Ancient regulatory evolution shapes individual language abilities in present-day humans

Language is a defining feature of our species, yet the genomic changes enabling it remain poorly understood. Despite decades of work since FOXP2 ’s discovery, we still lack a clear picture of which regions shaped language evolution and how variation contributes to present-day phenotypic differences. Using a novel evolutionary stratified polygenic score approach in nearly 40,000 individuals, we find that Human Ancestor Quickly Evolved Regions (HAQERs) are specifically associated with language but not general cognition. HAQERs evolved before the human–Neanderthal split, giving hominins increased binding of Forkhead and Homeobox transcription factors, and show balancing selection across the past 20,000 years. Remarkably, language variants in HAQERs appear more prevalent in Neanderthals and have convergently evolved across vocal-learning mammals. Our results reveal how ancient innovations continue shaping human language.