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 an evolutionary stratified polygenic score approach, we find that human ancestor quickly evolved regions (HAQERs) are associated with spoken language abilities (discovery N = 350, total replication N > 100,000). HAQERs evolved before the human-Neanderthal split, giving hominins increased binding of Forkhead and Homeobox transcription factors, and show evidence of balancing selection across the past 20,000 years. Language-associated variants in HAQERs appear more prevalent in Neanderthals, and HAQER-like sequences show convergent evolution across vocal-learning mammals. Our results reveal how ancient innovations continue shaping human language.