The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

Abstract

Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry-based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first direct evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.

Inclusion of variants discovered from diverse populations improves polygenic risk score transferability

“…In addition, our simulations assume random mating among admixed individuals and therefore do not reflect the more complex assortative mating that may be observed, which may impact the distribution of local ancestry tract lengths in our simulation and therefore hinder the improvement of PRS accuracy by local ancestry weighting. 31 Also, although we provide evidence to suggest the contribution of population differences in allele frequency and LD tagging of causal variants to loss of PRS accuracy with varying ancestry, we do not delineate how each of these factors decreases accuracy independently; this is a direction for future work. Finally, we have only simulated individuals from Yoruba, a West African population, which is not representative of the greater diversity in Sub-Saharan Africa.…”

Human genetic admixture

“…Theoretical work has sought to understand the relationship between demography and these summaries of genetic variation in admixed populations. Computational methods have built on this theory to infer population histories generating observed patterns of genetic ancestry [30][31][32][33]. Recent progress has focused on dynamic and complex population histories that may more accurately represent realistic population histories.…”

Racial and ethnic differences in preterm birth: A complex, multifactorial problem

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