Phenotypic covariance across the entire spectrum of relatedness for 86 billion pairs of individuals

Abstract

Attributing the similarity between individuals to genetic and non-genetic factors is central to genetic analyses. In this paper we use the genomic relationship (\(\pi\)) among 417,060 individuals to investigate the phenotypic covariance between pairs of individuals for 32 traits across the spectrum of relatedness, from unrelated pairs through to identical twins. We find linear relationships between phenotypic covariance and \(\pi\) that agree with the SNP-based heritability (\(\hat h_{SNP}^2\)) in unrelated pairs (\(\pi \, < \, 0.02\)), and with pedigree-estimated heritability in close relatives (\(\pi \, > \, 0.05\)). The covariance increases faster than \(\pi \hat h_{SNP}^2\) in distant relatives (\(0.02 \, > \, \pi \, > \, 0.05\)), and we attribute this to imperfect linkage disequilibrium between causal variants and the common variants used to construct \(\pi\). We also examine the effect of assortative mating on heritability estimates from different experimental designs. We find that full-sib identity-by-descent regression estimates for height (0.66 s.e. 0.07) are consistent with estimates from close relatives (0.82 s.e. 0.04) after accounting for the effect of assortative mating.