Autosomal Admixture Levels Are Informative About Sex Bias in Admixed Populations

Abstract

Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.

The time and place of European admixture in Ashkenazi Jewish history

“…Admixture parameters can also be inferred using more general demographic inference methods, e.g., based on the allele frequency spectrum [66, 67] or IBD sharing [60]; however, to use these methods one must specify and infer a model for the entire history. Recently, Rosenberg and colleagues [39, 68], Liang and Nielsen [69], and Gravel [35], derived analytical results for the moments of the ancestry proportion, namely the fraction of the chromosome that descends from each ancestral source. These ancestry proportions can be estimated (e.g., [63]) and matched to the theoretical moments for admixture time inference (e.g., [36, 37]).…”

Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes

“…Admixture models for migration from the Steppe. We used recursive expressions for X and autosomal ancestry as a function of sex-specific admixture rates to interpret observed ancestry (16,31). We considered four general models of admixture over time: 1) single admixture event, with no further migration, 2) constant migration over time, 3) increasing migration from SP over time, 4) decreasing migration from SP over time.…”

“…Therefore, we evaluated the magnitude of differences in male and female contributions that would be consistent with observed X to autosomal ancestry ratios. We determined this range of sex bias values by simulating ancestry under a mechanistic admixture model including genetic drift and sampling at specified sample sizes (16,30,31) (Fig. 3A, Materials and Methods).…”

Admixture Models and the Breeding Systems of H. S. Jennings: AGENETICSConnection

“…Because the X chromosome and autosomes have different modes of inheritance, X chromosomes record signatures of the founding females and males differently from autosomes. Having already built a general mathematical model of the effect of sex-biased admixture on autosomal markers (Goldberg et al 2014), our goal was to do the same for the X chromosome.…”

“…Indeed, Equations 3 and 4 give exactly the female and male frequencies of allele A in generation n $ 1 during the approach to Hardy-Weinberg equilibrium for a population that begins in generation 0 exclusively with AA females and aY males (Crow and Kimura 1970, p. 46). In parallel to the Hardy-Weinberg setting, unlike for autosomal loci (Goldberg et al 2014), the expected admixture on the X chromosome for a random female or male under hybrid isolation is not constant over time.…”