PT  - JOURNAL ARTICLE
AU  - Noah Zaitlen
AU  - Scott Huntsman
AU  - Donglei Hu
AU  - Melissa Spear
AU  - Celeste Eng
AU  - Sam S. Oh
AU  - Marquitta J White
AU  - Angel Mak
AU  - Adam Davis
AU  - Kelly Meade
AU  - Emerita Brigino-Buenaventura
AU  - Michael A LeNoir
AU  - Kirsten Bibbins-Domingo
AU  - Esteban G Burchard
AU  - Eran Halperin
TI  - The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium
AID  - 10.1101/056168
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 056168
4099  - http://biorxiv.org/content/early/2016/05/31/056168.short
4100  - http://biorxiv.org/content/early/2016/05/31/056168.full
AB  - 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 non-random 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 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.