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Imprint of assortative mating on the human genome
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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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Self-citationFrom R.A. Fisher’s 1918 Paper to GWAS a Century Later
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Howe, L. J., Battram, T., Morris, T., Hartwig, F. P., Hemani, G., Davies, N. M., & Smith, G. D. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009883 · Cited by 14
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Partner choice, confounding and trait convergence all contribute to phenotypic partner similarity
Sjaarda, J., & Kutalik, Z. (2023) · Nature Human Behaviour · doi:10.1038/s41562-022-01500-w · Cited by 16
Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective StudyPreprint
Ziyatdinov, A., Torres, J., Alegre-Díaz, J., Backman, J., Mbatchou, J. S., Turner, M., Gaynor, S. M., Joseph, T., Zou, Y., Liu, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.26.495014 · Cited by 15
Uffelmann, E., Posthuma, D., & Peyrot, W. J. (2023) · Scientific Reports · doi:10.1038/s41598-023-29428-9 · Cited by 16
How robust are cross-population signatures of polygenic adaptation in humans?
Refoyo-Martínez, A., Liu, S. M., Jørgensen, A. M., Jin, X., Albrechtsen, A., Martin, A. R., & Racimo, F. (2021) · Peer Community Journal · doi:10.24072/pcjournal.35 · Cited by 14
Cabrera‐Mendoza, B., Wendt, F. R., Pathak, G. A., Yengo, L., & Polimanti, R. A. (2024) · Nature Human Behaviour · doi:10.1038/s41562-024-01828-5 · Cited by 13
“GPD, WSib and WSps methods 3,24 have different expectations and statistical power depending on the sample size investigated.”
InfluentialSelf-citationKim, R., Lippert, A. M., Wedow, R., Jimenez, M. P., & Subramanian, S. V. (2020) · American Journal of Epidemiology · doi:10.1093/aje/kwaa058 · Cited by 12
“Assortative mating affects the distribution of allele frequencies at the population level and may lead to bias in genotype-phenotype associations (43, 44).”
BackgroundGenetic assortative mating for schizophrenia and bipolar disorder
Jefsen, O. H., Nudel, R., Wang, Y., Bybjerg‐Grauholm, J., Hemager, N., Christiani, C. J., Burton, B. K., Spang, K. S., Ellersgaard, D., Gantriis, D. L., et al. (2022) · European Psychiatry · doi:10.1192/j.eurpsy.2022.2304 · Cited by 12
“[13] ascertained partnership (and not all partners have children), and did so indirectly, with the potential for partnership misclassification.”
BackgroundInfluentialSunde, H. F., Eilertsen, E. M., & Torvik, F. A. (2025) · Nature Communications · doi:10.1038/s41467-025-60483-0 · Cited by 11
“I have only one outstanding comment: We engaged in a discussion on whether the are at 30 is the end of the observation window for educational attainment, and it turned out that some of the folks are even only observed until they are 27 years old.”
Axelrud, L. K., Hoffmann, M. S., Vosberg, D. E., Santoro, M. L., Pan, P. M., Gadelha, A., Belangero, S. I., Miguel, E. C., Shin, J., Thapar, A., et al. (2022) · Journal of Child Psychology and Psychiatry · doi:10.1111/jcpp.13708 · Cited by 15
“…adding the other parent PGS as a third mediator; (2) given that individuals often choose partners with similar phenotypes (i.e., assortative mating(Yengo et al., 2018)), we also repeated the multiple mediations described in step 2 adding the other parent phenotype as a third mediator; (3) we…”
BackgroundSelf-citationCausal inference methods for intergenerational research using observational data.
Frach, L., Jami, E. S., McAdams, T. A., Dudbridge, F., & Pingault, J. (2023) · Psychological Review · doi:10.1037/rev0000419 · Cited by 11
“Population stratification describes the fact that certain effect alleles vary in frequency between (sub-)populations, whereas assortative mating indicates that individual mating choices are not random but influenced by phenotypic similarities, for example, tall individuals choosing tall mates (Freedman et al., 2004; Y…”
Leigh, R. J., Corrigan, A., Murphy, R. A., Taylor-Pickard, J. A., Moran, C. A., & Walsh, F. (2024) · Animal Microbiome · doi:10.1186/s42523-024-00295-7 · Cited by 10
A Litmus Test for Confounding in Polygenic ScoresPreprint
Smith, S. P., Smith, O. S., Peng, D., Miao, X., Mostafavi, H., Berg, J. J., Edge, M. D., & Harpak, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.01.635985 · Cited by 12
“A second source of confounding that may act isotropically is assortative mating, or the tendency toward the formation of mating pairs with similar phenotypes, which plays a role in complex trait vari-451 ation in human populations 55,79–84 .”
Genetic nurture: estimating the direct genetic effects of pediatric anthropometric traits
Ghatan, S., de Vries, J., Pingault, J., Jaddoe, V. W. V., Cecil, C. A. M., Felix, J. F., Rivadeneira, F., & Medina‐Gómez, C. (2025) · Human Molecular Genetics · doi:10.1093/hmg/ddaf117 · Cited by 7
“BMD, on the other hand, displayed no evidence of assortative mating in our study, in accordance with previous estimations [23].”
Gorelik, A. J., Paul, S. E., Miller, A. P., Baranger, D. A. A., Lin, S., Zhang, W., Elsayed, N. M., Modi, H., Addala, P., Bijsterbosch, J. D., et al. (2024) · Psychological Medicine · doi:10.1017/s0033291724002174 · Cited by 9
“…as prior research has shown that confounds such as assortative mating (Horwitz, Balbona, Paulich, & Keller, 2023) can inflate GWAS test statistics (Yengo et al., 2018) and polygenic score associations (Okbay et al., 2022), we performed post hoc within-sibling analyses to assess whether any…”
MethodZeng, J., Xue, A., Jiang, L., Lloyd‐Jones, L. R., Wu, Y., Wang, H., Zheng, Z., Yengo, L., Kemper, K. E., Goddard, M. E., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/752527 · Cited by 7
Self-citationThe contribution of gametic phase disequilibrium to the heritability of complex traits
Zhang, Y., Sakaue, S., Morris, S., Graff, M., The Biobank Japan Project, Okada, Y., Yamamoto, K., Chen, Z., Li, L., Keller, M. C., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02192-4 · Cited by 6
“We further discuss the lack of evidence of AM for height in Chinese populations and explored other approaches based on polygenic scores 30,39 (Supplementary Note 9).”
Self-citationNot by Selection Alone: Expanding the Scope of Gene‐Culture Coevolution
Kasser, S. M., Laland, K. N., Fortunato, L., & Feldman, M. W. (2025) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.70007 · Cited by 8
“…include genetic structure being shaped by linguistic boundaries [144, 184, 185], postmarital residence norms [145, 146, 153], subsistence transitions [104], assortative mating [186, 187], culturally determined social stratification [188, 189], or endogamy and consanguineous marriage norms [190].”
Assortative mating on complex traits revisited: Double first cousins and the X-chromosome
Yengo, L., & Visscher, P. M. (2018) · Theoretical Population Biology · doi:10.1016/j.tpb.2018.09.002 · Cited by 6
Self-citationA General Approach to Adjusting Genetic Studies for Assortative MatingPreprint
Bilghese, M., Manansala, R., Jaishankar, D., Jala, J., Benjamin, D. J., Kimball, M., Auer, P. L., Livermore, M. A., & Turley, P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.01.555983 · Cited by 6
Self-citationNudel, R., HOUGAARD, D. M., Werge, T. M., & Benros, M. E. (2023) · Epidemiology and Infection · doi:10.1017/s0950268823000687 · Cited by 5
“It was shown that, for a single trait, assortativemating would induce a correlation between a PRS generated using only odd- or only even-numbered chromosomes (in the target sample) at a time and that, under random mating, these scores should not be correlated [40].”
BackgroundConfounding fuels misinterpretation in human genetics
Benning, J. W., Carlson, J., Smith, O. S., Shaw, R. G., & Harpak, A. (2025) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2025.1615 · Cited by 6
“While researchers often use methods that adjust for population structure in an attempt to avoid spurious associations, the extent of residual confounding in GWAS remains unclear.”
Wolfram, T., & Morris, D. M. (2022) · PsyArXiv (OSF Preprints) · doi:10.31234/osf.io/m4eqv · Cited by 7
Smolen, C., Jensen, M., Dyer, L. M., Pizzo, L., Tyryshkina, A., Banerjee, D., Rohan, L., Huber, E., Khattabi, L. E., Prontera, P., et al. (2023) · medRxiv · doi:10.1101/2023.05.18.23290169 · Cited by 5
“Partner assortment will result in positive correlations between their risk alleles, which underly the phenotypes driving assortment 60 .”
Dissecting the contribution of common variants to risk of rare neurodevelopmental conditionsPreprint
Huang, Q. Q., Wigdor, E. M., Campbell, P. H., Malawsky, D. S., Samocha, K. E., Chundru, V. K., Danecek, P., Lindsay, S., Marchant, T., Koko, M., et al. (2024) · medRxiv · doi:10.1101/2024.03.05.24303772 · Cited by 5
“…on cognitive ability or correlated traits (e.g. educational attainment) would be expected to lead to individuals with inherited rare variants associated with reduced cognitive ability 8,9,12,69 also having a polygenic background of common variants associated with reduced cognitive ability 57,68 .”
BackgroundInfluentialPartners in Health: Investigating Social Genetic Effects Among Married and Cohabiting Couples
Otten, K., & Mandemakers, J. J. (2023) · Behavior Genetics · doi:10.1007/s10519-023-10147-w · Cited by 6
Use of genetic correlations to examine selection bias
Shapland, C. Y., Gkatzionis, A., Hemani, G., & Tilling, K. M. (2024) · Genetic Epidemiology · doi:10.1002/gepi.22584 · Cited by 4
Lu, T., Zhang, W., Hamilton, F., Butler‐Laporte, G., Timpson, N. J., Smith, G. D., & Richards, J. B. (2025) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaf305 · Cited by 5
Valdes, V., Craighead, L. W., Nelson, C. A., & Enlow, M. B. (2024) · Infancy · doi:10.1111/infa.12628 · Cited by 4
Assortative Mating, Autistic Traits, Empathizing, and SystemizingPreprint
Richards, G., Baron‐Cohen, S., Stokes, H., Warrier, V., Mellor, B., Winspear, E., Davies, J., Gee, L., & Galvin, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.28.358895 · Cited by 4
“Furthermore, although a study utilising genome wide association study (GWAS) data (Yengo et al., 2018) lacked the statistical power required to detect a significant genotypic correlation, a more recent study by Connolly et al.”
BackgroundGenetic basis of partner choicePreprint
Zheng, Q., van Alten, S., Lyngstad, T. H., Ciscato, E., Sun, Z., Miao, J., Wu, Y., Dorn, S., Zheng, B., Havdahl, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.03.636375 · Cited by 5
“Additional details of phenotypic definition in each cohort are provided in Supplementary Table 22 .”
InfluentialSelf-citationBorder, R., & Malik, O. A. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05442-6 · Cited by 3
“On the other hand, there is substantial recent evidence that AM is widespread [8–10] and complicates the interpretation of many commonly applied methods in statistical genetics, including heritability estimation [11], genetic correlation estimation [8, 12], and Mendelian randomization [13].”
BackgroundD’Urso, S., Wootton, R. E., Ask, H., Nunes, C. B., Andreassen, O. A., Hwang, L., Moen, G.-H., Evans, D. M., & Havdahl, A. (2024) · Psychological Medicine · doi:10.1017/s0033291724002216 · Cited by 4
“…(Haworth et al., 2019), assortative mating (Domingue, Fletcher, Conley, & Boardman, 2014; Howe, Nivard, et al., 2022; Robinson et al., 2017; Yengo et al., 2018), and involve indirect genetic effects (Howe, Evans, Hemani, Davey Smith, & Davies, 2022; Howe, Nivard, et al., 2022; Kong et al.,…”
Sosa, R. (2022) · Adaptive Behavior · doi:10.1177/10597123221097451 · Cited by 5
“Yet another problem is that twin studies often rely on the assumption of random mating between parents, for which there is evidence that it is not met (Yengo et al., 2018).”
BackgroundThe 20-year documentary of genetic nurturing: The realization of Harris’s insight
Grigorenko, E. L. (2024) · Developmental Review · doi:10.1016/j.dr.2024.101151 · Cited by 3
Wray, N. R., & Yengo, L. (2019) · Biological Psychiatry · doi:10.1016/j.biopsych.2019.06.007 · Cited by 3
Self-citation
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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