Fig 3. Scaled density plot of Δ log R distributions for discovery panel dogs with zero, one, or two copies of the associated haplotype, demonstrating that the presence of the haplotype tracks the presence of the duplication in almost all cases.

Dogs carrying the haplotype exhibited elevated log R at SNPs within the duplicated region compared to flanking regions (high Δ log R) relative to non-carriers, and dogs heterozygous vs. homozygous for the haplotype exhibited distinct distributions, consistent with being heterozygous vs. homozygous for the duplication itself. Although the duplication appeared to act dominantly in Siberian Huskies, brown-eyed heterozygotes in other breeds or mixed breed dogs also had log R data consistent with carrying the duplication. Exceptions included three high-log R dogs with alternative, recombinant versions of the associated haplotype (asterisks, top panel; S7 Fig) and one low-log R dog with a partial duplication (asterisk, middle panel; Supplementary Information). Individual log R values contributing to each density curve are represented with vertical ticks, and counts of blue-eyed vs. brown-eyed dogs are indicated for each haplotype category.