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Imprint of assortative mating on the human genome
Open accessPublished version of a preprint
Abstract
Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans 1-5 and has evolutionary consequences 6-8. Under Fisher's classical theory 6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes.
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“The primary explanation is likely AM, which is strong for EA and height25,31, although IGEs that are positively correlated with DGEs could also contribute3.”
From Family-GWAS reveals effects of environment and mating on genetic associations (2024) · cites this paper as [25]
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“However, there is growing evidence that GWAS associations for some phenotypes estimated from samples of unrelated individuals also capture effects of demography7,8 (assortative mating9–11 and population stratification12) and indirect genetic effects of relatives13–19 (Fig. 1).”
From Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects (2022) · cites this paper as [11]
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BackgroundPhenotypic and ancestry-related assortative mating in autism
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“The change in variance due to AM induced correlations between alleles of mates at a locus and also between loci has been shown by previous theory (Crow and Kimura 1970) and empirical research (Yengo et al. 2018).”
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Consequences of assortative mating for genetic similarities between partners, siblings, and in-lawsPreprint
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The contribution of mate-choice, couple convergence and confounding to assortative matingPreprint
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“…mating can be estimated in admixed populations by calculating ancestry correlations within mating pairs (e.g., Risch et al. 2009) or between mothers and offspring (e.g., Schumer et al. 2017, Powell et al. 2020), or by measuring ancestry disequilibria between unlinked loci (e.g., Yengo et al. 2018).”
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Additional file 1 of Phenotypic and ancestry-related assortative mating in autism
Zhang, J., Weissenkampen, J. D., Kember, R. L., Grove, J., Børglum, A. D., Robinson, E., Brodkin, E. S., Almasy, L. A., Bućan, M., & Sebro, R. (2024) · Figshare · doi:10.6084/m9.figshare.26043692
Additional file 2 of Phenotypic and ancestry-related assortative mating in autism
Zhang, J., Weissenkampen, J. D., Kember, R. L., Grove, J., Børglum, A. D., Robinson, E., Brodkin, E. S., Almasy, L. A., Bućan, M., & Sebro, R. (2024) · Figshare · doi:10.6084/m9.figshare.26043803
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Self-citationHofmeister, R. J., Marnetto, D., Cavinato, T., Knüsel, L., Modenini, G., Pennarun, E., Metspalu, A., Milani, L. A., Esko, T., Nelis, M., et al. (2026) · Nature Human Behaviour · doi:10.1038/s41562-026-02556-8 · Cited by 3
Genetic similarity between partners has intensified throughout the 20th century
(2026) · Nature Human Behaviour · doi:10.1038/s41562-026-02555-9
Dehkordi, S. R., Meijsen, J. J., Waples, R. K., Zetterberg, R., Helenius, D., Athanasiadis, G., Vaez, M., Shorter, J. R., Montalbano, S., Hellberg, K.-L. G., et al. (2026) · JAMA Psychiatry · doi:10.1001/jamapsychiatry.2026.2712
Changing Patterns of Assortative Mating for Educational, Substance Use, and Anthropometric Traits
Saunders, G. (2026) · Behavior Genetics · doi:10.1007/s10519-026-10285-x
Metadata
- Authors
- Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., Gratten, J., Turley, P., Cesarini, D., Benjamin, D. J., Wray, N. R., Goddard, M. E., Yang, J., & Visscher, P. M.
- Affiliations
- The University of Queensland (AU)
- University of Colorado Boulder (US)
- Translational Research Institute (AU)
- Broad Institute (US)
- National Bureau of Economic Research (US)
- University of Southern California (US)
- The University of Melbourne (AU)
- Corresponding author
- Visscher, Peter M.
- ORCID
- Venue
- Nature Human Behaviour
- Published
- 2018-11-26
- Volume
- 2
- Issue
- 12
- Pages
- 948-954
- ISSN
- 2397-3374 (ISSN-L)
- PMC
- PMC6705135
- OpenAlex
- W2952585581
- Cited by
- 148
- References
- 54
- Citations by year
- 2026: 12 · 2025: 20 · 2024: 27 · 2023: 22 · 2022: 26 · 2021: 17 · 2020: 9 · 2019: 13 · 2018: 2
- FWCI
- 6.27
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Human Behaviour (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Funders
- National Institutes of Health
- Medical Research Council (1107258, 1113400, 1078037, 1078901, 1127440, 1103418)
- Australian Research Council (DP160103860, DP160102400, DP130102666, 1113400)
- National Health and Medical Research Council (1113400, 1078901, 1127440, 1107258, 1078037, 1103418)
- National Institute on Aging (RC2AG036607, R56AG042568, R01AG042568)
- National Institute of Mental Health (R01MH100141)
- National Institute of General Medical Sciences (P01GM099568)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- assortative mating, mate choice, human genome, single nucleotide polymorphisms, population stratification, height, educational attainment, complex traits, genome organization
- MeSH terms
- Alleles, Body Height, Educational Status, Female, Humans, Male, Marriage, Genome, Human, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, White People
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