Modeling Continuous Admixture Using Admixture-Induced Linkage Disequilibrium

Abstract

Recent migrations and inter-ethnic mating of long isolated populations have resulted in genetically admixed populations. To understand the complex population admixture process, which is critical to both evolutionary and medical studies, here we used admixture induced linkage disequilibrium (LD) to infer continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general scenario with isolation after a certain duration of continuous gene flow. Based on the new models, we developed a method, CAMer, to infer the admixture history considering continuous and complex demographic process of gene flow between populations. We evaluated the performance of CAMer by computer simulation and further applied our method to real data analysis of a few well-known admixed populations.

Figure 1. Classic admixture models (HI, GA and CGF) and the models we extended (GA-I and CGF-I).

For each model, the simulated admixed population (Hybrid) is in the middle of two source populations (POP1 and POP2). Each horizontal arrow represents the direction of gene flow from the source populations to the admixed population. Once the genetic components flow into the admixed population, the admixed population randomly hybridizes with other existing components. The existence of horizontal arrows indicates gene flow from the corresponding source population.

Figure 2. Coefficient vector of polynomial functions for each model.

For each admixture model, the starting time of the population admixture is 50 generations ago. The admixture proportion in the final admixed population is set as 0.3:0.7 for population 1 and population 2.

Figure 3. Evaluation of CAMer under various simulated admixture models.

Here, the core models are HI, GA-I, CGF1-I, and CGF2-I. The simulated models (True Model) are listed on the left, with the admixture time interval depicted in the parentheses. The gray area on the middle vertical panel is the simulated time interval, whereas colored lines indicate the estimated time intervals under different core models. HI: pink; CGF1-I: green; CGF2-I: purple; GA-I: blue. The intensity of lines means the number each point is covered by the time intervals estimated from all jackknives. Lighter colors represent fewer covers while darker colors indicate more.