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bioRxiv2026

Tracing Neanderthal ancestry patterns through successive population expansions in Europe

During their expansion out of Africa, modern humans interbred with Neanderthals, leading to the introgression of Neanderthal DNA into their genomes. This initial dispersal created, in Europe, a Southeast-to-Northwest gradient of Neanderthal ancestry in European populations, which was preserved through later Neolithic migration. Here, we investigate the population dynamics that created and maintained this gradient across two successive expansions. We developed a three-population layered simulation framework to track the spatiotemporal evolution of Neanderthal ancestry under a model of interactions between Neanderthals, Palaeolithic hunter-gatherers, and Neolithic farmers. Our results indicate that the Neanderthal ancestry cline was shaped by the direction of the early hunter-gatherer expansion, the northern limit of the Neanderthal range, and strong reproductive isolation between lineages. We estimated that admixture between hunter-gatherers and Neolithic populations was an order of magnitude higher than that between Neanderthals and modern humans. These findings demonstrate how spatiotemporal analyses of ancient DNA provide insights into the dynamics and interactions of ancestral populations.

genomics↗

bioRxiv2022

Past human expansions shaped the spatial pattern of Neanderthal ancestry

The worldwide expansion of modern humans (Homo sapiens) from Africa started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, as revealed by the sequencing of Neanderthal genomes, leading to ~2% Neanderthal DNA in modern Eurasians1,2, with slightly higher introgression in East Asians than in Europeans3-6. These distinct levels of ancestry have been argued to result from selection processes7,8. However, recent theoretical simulations have shown that range expansions could be another explanation9,10. This hypothesis would lead to the generation of spatial gradients of introgression, increasing with the distance from the source of the expansion, i.e., Africa for modern humans. Here, we investigate the presence of Neanderthal introgression gradients after past human expansions by analysing an extended palaeogenomic dataset of Eurasian populations. Our results show that the Out-of-Africa expansion of modern humans into Eurasia resulted in spatial gradients of Neanderthal ancestry that persisted through time. Moreover, while keeping the same gradient orientation, the expansion of early Neolithic farmers into western Eurasia contributed decisively to reducing the average level of Neandertal genomic introgression in European compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Palaeolithic hunter-gatherers. This study shows that inferences about past population dynamics within our species can be made from the spatiotemporal variation in archaic introgression.

evolutionary biology↗