Selection at LCT locus began thousands of years before lactase persistence allele emerged. FADS cluster selection for vegetarian diet started in Neolithic before Europe. HLA region shows strong Bronze Age selection from pathogen exposure. Lighter skin alleles fixed early from vitamin D needs in northern groups. Steppe ancestry causes taller height in Northern vs Southern Europeans. Neolithic farmer ancestry enriches mood disorder risk alleles like anxiety and irritability. Western hunter-gatherer ancestry enriches diabetes and Alzheimer's risk alleles. Steppe ancestry boosts anthropometric traits like mass and lung capacity. Neolithic ancestry raises skin cancer risk and light hair. Hunter-gatherer ancestries link to darker skin and hair. ApoE4 Alzheimer's risk allele ties to WHG/EHG ancestry. WHG ancestry elevates cholesterol and blood pressure risks. Admixture masks selection signals in modern genomes. Agriculture triggered selection for new diet, immunity, and metabolism. Pathogen protection alleles increase autoimmune disease risks. KANSL1 duplications spread with Neolithic farmers, rare outside Europe/Mideast. Recurrent CNVs causing neurodevelopmental disorders stable since ancient times. Bronze Age shifts selected STD protections at cost of other diseases. Hunter-gatherer differentiation predates Neolithic in metabolic loci.