The dynamic genomic prehistory of glacial western Europe

Southwestern Europe has long been looked upon as the exemplar of a glacial refugium where humans have continuously survived climatic challenges1. Consequently, the rich archaeological record of Southwestern France is key to understanding European Upper Palaeolithic population dynamics. We present a genomic transect (23–13 ka BP) showing the persistence of a Franco-Iberian glacial refugium legacy, but one unexpectedly punctuated by pulses of non-local ancestry. The earliest, Badegoulian2, genome contains unexpected Ancient North Eurasian ancestry of Siberian origin during the Last Glacial Maximum and separately provides the earliest evidence of Balko-Italian refugium ancestry. This three-way mix subsequently disappears. However, persistent Franco-Iberian ancestry is later perturbed by two separate influxes of Balko-Italian ancestry, each of which coincided with climate upturns, one during the Middle Magdalenian (~19.2 ka BP) and another at ~14.2 ka BP which was part of a major population turnover at the end of the Upper Palaeolithic. These transient admixtures speak to the long distance connectivity but ultimate fragility of human populations in glacial Europe. A higher level of Neanderthal ancestry persists in genomes with Franco-Iberian ancestry, suggesting this refugium avoided a dilution of archaic heritage that affected other ancient Eurasian populations.