title: 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.
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158 noah.zaitlen@ucsf.edu heran@post.tau.ac.il.
authors.forename: Noah
authors.initials: N
authors.lastname: Zaitlen
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Scott
authors.initials: S
authors.lastname: Huntsman
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Donglei
authors.initials: D
authors.lastname: Hu
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Melissa
authors.initials: M
authors.lastname: Spear
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Celeste
authors.initials: C
authors.lastname: Eng
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Sam S
authors.initials: SS
authors.lastname: Oh
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Marquitta J
authors.initials: MJ
authors.lastname: White
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Angel
authors.initials: A
authors.lastname: Mak
authors.affiliation: Childrens Hospital and Research Center Oakland, California 94609.
authors.forename: Adam
authors.initials: A
authors.lastname: Davis
authors.affiliation: Childrens Hospital and Research Center Oakland, California 94609.
authors.forename: Kelly
authors.initials: K
authors.lastname: Meade
authors.affiliation: Department of Allergy and Immunology, Kaiser Permanente Vallejo Medical Center, California 94589.
authors.forename: Emerita
authors.initials: E
authors.lastname: Brigino-Buenaventura
authors.affiliation: Bay Area Pediatrics, Oakland, California 94601.
authors.forename: Michael A
authors.initials: MA
authors.lastname: LeNoir
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Bibbins-Domingo
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158.
authors.forename: Esteban G
authors.initials: EG
authors.lastname: Burchard
authors.affiliation: Department of Medicine, University of California, San Francisco, California 94158 noah.zaitlen@ucsf.edu heran@post.tau.ac.il.|Department of Computer Science, Tel Aviv University, Israel.
authors.forename: Eran
authors.initials: E
authors.lastname: Halperin
mesh_terms: D001741:Black or African American / Q000235:genetics*; D000483:Alleles; D066264:Datasets as Topic; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods; D023281:Genomics / Q000379:methods; D063426:Human Migration; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide
keywords: admixture; assortative mating; demography; migration; population genetics