Additional file 10.

Figure S3. Parental similarity versus offspring heterozygosity. When parents choose mates that are similar to self at a given SNP, the result is excessive homozygosity in the children (an excess of homozygous genotypes at that SNP). Conversely, when parents choose mates that are dissimilar to self, the result is excessive heterozygosity in the children. In a simulation, random genotypes for 22,500 SNPs (2,500 with each MAF ϵ(0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45)) were generated for 1,000 sets of parents. At each SNP, the similarity measure (Pearson correlation) was calculated between the vectors of parental genotypes (shown on the y-axis). For each SNP, the genotypic frequencies of the offspring of the 1,000 sets of parents were calculated based on Mendelian inheritance. The observed frequency of heterozygotes in the offspring was divided by the expected frequency of heterozygotes, assuming Hardy Weinberg equilibrium (x-axis). A value higher than 1 on the x-axis means that offspring have a greater than expected frequency of heterozygotes, while a value smaller than 1 on the x-axis means that offspring display excessive homozygosity. These plots show that SNPs which show similarity between parents (high values on the y-axis) are more likely to show excessive homozygosity in the offspring (low values on the x-axis). To extend the concept: if parents select mates that are similar to self at a given SNP, over many generations we expect excessive homozygosity in the general population compared to Hardy Weinberg equilibrium.

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Khankhanian et al. BMC Genomics 2010 11:626   doi:10.1186/1471-2164-11-626