Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Abstract

AbstractGenetic data can provide insights into population history, but first we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and for genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating non-random mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs-of-homozygosity (ROH). While summaries of ROH may be difficult to interpret in admixed populations, differentiating ROH by length class shows that ROH reflect historical differences between the islands in their contributions from the source populations and post-admixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.Author SummaryPatterns of genetic variation are often used to infer human population histories; however population-genetic models make a variety of simplifying assumptions that often neglect the demographic and social dynamics of human populations. Here, we use the population of Cabo Verde as a case study to understand the patterns of genetic variation left by social and demographic processes. The islands of Cabo Verde were first settled in the late 1400s by Portuguese colonizers and enslaved West African people. We consider genomic data from four regions within the archipelago alongside historical records that document settlement patterns, timing, and sociocultural dynamics within the islands. We use genetic ancestry to test for nonrandom mating and sex-specific demography. We show that these sociocultural processes may bias inference of population history parameters and distributions of shared ancestry in the region. Overall, by providing insights into the patterns of genetic variation social processes leave in human genomes for a population with a well-studied historical record, we highlight processes to consider in order to more accurately understand the history of populations without extensive records.