Tracing Neanderthal ancestry patterns through successive population expansions in Europe

During their expansion from Africa, modern humans interbred with Neanderthals, resulting in introgression of Neanderthal DNA into their genomes. This process contributed to a Southeast-to-Northwest gradient of Neanderthal ancestry across Europe. We investigate the population dynamics underlying the emergence and persistence of this gradient through two successive human range expansions. We developed a three-population, layered, spatially explicit simulation framework to track the spatiotemporal evolution of Neanderthal ancestry under a model of interactions among Neanderthals, pre-Neolithic hunter-gatherers, and Neolithic farmers. Our results indicate that the ancestry cline emerged from the interplay between the direction of the initial hunter-gatherer expansion, the northern limit of the Neanderthal range, and strong reproductive isolation, without requiring natural selection. The similar direction of the subsequent Neolithic expansion explains the cline’s persistence and Neanderthal ancestry differences between hunter-gatherers and farmers. These findings demonstrate how spatiotemporal patterns in ancient DNA provide insights into past population dynamics.