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 presentday 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. Remarkably, language-associated variants in HAQERs appear more prevalent in Neanderthals and HAQER-like sequences show convergent evolution across vocallearning mammals. Our results reveal how ancient innovations continue shaping human language.