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Abstract
Human populations across multiple regions transitioned from hunting and foraging to sedentary farming societies starting ~10 to 12kya, narrowing dietary diversity and transforming relationships with animals and pathogens. To investigate how these ecological changes during the Neolithic shaped human adaptations, I analysed high-coverage whole-genome sequence data from 1,092 individuals practising hunter-gatherer, agriculturalist, and pastoralist lifestyles across eight geographic regions spanning Africa, Asia, and Oceania. Haplotype-based scans revealed pervasive recent positive selection on regulatory variation and genes associated with immune function across all subsistence modes, challenging the notion that agriculturalists alone experienced uniquely strong pathogenic pressures. By explicitly modelling correlations between allele frequencies and subsistence strategy, I uncovered convergent adaptations at a cross-continental scale in pathways beyond immunity, including metabolic, spermatogenesis, and developmental pathways, supporting the life-history hypothesis that energy allocation to growth, reproduction, and maintenance shifted with the adoption of agriculture. Collectively, these findings illuminate the genetic legacy of ecological changes associated with the foraging-to-farming transition and highlight the central role of non-coding regulatory variation in human adaptation.