Most American populations descend from indigenous Americans, European colonisers and sub-Saharan African slaves. However, the admixture process resulting from the colonisation of the Americas is constrained by socioeconomic and cultural stratification.

By analysing the DNA fragments of each individual that are inherited from each of these three ancestral populations, we quantify how much the mating has not been random related to the genetic ancestry proportions of males and females.

In this way, we reconstruct how interactions between racial and gender hierarchies shaped population stratification since the colonisation of the Americas. We challenge the oversimplified understanding that mestizaje reduces population stratification: a high degree of mixture cannot translate into a decrease in inequality if it occurs with strongly gendered patterns. Finally, we analyse the role of racialised phenotypes in stratifying the population beyond the effect of socioeconomic stratification.

Overall, we show how social stratification leaves a footprint in the genetic structure of human populations and how, by studying it, we can reconstruct the evolution of inequalities throughout human history.