Phylogenetic tree of domestic horse breeds and Przewalski's Horse.

<p>Parsimony analysis across 46,244 autosomal loci in the Domestic and Przewalski's Horse. The tree is rooted with the domestic ass.</p

Phylogenetic tree of extant Hippomorpha.

<p>Unrooted cladogram constructed via parsimony analysis, considering only the Hippomorpha, using 40,697 autosomal markers. Bootstrap support >50% calculated from 1000 replicates is shown.</p

Allele association analysis for three known equine coat color loci.

<p>a), mapping of the chestnut locus across breeds, based on inferred coat color phenotype; b), mapping of the black (agouti) locus across breeds, based on inferred black coat color; c), mapping of the gray locus across breeds. Phenotypes were inferred from the genotypes at 9 known coat color loci and known inheritance models as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>. Unstructured case control association analyses using chi-square tests for allelic association were then performed on a pruned SNP set also as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>. SNPs on each chromosome are labeled with a different color on the X axis as indicated.</p

Multidimensional scaling with 14 domestic horse breeds.

<p>Metric multidimensional scaling analysis of pair-wise genetic distance was used as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a> to identify relationships between the 14 domestic horse breeds.</p

Distribution of pair-wise genetic distances.

<p>a), within and between domestic horse breeds; b), between domestic horse breeds and between domestic horse breeds and Przewalski's Horse. Genetic distance (D) between pair-wise combinations of individuals was calculated as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>.</p

Decline in genome-wide linkage disequilibrium across and within breeds.

<p>Genome-wide linkage disequilibrium (LD) was estimated both within a given breed, and across all breeds, by calculating <i>r²</i> values between all pairs of SNPs with inter-SNP distances of less than 4 Mb as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>.</p

Individual and breed relationships among 814 horses illustrated by parsimony.

<p>Parsimony tree created from 10,066 SNPs and rooted by the domestic ass. Breeds are listed in the legend in order starting from the root and working counterclockwise. Individual outliers with respect to their breeds are noted with arrows. Bootstrap support calculated from 1,000 replicates is shown for major branches when greater than 50%.</p

Number of samples (N), effective population size (N_e), individual inbreeding estimates (f), inbreeding coefficient (F_IS), and expected heterozygosity (H_e) from four SNP sets pruned based upon varying levels of LD.

a<p>Individuals from this breed also included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>b<p>20 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>c<p>17 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>d<p>21 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>e<p>19 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>.</p><p>F_IS and f were calculated based upon the primary SNP set (10,536 loci). Samples also used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a> are indicated in the footnotes.</p>*<p>indicates significance at α<0.05 determined by 10,000 permutations.</p

Pairwise F_ST values based upon 10,536 SNPs in 37 horse populations.

<p>Pairwise F_ST values as calculated in Arlequin using 10,536 autosomal SNPs and significance tested using 20,000 permutations. All pairwise values are significantly different from zero. (individual outliers were removed from this analysis).</p

Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.

<p>Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.</p