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 and the SNP similarity matrix for ‘related' individuals. Note that estimates of variance from analyses including close relatives are increased by the effects of (i) possible environmental factors that render phenotypic similarity between genetically more similar individuals and (ii) by causal variants that are not correlated with genotyped SNPs but are captured by pedigree structure. Close relatives share a substantial proportion of their segregating genes on all chromosomes (for example, ∼50% for full siblings), consequently, variance attributable to causal variants on one chromosome will be captured by SNPs on other chromosomes.43, 52
