Tracing the Neanderthal–Modern Human hybrid zone using paleogenomic data

Abstract Interbreeding between closely related lineages is a pervasive evolutionary feature across taxa 1 , including modern humans, who admixed with Neanderthals and other archaic hominins 2,3 . Identifying where gene flow between these lineages happened can shed light on ecological and adaptive contexts in which introgressed genes were acquired. However, mapping ancient hybrid zones is challenging because post-admixture population dynamics obscure their genetic signatures. Here, we determine the conditions under which spatial patterns of introgressed DNA in ancient genomes allow the inference of the geographic location of past hybridization events during population expansions. Using computational simulations, we identify the conditions under which introgression-based statistics provide informative signals about past hybridization events. We show that the mean genomic proportion of introgressed DNA, which can be readily calculated from low-coverage ancient genomes, reveals a cline that increases with distance from the population expansion source until reaching the hybrid zone boundary and persists over time. Comparison with empirical Neanderthal introgression distribution from an extended Eurasian paleogenomic dataset supports a prolonged admixture pulse extending far beyond the Levant in western Eurasia. Our findings highlight the power of paleogenomics to reconstruct the spatiotemporal dynamics of species interactions.