture on the genetic diversity of European breeds. Breed-specific values for expected heterozygosity and haplotype sharing are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001258#pbio.1001258.s015" target="_blank">Table S4</a> to allow identification of populations with outlier values.</p

Genome-wide distribution of global <i>F</i>_ST.

<p>The amount of differentiation, measured as <i>F</i>_ST, was estimated within each breed by comparison to all other breeds. Global <i>F</i>_ST is the average for each SNP across all 74 HapMap breeds, meaning common signals present in multiple breeds are preferentially detected. SNP were ordered in genomic order with OAR1 at left. The highest peak is on OAR10.</p

Selection for sheep without horns (poll).

<p>Animals from two breeds with horns (Dorset Horn and Merino) were pooled and compared with two polled breeds (Poll Dorset and Poll Merino). Pairwise <i>F</i>_ST was calculated between the two groups of animals for all 49,034 SNP, before smoothed values were plotted in order across the genome (top panel). A strong selection signal was observed on Chromosome 10 (SNP number 27,878–29,558 with the signal peak at SNP <i>OAR10_29546872</i>). Pairwise <i>F</i>_ST was also calculated between horned breeds (green line) or between polled breeds (blue line) before the smoothed values were plotted across Chromosome 10 (bottom panel). The peak was only observed where horned breeds were compared with polled breeds, verifying that the signal relates to the long-standing husbandry practise of selecting animals for the absence of horns.</p