the realized genetic similarity, which vary around the expected values from pedigrees (See Supplementary Information Figure S2). The genetic variation around the expected values (for example, 0, 50 or 100%) is not captured by pedigree studies but can be captured by the SNP data. In order to partition the genetic variance into variance explained by pedigree data and variance explained by SNP data, genetic similarity was estimated from pedigree information (expected genetic similarity) and from SNP data (realized genetic similarity) in a series of separate and joint analyses of the pedigree and SNP data. The analyses are described in detail in the Supplementary Information Section 1. Briefly, we (1) estimated variance explained by all SNPs based on ‘unrelated' individuals using genome-wide SNP date, as above; (2) estimated variance explained by all SNPs based on all individuals using genome-wide SNP data; (3) estimated heritability from all individuals using expected genetic similarity (pedigree similarity matrix); (4) partitioned the variance into variance captured by the SNP similarity matrix and variance captured by the pedigree similarity matrix from all individuals; and (5) partitioned the variance further into variance captured by the pedigree similarity matrix from all individuals, the SNP similarity matrix for ‘unrelated' individuals
