Population Admixture Dynamics
Human diasporas over the past millennia have resulted in even more frequent intercontinental marriages and population admixtures. Many recently admixed populations, such as AfAs and Mestizos, have received much attention due to their potential advantages in the discovery of disease-associated genes. Particularly, a disease gene mapping strategy, named admixture mapping or MALD, as aforementioned, has been developed [1, 7, 11, 47]. The statistical power of admixture mapping or MALD relies on the fact that population admixture creates extended and elevated LD between loci with different allele frequencies among the parental source populations [7, 10, 48], while the historical population admixture processes determine the LD pattern in an admixed population. Therefore, as shown in several theoretical and simulation studies, population admixture dynamics have a strong effect on the power of admixture mapping [48-51].
In fact, accurate understanding of population admixture dynamics is important not only to admixture mapping but also to other applications, such as elucidating population history [52] and detecting natural selection signatures in admixed populations [49, 53]. However, the fine admixture dynamics of recently admixed populations has not been well established, even though some studies have examined the simulated data [54, 55] or experimental data with sparse markers [48, 51]. In addition, admixture dynamics of relatively ancient admixed populations has rarely been studied. Recently, the availability of genomewide high-density SNPs data has facilitated the study on detailed genetic structures of admixed populations [35, 44, 56-61]. However, most of these studies relied on simplified models that do not take into account the inherent complexity of the admixture processes. Moreover, the haplotype and chromosomal segment patterns shaped by recombination within each individual have been deliberately ignored in most studies due to many inherent challenges [62].
For individuals from admixed populations that have existed for a long time, their chromosomes resemble a mosaic of chromosomal segments of distinct ancestry (CSDA). The CSDA in the admixed population would have been reshaped and rearranged by recombination in each generation, which should provide some information about the population history. In other words, the CSDA will be spliced into smaller pieces as the number of generations since admixture increases, while the chromosomes from recently admixed individuals contain much longer CSDAs. Information regarding the average CSDA length has been used to infer the number of generations since admixture in various studies [57, 63-66]. However, the distribution of CSDA length may contain more valuable information concerning population admixture history and admixture dynamics, which has not yet been explored.
In a recent study [67], we proposed 2 approaches to explore population admixture dynamics and, by analyzing genomewide empirical and simulated data, demonstrated that the approach based on the distribution of CSDA was more powerful than that based on the distribution of individual ancestry proportions. As a result, analysis of 1,890 AfAs showed that a continuous gene flow (CGF) model (Fig. 3), in which AfAs continuously received gene flow from EUR populations over about 14 generations, best explained the admixture dynamics of AfAs among several putative models. Interestingly, we observed that some AfAs had much more EUR ancestry than the simulated samples, indicating substructures of local ancestries in AfAs that could have been caused by individuals from some particular lineages having continuously inter-married with people of EUR ancestry. On the contrary, the admixture dynamics of Mexicans was more likely to be explained by a gradual admixture (GA) model (Fig. 3), in which Mexicans continuously received gene flow from both EUR and Amerindian populations for about 24 generations. The higher proportion of long CSDAs observed in Mexican-Americans relative to Mexican-Mestizos suggested recent gene flow from EUR-Americans to Mexican-Americans. The genetic components of sub-Saharan Africans in Middle Eastern populations, such as Mozabite, Bedouin, and Palestinians, could be explained by one early admixture followed by some recent gene flow from Africans. In summary, this study not only provides new approaches to explore population admixture dynamics but also advances our understanding on historical admixture processes of AfAs, Mexicans, and Middle Eastern populations.
Again, since admixed populations in Asia have not been studied, I will not go further into details. This approach can be also applied in admixed populations in Asia to explore the admixture dynamics of admixed populations in Asia.