Parental haplotype reconstruction in up to 440,209 UK and Estonian individuals reveals recent assortative mating dynamics

Assortative mating (AM), the tendency to choose partners with similar traits, contributes to the genetic architecture of human traits. Detecting its genetic footprint (genetic AM) requires either genotyped couples or detection of gametic phase disequilibrium (which is insensitive to recent changes). We introduce an inter-chromosomal phasing approach that reconstructs parental haplotypes from close relatives and correlates maternally and paternally inherited polygenic scores to provide estimates enriched for recent AM. Applied to 69 traits in 245,884 UK Biobank and 194,325 Estonian Biobank individuals, our approach showed concordance with mate-pair-based estimates comparable to or better than existing approaches, significantly outperforming them in the Estonian Biobank (through-origin r 2 = 0.638 versus 0.479, P = 0.005) and performing comparably in the UK Biobank ( r 2 = 0.737 versus 0.731). We identified genetic AM for traits such as height, education, overall health and time spent watching TV, with assortment for height and education accelerating in recent generations (for example, θ HAP = 0.041 (0.034–0.048) versus 0.015 (0.007–0.024) for height in post-1980 versus pre-1960 Estonian Biobank cohorts).