Analytical expectations for ancestry junction accumulation in admixed genomes

Abstract

Complex demographic events have shaped human history, leaving signatures of genetic variation across the genome. Here, we investigate the recent evolutionary dynamics of admixed populations that descend from distinct ancestral sources. We present a discrete, generalizable model of admixture that leverages ancestry switches, which are recombination breakpoints that mark changes in ancestral origin along a chromosome. We derive analytical expectations for the number of ancestry switches within a genomic segment as functions of recombination rate, ancestry heterozygosity, and effective population size. We then extend these expectations to incorporate population-specific recombination maps. Our theoretical predictions are in close agreement with forward-in-time simulations that trace ancestry junction accumulation following an initial admixture event under both constant and variable recombination models. We observe minimal variability in switch counts across ten simulation replicates, underscoring the robustness of the theoretical expectation. Furthermore, model-based switch counts, parameterized using literature-informed demographic values, agree with empirical observations from African-American individuals in the 1000 Genomes Project. For example, when modeling human chromosome 1, we found a mean of approximately six switches per haplotype, which aligns with the theoretical expectation under an initial African ancestry proportion of 0.85 and agrees with published estimates from other African-American cohorts. Overall, the model provides a new route for using ancestry switches to understand how recombination and demography jointly shape ancestry patterns in admixed populations without requiring separation into parental sources. Keywords: ancestry junctions, admixture, recombination, population genetics, PEQG2026